https://pymolwiki.org/api.php?action=feedcontributions&user=Inchoate&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T21:51:13ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=File:Test.jpg&diff=12333File:Test.jpg2016-04-12T17:24:51Z<p>Inchoate: </p>
<hr />
<div></div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=12265Main Page2016-01-04T22:36:13Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[PyMOL_mailing_list|Getting Help]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.<br />
|-<br />
! PyMOL Open-Source Fellowship<br />
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.<br />
|-<br />
! New Plugin<br />
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DynamicPageList><br />
randomcount=1<br />
category=Commands|Plugins|Script_Library|Settings<br />
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|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=12264Main Page2016-01-04T22:34:46Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[PyMOL_mailing_list|Getting Help]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.<br />
|-<br />
! PyMOL Open-Source Fellowship<br />
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.<br />
|-<br />
! New Plugin<br />
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DynamicPageList><br />
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category=Commands|Plugins|Script_Library|Settings<br />
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<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Draw_Protein_Dimensions&diff=12263Draw Protein Dimensions2016-01-03T03:52:43Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = Draw_Protein_Dimensions.py<br />
|author = [[User:PabloGuardado|Pablo Guardado Calvo]]<br />
}}<br />
<br />
This script will draw the dimensions of a protein based on an Inertia Axis Aligned Bounding Box (IABB).<br />
<br />
<br />
The idea behind this script is to calculate an approximate minimal bounding box (MBB) to extract the cell dimensions of a protein. To calculate the MBB is not trivial and usually the Axis Aligned Bounding Box (AABB) does not show up the real dimensions of the protein. This script calculates the inertia tensor of the object, extract the eigenvectors and use them to rotate the molecule (using as rotation matrix the transpose of the eigenvector matrix). The result is a molecule oriented with the inertia axis aligned with the cartesian axis. A new Bounding Box is calculated, which is called Inertia Axis Aligned Bounding Box (IABB), with a volume always lower than the AABB volume, and in many cases may correspond with the MBB. <br />
<br />
As always with these type of things, you have to use at your own risk. I did not try all the possible combinations, but if you find a bug, do<br />
not hesitate to contact me (pablo.guardado (at) gmail.com) or try to modify the code for yourself to correct it.<br />
<br />
To load the script just type:<br />
<br />
'''run path-to-the-script/Draw_Protein_Dimensions.py'''<br />
<br />
or if you want something more permanent add the previous line to your .pymolrc file<br />
<br />
The script works just typing:<br />
<br />
'''draw_Protein_Dimensions ''selection'''''<br />
<br />
This will draw the cell dimensions of your selection based on a IABB box. It also generates the IABB box and the inertia axis, you just need to do "show cgo" to display them.<br />
<br />
You could also try:<br />
<br />
'''draw_BB ''selection'''''<br />
<br />
This will draw the AABB and IABB boxes with their cell dimensions and show up their volumes, you can compare them.<br />
<br />
<br />
= Examples =<br />
<source lang="python"><br />
# download the source and save as Draw_Protein_Dimensions.py<br />
run Draw_Protein_Dimensions.py<br />
fetch 2vak<br />
# calculate the dimensions of the full ASU<br />
draw_Protein_Dimensions 2vak<br />
</source><br />
<br />
<gallery perrow=3 widths=350 heights=350> <br />
File:2vak_ASU.png |Dimensions of 2vak ASU<br />
</gallery><br />
<br />
<source lang="python"><br />
# you can extract only one chain and calculates the dimensions<br />
draw_Protein_Dimensions obj01<br />
</source><br />
<br />
<gallery perrow=3 widths=350 heights=350> <br />
File:2vak_A.png |Dimensions of one protomer (chain A - 2vak)<br />
</gallery><br />
<br />
<source lang="python"><br />
# You can also draw the Bounding boxes (AABB and IABB) to compare them.<br />
fetch 2vak<br />
draw_BB 2vak<br />
</source><br />
<br />
<br />
<br />
<gallery perrow=3 widths=350 heights=350> <br />
File:2vak_AABB.png |Axis-aligned bounding box <br />
File:2vak_IABB.png |Inertia-axis-aligned bounding box<br />
</gallery><br />
<br />
<br />
[[Category:Script_Library]]<br />
[[Category:Math_Scripts]]<br />
[[Category:Structural_Biology_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=12262Main Page2016-01-03T03:16:58Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[PyMOL_mailing_list|Getting Help]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.<br />
|-<br />
! PyMOL Open-Source Fellowship<br />
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.<br />
|-<br />
! New Plugin<br />
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DynamicPageList><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
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<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=File:J_square.jpg&diff=12114File:J square.jpg2015-09-09T02:33:28Z<p>Inchoate: Testing upload.</p>
<hr />
<div>Testing upload.</div>Inchoatehttps://pymolwiki.org/index.php?title=Stereo_Mode&diff=11520Stereo Mode2014-02-04T15:03:28Z<p>Inchoate: </p>
<hr />
<div>[[Image:Anaglyph1.png|Example of Anaglyph 3D in PyMOL|450px|right|thumb]]<br />
[[Image:Ana4 focal ray.png|Example of a ray traced, focal blurred, anaglyph image.|450px|right|thumb]]<br />
[[Image:3D-B-DNA.png|3D B-DNA Example|450px|right|thumb]]<br />
[[Image:Amyloid.png|Amyloid beta example|450px|right|thumb]]<br />
<br />
The [[stereo_mode]] setting sets the type of stereo mode, if the [[stereo]] setting is enabled.<br />
<br />
''You can also control both settings with the [[stereo]] command, which is more convenient!''<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set stereo_mode, integer<br />
</source><br />
<br />
Valid values for the '''integer''' argument are listed in the following table.<br />
<br />
== Supported Stereo Modes ==<br />
<br />
Corresponding keyword arguments (instead of numeric values) can be passed to the [[stereo]] command.<br />
<br />
{| border=1 cellspacing=0 cellpadding=4 class=wikitable<br />
! value !! description<br />
|-<br />
| 1 || '''quad-buffered'''<br />
|-<br />
| 2 || '''cross-eyed'''<br />
|-<br />
| 3 || '''walleye'''<br />
|-<br />
| 4 || '''geowall'''<br />
|-<br />
| 5 || '''sidebyside'''<br />
|-<br />
| 6 || '''stencil by row''', Zalman<br />
|-<br />
| 7 || '''stencil by col'''<br />
|-<br />
| 8 || '''stencil checkerboard'''<br />
|-<br />
| 9 || '''stencil custom''' for developers<br />
|-<br />
| 10 || '''anaglyph''' (requires green/magenta glasses)<br />
|-<br />
| 11 || '''dynamic polarization'''<br />
|-<br />
| 12 || '''clone dynamic'''<br />
|}<br />
<br />
== Notes ==<br />
=== Anaglyph Color Quality and Ghosting ===<br />
To test the quality of your glasses and coloring, you can test for "ghosting". Choose a part of the structure where the channels for the left and right eye are nicely separated in space. Hold one lens over the part of the structure and see you see one image or if there is a faint second image for the other channel. Then hold the other other lens over the image and see if there is a faint second image.<br />
<br />
== See Also ==<br />
* [[Stereo]]<br />
* [[Stereo_angle]]<br />
<br />
[[Category:Settings|Settings]]<br />
[[Category:Stereo|Stereo]]</div>Inchoatehttps://pymolwiki.org/index.php?title=File:Amyloid.png&diff=11519File:Amyloid.png2014-02-04T15:02:56Z<p>Inchoate: Example (simulated) amyloid beta.</p>
<hr />
<div>Example (simulated) amyloid beta.</div>Inchoatehttps://pymolwiki.org/index.php?title=File:3D-B-DNA.png&diff=11518File:3D-B-DNA.png2014-02-04T14:59:58Z<p>Inchoate: Anaglyph image of DNA</p>
<hr />
<div>Anaglyph image of DNA</div>Inchoatehttps://pymolwiki.org/index.php?title=User:PietroGattiLafranconi&diff=11504User:PietroGattiLafranconi2014-01-14T20:28:34Z<p>Inchoate: </p>
<hr />
<div>* Is new to PyMOLWiki<br />
* Submitted [[DistancesRH]], [[ListSelection2]] and [[Pairwise_distances]]<br />
* Will be happy to receive feedbacks/suggestions<br />
* can be found [http://www2.bio.cam.ac.uk/~fhlab/pg356.php here]</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11503Main Page2014-01-14T19:59:49Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
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randomcount=1<br />
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addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11502Main Page2014-01-14T19:38:41Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! Official Release<br />
| [http://pymol.org|PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11501Main Page2014-01-14T19:38:27Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! Official Release<br />
| [[http://pymol.org|PyMOL, AxPyMOL, and JyMO v1.7 have all been released]] today, January 14, 2014.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
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randomcount=1<br />
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addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11500Main Page2014-01-14T19:38:09Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! Official Release<br />
| [[PyMOL, AxPyMOL, and JyMO v1.7 have all been released|http://pymol.org]] today, January 14, 2014.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Stereo_Mode&diff=11488Stereo Mode2013-12-17T15:49:54Z<p>Inchoate: </p>
<hr />
<div>[[Image:Anaglyph1.png|Example of Anaglyph 3D in PyMOL|450px|right|thumb]]<br />
[[Image:Ana4 focal ray.png|Example of a ray traced, focal blurred, anaglyph image.|450px|right|thumb]]<br />
The [[stereo_mode]] setting sets the type of stereo mode, if the [[stereo]] setting is enabled.<br />
<br />
''You can also control both settings with the [[stereo]] command, which is more convenient!''<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set stereo_mode, integer<br />
</source><br />
<br />
Valid values for the '''integer''' argument are listed in the following table.<br />
<br />
== Supported Stereo Modes ==<br />
<br />
Corresponding keyword arguments (instead of numeric values) can be passed to the [[stereo]] command.<br />
<br />
{| border=1 cellspacing=0 cellpadding=4 class=wikitable<br />
! value !! description<br />
|-<br />
| 1 || '''quad-buffered'''<br />
|-<br />
| 2 || '''cross-eyed'''<br />
|-<br />
| 3 || '''walleye'''<br />
|-<br />
| 4 || '''geowall'''<br />
|-<br />
| 5 || '''sidebyside'''<br />
|-<br />
| 6 || '''stencil by row''', Zalman<br />
|-<br />
| 7 || '''stencil by col'''<br />
|-<br />
| 8 || '''stencil checkerboard'''<br />
|-<br />
| 9 || '''stencil custom''' for developers<br />
|-<br />
| 10 || '''anaglyph''' (requires green/magenta glasses)<br />
|-<br />
| 11 || '''dynamic polarization'''<br />
|-<br />
| 12 || '''clone dynamic'''<br />
|}<br />
<br />
== Notes ==<br />
=== Anaglyph Color Quality and Ghosting ===<br />
To test the quality of your glasses and coloring, you can test for "ghosting". Choose a part of the structure where the channels for the left and right eye are nicely separated in space. Hold one lens over the part of the structure and see you see one image or if there is a faint second image for the other channel. Then hold the other other lens over the image and see if there is a faint second image.<br />
<br />
== See Also ==<br />
* [[Stereo]]<br />
* [[Stereo_angle]]<br />
<br />
[[Category:Settings|Settings]]<br />
[[Category:Stereo|Stereo]]</div>Inchoatehttps://pymolwiki.org/index.php?title=File:Ana4_focal_ray.png&diff=11487File:Ana4 focal ray.png2013-12-17T15:48:52Z<p>Inchoate: Ray trace with anaglyph and focal blur.</p>
<hr />
<div>Ray trace with anaglyph and focal blur.</div>Inchoatehttps://pymolwiki.org/index.php?title=Perp_maker&diff=11486Perp maker2013-12-09T22:06:03Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = perp_maker.py<br />
|author = [[User:Inchoate|Jason Vertrees]]<br />
|license = MIT<br />
}}<br />
<br />
The '''perp_maker.py''' script creates perpendicular planes.<br />
<br />
Nothing to do with cops. Given a simple PyMol scene, attempts to create a CGO background triangle perpendicular to the vector created - which is parallel to the line segment drawn through the camera point and current center of mass - as obtained by "get_position," or "get_view."<br />
<br />
== Usage ==<br />
<br />
* Load your scene<br />
* Orient the scene as you wish<br />
* [[Running Scripts|Run]] the script<br />
<br />
Could it be any simpler?<br />
<br />
You can rotate and move the plane using the editing features (A > drag, Shift+Drag with right, middle or left mouse button).<br />
<br />
[[Category:Script_Library]]<br />
[[Category:Math_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Bondpack&diff=11471Bondpack2013-11-18T16:47:26Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = https://github.com/rasbt/BondPack<br />
|author = Sebastian Raschka<br />
|license = GNU GENERAL PUBLIC LICENSE<br />
}}<br />
<br />
== BondPack ==<br />
<br />
<br />
A collection of PyMOL plugins to visualize atomic bonds.<br><br />
<br />
<br />
<br />
== Introduction ==<br />
PyMOL is without any doubt a great tool to visualize protein and ligand molecules.<br><br />
However, drawing interactions between atoms can be often quite cumbersome when done manually.<br><br />
For the sake of convenience, I developed three plugins for PyMOL that will make our life as protein biologists a little bit easier.<br><br />
All three PyMOL plugins can be installed and used separately; they don't depend on each other, but rather complement each other.<br><br />
At the end of this article, you will find brief instructions on how to install plugins in PyMOL - a very quick and simple process.<br> <br />
<br />
== HydroBond ==<br />
HydroBond visualizes all potential polar contacts between protein and ligand molecules within a user-specified distance.<br> <br />
The underlying function is based on the different atom types, such as hydrogen bond acceptor and donor atoms,<br><br />
and thus it is required to have hydrogen atoms present in the structure. <br><br />
If your structure file doesn't contain hydrogen atoms already, you can add them directly in PyMOL as shown in the image below.<br><br><br />
[[File:add_hydrogens.png]]<br />
<br><br>HydroBond is related to PyMOLs "[A]->find->polar contacts" command, however,<br><br />
it doesn't consider geometry criteria and angle thresholds,<br> but is rather based on atom types.<br> <br />
When you select HydroBond from the "Plugin" menu, you will be prompted to enter the name of the protein object,<br><br />
the ligand object, and a distance cutoff as shown in the figure below.<br><br />
If HydroBond was able to detect hydrogen bond and acceptor atoms within the<br><br />
specified distance, potential interactions will be visualized as yellow dashed lines.<br><br><br />
[[File:hydrobond_action.png]]<br />
<br><br><br />
<br />
== BondVis ==<br />
The BondVis plugin lets you visualize interactions between any pair of atoms you specified.<br> <br />
Often I find it helpful for my understanding (and for verification) to visualize the bonds between certain atoms<br><br />
that were assigned in docking or any other prediction software.<br><br />
Most software will provide you with information about the atoms that were "connected" to perform the analysis.<br><br />
If you run BondVis from the "Plugin" menu, it will ask you to select a "bond info file."<br><br><br />
[[File:bondinfo.png]]<br />
<br><br><br />
This is just a simple text file that contains the atom numbers of connected atoms in pairs.<br><br />
Those can be separated by spaces, tabs, or commas. An example file with bond information could look like this:<br> <br />
<code><pre>1174 1357<br />
1175 1358<br />
1176 1359<br />
</pre></code><br />
<br><br />
When you selected a "bond info" file, BondVis will connect all atom pairs by yellow dashed lines<br><br />
and print out the connected atoms in the command field.<br><br><br />
[[File:bondvis.png]]<br />
<br><br><br />
<br />
== BondLab ==<br />
If you are not happy with the looks of the lines that were drawn to visualize connections between atoms,<br><br />
you will like to use BondLab.<br> This plugin offers a simple interface that allows you to change the diameter,<br><br />
gap width, and color of the lines. <br><br><br />
[[File:bondlab.png]]<br><br />
The following video demonstrates the different features of BondLab:<br><br />
http://youtu.be/14UZctxtK3w<br />
<br><br />
== Github ==<br />
If you are interested, you can follow the BondPack Github repository<br><br />
https://github.com/rasbt/BondPack for updates<br />
<br />
[[Category:Script_Library]]<br />
[[Category:Structural_Biology_Scripts]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Older_News&diff=11470Older News2013-11-18T16:46:16Z<p>Inchoate: </p>
<hr />
<div>= Older News=<br />
* [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.<br />
* [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.<br />
* [[DistancesRH|Distances RH]]<br />
* PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
* Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
* [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
* [[b2transparency]] can set surface transparency based on atom b-factor<br />
* [[psico]] is a python module which extends PyMOL with many commands<br />
* [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
* [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
* [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
* [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
* [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
* [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
* [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].<br />
* [[spectrum_states]] colors states of multi-state object<br />
* [[TMalign]] is a wrapper for the TMalign program<br />
* The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
* [[save_settings]] can dump all changed settings to a file<br />
* Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
* Wiki has been updated. Please report any problems to the sysops.<br />
* Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
* [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
* [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
* [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
* [[PluginDirectory]]: How to set up a personal plugin directory<br />
* Add focal blur to images [[FocalBlur]].<br />
* Visualize VDW clashes with [[show bumps]]<br />
* Color by [[DSSP]] or [[Stride]] secondary structure assignment<br />
* There is a new script to calculate the [[Radius of gyration]]<br />
* New Command<br />
* [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.<br />
* [[ColorByDisplacement]] Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.<br />
* [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.<br />
* Two new scripts: [[AAindex]] and [[Sidechaincenters]]<br />
* [[CAVER_2.0]] update to the CAVER plugin.<br />
* [[AngleBetweenHelices]] calculates the angle between two helices.<br />
* [[GoogleSearch]] widget fixed.<br />
* [[Spectrumany]] creates color gradients with arbitrary color sequences.<br />
* [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.<br />
* [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). <br />
* [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.<br />
* [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.<br />
* See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.<br />
* See [[Supercell]], the new script for making XxYxZ supercells.<br />
* See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.<br />
* See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.<br />
* The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.<br />
* [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.<br />
* [[Fetch]] has been updated to also load electron density maps.<br />
* Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].<br />
* One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. <br />
* [[surface_cavity_mode]] to change how PyMOL displays cavities.<br />
* Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.<br />
* [[Cache]]&mdash;stores information on structures, so we don't have to recompute them.<br />
* News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].<br />
* [[Fetch_Path]]&mdash;Sets the default path for the [[fetch]] command.<br />
* [[SelInside]]&mdash;Creates a custom selection of all atoms spatially inside some user-defined box.<br />
<br />
* [[ContactsNCONT]]&mdash;The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite<br />
* [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).<br />
* Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.<br />
* New &mdash; Search the PyMOLWiki via [[GoogleSearch]]<br />
* PyMOL is known to work under Mac OS X 10.6+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].<br />
* PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.<br />
* PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.<br />
* [[group]] command has been added.<br />
* The truly awesome [[grid_mode]] setting has been added.<br />
* [[Ellipsoids]] representation added for drawing thermal ellipsoids.<br />
* [[GetNamesInSel]] &#8212; find the names of all objects in a selection.<br />
* [[CalcArea]] &#8212; find the area of any given object/selection;<br />
* [[ConnectedCloud]] &#8212; find connected clouds of objects in PyMOL.<br />
* [[MakeVinaCommand]] &#8212; Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.<br />
* [[DrawBoundingBox]] &#8212; Draw a bounding box around your selection.<br />
* Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].<br />
* Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with [[LoadDir]].<br />
* [[PDB Web Services Script]] &#8212; Example using PyMOL and the PDB Web Services.<br />
* [[LigAlign]] &#8212; Ligand-based active site alignment and comparison.<br />
* Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.<br />
* Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests. &diams; New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).<br />
* New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.<br />
<br />
<br />
* [[ImmersiveViz]] -- Headtracking user interface for PyMOL (watch the video)!<br />
* [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars<br />
* [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added. Catalytic site prediction, other tools. Redirects to website.<br />
* [[EMovie]] plugin added. Easy movies in PyMol using a GUI.<br />
* [[DYNMAP]] plugin page created. Check it out!<br />
* [[EZ-Viz]]<br />
<br />
* [[3D_Display_Options|Stereo 3D Displays]].<br />
* Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version. Still need to add more content to the [[TOPTOC]].<br />
* Added a simple script for [[removeAlt|removing specific alternately located atoms]].<br />
* Added a starter gallery of PyMOL-created Journal [[Covers]].<br />
* Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].<br />
* Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!<br />
* [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).<br />
<br />
* Updated the wiki. Also installed the newer GeSHI extension. Please keep an eye out for source code that is improperly tagged and so improperly formatted. See [http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi#Parameters GeSHI Parameters].<br />
* Adding a special category/section for active PyMOL [[:Category:Development|Development]].<br />
* PyMOL 1.0 has been released!<br />
* [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.<br />
<br />
<br />
* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.<br />
* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].<br />
* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]<br />
* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.<br />
* Added [[Kabsch]] script for optimal alignment of two sets of vectors.<br />
* Some details have been released about [[0.99beta11]]'s release and new features.<br />
<br />
<br />
* A new map function is in the beta build, [[Map_Trim]].<br />
* Details on how to build [[Peptide_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| nucleic acid sequences]] by hand.<br />
* New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN<br />
<br />
<br />
* How to create multiple [[Distance]] objects.<br />
* [[Nuccyl]]'s address changed.<br />
<br />
<br />
* PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new <br />
# [[Draw]] command and,<br />
# [[Spheres]] Shader Spheres represenation<br />
* Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.<br />
<br />
* [[Cealign|CE Align v0.8-RBS]] released. Better than before. See test case comparisons.<br />
* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.<br />
* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11469Main Page2013-11-18T16:45:49Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Older_News&diff=11468Older News2013-11-18T16:45:15Z<p>Inchoate: </p>
<hr />
<div>= Older News=<br />
* [[b2transparency]] can set surface transparency based on atom b-factor<br />
* [[psico]] is a python module which extends PyMOL with many commands<br />
* [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
* [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
* [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
* [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
* [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
* [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
* [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].<br />
* [[spectrum_states]] colors states of multi-state object<br />
* [[TMalign]] is a wrapper for the TMalign program<br />
* The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
* [[save_settings]] can dump all changed settings to a file<br />
* Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
* Wiki has been updated. Please report any problems to the sysops.<br />
* Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
* [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
* [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
* [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
* [[PluginDirectory]]: How to set up a personal plugin directory<br />
* Add focal blur to images [[FocalBlur]].<br />
* Visualize VDW clashes with [[show bumps]]<br />
* Color by [[DSSP]] or [[Stride]] secondary structure assignment<br />
* There is a new script to calculate the [[Radius of gyration]]<br />
* New Command<br />
* [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.<br />
* [[ColorByDisplacement]] Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.<br />
* [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.<br />
* Two new scripts: [[AAindex]] and [[Sidechaincenters]]<br />
* [[CAVER_2.0]] update to the CAVER plugin.<br />
* [[AngleBetweenHelices]] calculates the angle between two helices.<br />
* [[GoogleSearch]] widget fixed.<br />
* [[Spectrumany]] creates color gradients with arbitrary color sequences.<br />
* [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.<br />
* [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). <br />
* [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.<br />
* [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.<br />
* See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.<br />
* See [[Supercell]], the new script for making XxYxZ supercells.<br />
* See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.<br />
* See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.<br />
* The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.<br />
* [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.<br />
* [[Fetch]] has been updated to also load electron density maps.<br />
* Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].<br />
* One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. <br />
* [[surface_cavity_mode]] to change how PyMOL displays cavities.<br />
* Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.<br />
* [[Cache]]&mdash;stores information on structures, so we don't have to recompute them.<br />
* News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].<br />
* [[Fetch_Path]]&mdash;Sets the default path for the [[fetch]] command.<br />
* [[SelInside]]&mdash;Creates a custom selection of all atoms spatially inside some user-defined box.<br />
<br />
* [[ContactsNCONT]]&mdash;The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite<br />
* [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).<br />
* Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.<br />
* New &mdash; Search the PyMOLWiki via [[GoogleSearch]]<br />
* PyMOL is known to work under Mac OS X 10.6+ (Snow Leopard) using the new Fink and incentive builds. See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].<br />
* PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.<br />
* PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.<br />
* [[group]] command has been added.<br />
* The truly awesome [[grid_mode]] setting has been added.<br />
* [[Ellipsoids]] representation added for drawing thermal ellipsoids.<br />
* [[GetNamesInSel]] &#8212; find the names of all objects in a selection.<br />
* [[CalcArea]] &#8212; find the area of any given object/selection;<br />
* [[ConnectedCloud]] &#8212; find connected clouds of objects in PyMOL.<br />
* [[MakeVinaCommand]] &#8212; Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.<br />
* [[DrawBoundingBox]] &#8212; Draw a bounding box around your selection.<br />
* Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].<br />
* Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with [[LoadDir]].<br />
* [[PDB Web Services Script]] &#8212; Example using PyMOL and the PDB Web Services.<br />
* [[LigAlign]] &#8212; Ligand-based active site alignment and comparison.<br />
* Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.<br />
* Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests. &diams; New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).<br />
* New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.<br />
<br />
<br />
* [[ImmersiveViz]] -- Headtracking user interface for PyMOL (watch the video)!<br />
* [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars<br />
* [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added. Catalytic site prediction, other tools. Redirects to website.<br />
* [[EMovie]] plugin added. Easy movies in PyMol using a GUI.<br />
* [[DYNMAP]] plugin page created. Check it out!<br />
* [[EZ-Viz]]<br />
<br />
* [[3D_Display_Options|Stereo 3D Displays]].<br />
* Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version. Still need to add more content to the [[TOPTOC]].<br />
* Added a simple script for [[removeAlt|removing specific alternately located atoms]].<br />
* Added a starter gallery of PyMOL-created Journal [[Covers]].<br />
* Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].<br />
* Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!<br />
* [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).<br />
<br />
* Updated the wiki. Also installed the newer GeSHI extension. Please keep an eye out for source code that is improperly tagged and so improperly formatted. See [http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi#Parameters GeSHI Parameters].<br />
* Adding a special category/section for active PyMOL [[:Category:Development|Development]].<br />
* PyMOL 1.0 has been released!<br />
* [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.<br />
<br />
<br />
* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.<br />
* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].<br />
* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]<br />
* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.<br />
* Added [[Kabsch]] script for optimal alignment of two sets of vectors.<br />
* Some details have been released about [[0.99beta11]]'s release and new features.<br />
<br />
<br />
* A new map function is in the beta build, [[Map_Trim]].<br />
* Details on how to build [[Peptide_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| nucleic acid sequences]] by hand.<br />
* New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN<br />
<br />
<br />
* How to create multiple [[Distance]] objects.<br />
* [[Nuccyl]]'s address changed.<br />
<br />
<br />
* PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new <br />
# [[Draw]] command and,<br />
# [[Spheres]] Shader Spheres represenation<br />
* Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.<br />
<br />
* [[Cealign|CE Align v0.8-RBS]] released. Better than before. See test case comparisons.<br />
* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.<br />
* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.</div>Inchoatehttps://pymolwiki.org/index.php?title=Find_symbol&diff=11434Find symbol2013-09-27T13:51:10Z<p>Inchoate: Created page with "= Overview = This script looks for the given symbol in a given module(s). This can be handy if you forgot which module something is in or just want to query for a substring in a..."</p>
<hr />
<div>= Overview =<br />
<br />
This script looks for the given symbol in a given module(s). This can be handy if you forgot which module something is in or just want to query for a substring in a set of modules.<br />
<br />
= Usage =<br />
<source lang="python"><br />
# search pymol and pymol.cmd for any symbol starting with 'mov'<br />
<br />
fs("mov")<br />
['cmd.get_movie_length',<br />
'cmd.get_movie_locked',<br />
'cmd.get_movie_playing',<br />
'cmd.mmove',<br />
'cmd.move',<br />
'cmd.movie',<br />
'cmd.moving',<br />
'cmd.remove',<br />
'cmd.remove_picked']<br />
<br />
# Search PyMOL's CMD module for something called align<br />
<br />
fs("align", "cmd")<br />
['cmd.align', 'cmd.alignto', 'cmd.cealign', 'cmd.get_raw_alignment']<br />
</source><br />
<br />
= The Code =<br />
<source lang="python"><br />
import pymol<br />
import inspect<br />
import pprint<br />
<br />
def fs(needle,haystack=["pymol","cmd"]):<br />
"""<br />
This script will find the 'needle' in the 'haystack,' where the former is<br />
a symbol to be found in the latter, which is a module.<br />
"""<br />
<br />
if type("") == type(haystack):<br />
<br />
haystack = [haystack,]<br />
<br />
for mod in haystack:<br />
<br />
found_list = map(lambda x: "%s.%s" % (mod,x), [name for name,obj in inspect.getmembers(eval(mod)) if needle in name])<br />
<br />
pprint.pprint(found_list)<br />
<br />
return found_list<br />
</source><br />
<br />
[[Category:System_Scripts]]<br />
[[Category:Script_Library]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11387Main Page2013-08-13T19:28:30Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! New Script<br />
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.<br />
|-<br />
! New Script<br />
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.<br />
|-<br />
! New Script<br />
| [[DistancesRH|Distances RH]]<br />
|-<br />
! PyMOL on the iPad<br />
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
|-<br />
! OS X Compatibility<br />
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
|-<br />
! New Script<br />
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
|-<br />
! New Script<br />
| [[b2transparency]] can set surface transparency based on atom b-factor<br />
|-<br />
! New Extension<br />
| [[psico]] is a python module which extends PyMOL with many commands<br />
|-<br />
! New Script<br />
| [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
|-<br />
! New Plugin<br />
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
|-<br />
! New Script<br />
| [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
|-<br />
! New Script<br />
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
|-<br />
! New Script<br />
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
|-<br />
! New Script<br />
| [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
|-<br />
! New Plugin<br />
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].<br />
|-<br />
! New Script<br />
| [[spectrum_states]] colors states of multi-state object<br />
|-<br />
! New Script<br />
| [[TMalign]] is a wrapper for the TMalign program<br />
|-<br />
! Gallery Updates<br />
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
|-<br />
! New Script<br />
| [[save_settings]] can dump all changed settings to a file<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
|-<br />
! Wiki Update<br />
| Wiki has been updated. Please report any problems to the sysops.<br />
|-<br />
! New Scripts<br />
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
|-<br />
! New Script<br />
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
|-<br />
! New Script<br />
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
|-<br />
! New Script<br />
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Ray_Trace_Fog&diff=11385Ray Trace Fog2013-08-09T21:23:59Z<p>Inchoate: </p>
<hr />
<div>== Overview ==<br />
The '''ray_trace_fog''' setting forces PyMol to render '''fog''' over objects further from the camera. This adds a sense of depth and brings the attention to foreground objects.<br />
<br />
== Examples ==<br />
<gallery><br />
Image:Fogon.png|Setting on<br />
Image:Fogoff.png|Setting off<br />
</gallery><br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set ray_trace_fog, 0 # off<br />
set ray_trace_fog, 1 # on<br />
</source><br />
<br />
[[Category:Settings]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=11374Main Page2013-07-29T19:02:38Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! New Script<br />
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.<br />
|-<br />
! New Script<br />
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.<br />
|-<br />
! New Script<br />
| [[DistancesRH|Distances RH]]<br />
|-<br />
! PyMOL on the iPad<br />
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
|-<br />
! OS X Compatibility<br />
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
|-<br />
! New Script<br />
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
|-<br />
! New Script<br />
| [[b2transparency]] can set surface transparency based on atom b-factor<br />
|-<br />
! New Extension<br />
| [[psico]] is a python module which extends PyMOL with many commands<br />
|-<br />
! New Script<br />
| [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
|-<br />
! New Plugin<br />
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
|-<br />
! New Script<br />
| [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
|-<br />
! New Script<br />
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
|-<br />
! New Script<br />
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
|-<br />
! New Script<br />
| [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
|-<br />
! New Plugin<br />
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].<br />
|-<br />
! New Script<br />
| [[spectrum_states]] colors states of multi-state object<br />
|-<br />
! New Script<br />
| [[TMalign]] is a wrapper for the TMalign program<br />
|-<br />
! Gallery Updates<br />
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
|-<br />
! New Script<br />
| [[save_settings]] can dump all changed settings to a file<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
|-<br />
! Wiki Update<br />
| Wiki has been updated. Please report any problems to the sysops.<br />
|-<br />
! New Scripts<br />
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
|-<br />
! New Script<br />
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
|-<br />
! New Script<br />
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
|-<br />
! New Script<br />
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Xpyder&diff=11359Xpyder2013-07-16T21:08:13Z<p>Inchoate: </p>
<hr />
<div>[http://pubs.acs.org/doi/abs/10.1021/ci300213c xPyder] is a PyMOL plugin for analyzing coupled residued and their networks in proteins.<br />
<br />
You can download it [http://linux.btbs.unimib.it/xpyder/ here].<br />
<br />
[[Category:Plugins]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Xpyder&diff=11358Xpyder2013-07-16T21:05:15Z<p>Inchoate: Created page with "[http://pubs.acs.org/doi/abs/10.1021/ci300213c xPyder] is a PyMOL plugin for analyzing coupled residued and their networks in proteins. Category:Plugins"</p>
<hr />
<div>[http://pubs.acs.org/doi/abs/10.1021/ci300213c xPyder] is a PyMOL plugin for analyzing coupled residued and their networks in proteins.<br />
<br />
[[Category:Plugins]]</div>Inchoatehttps://pymolwiki.org/index.php?title=GROMACS_Plugin&diff=11357GROMACS Plugin2013-07-16T20:59:43Z<p>Inchoate: Created page with "A new plugin that connects GROMACS and PyMOL has been [http://pubs.acs.org/doi/abs/10.1021/ci400071x published]. Category:Plugins"</p>
<hr />
<div>A new plugin that connects GROMACS and PyMOL has been [http://pubs.acs.org/doi/abs/10.1021/ci400071x published].<br />
<br />
[[Category:Plugins]]</div>Inchoatehttps://pymolwiki.org/index.php?title=File:Cover_Paunescu.jpg&diff=11263File:Cover Paunescu.jpg2013-05-17T13:12:10Z<p>Inchoate: Paunescu's Cover</p>
<hr />
<div>Paunescu's Cover</div>Inchoatehttps://pymolwiki.org/index.php?title=FocalBlur&diff=11167FocalBlur2013-04-17T14:57:14Z<p>Inchoate: </p>
<hr />
<div>[[Image:StylizedFocalBlur.png|550px|right]]<br />
<br />
<br />
<br />
==Description==<br />
<br />
This script creates fancy figures by introducing a focal blur to the image. The object at the origin will be in focus. <br />
<br />
===Usage===<br />
<br />
Load the script using the [[run]] command. Execute the script using PyMOL syntax:<br />
<source lang="python"><br />
FocalBlur aperture=2.0,samples=20,ray=1<br />
</source><br />
or using python syntax:<br />
<source lang="python"><br />
FocalBlur(aperture=2.0,samples=20,ray=1)<br />
</source><br />
<br />
<br />
For additional options, see the script comments.<br />
<br />
===Notes===<br />
<br />
* When using raytracing, the image creation will take ''n'' times longer than normal, where ''n'' is the number of samples.<br />
* The aperture is related to the aperture on a camera.<br />
<br />
===Bugs===<br />
<br />
* FocalBlur uses the Python Image Library (PIL), a necessary components of PIL is missing in the Windows version of PyMOL<br />
* There is a bug when not using ray tracing with the free version of PyMOL<br />
<br />
===Examples===<br />
<br />
<gallery perrow=3 widths=300 heights=240><br />
Image:FocalBlur_a1.0_r1.png|FocalBlur aperture=1,samples=100,ray=1<br />
Image:FocalBlur_a2.0_r1.png|FocalBlur aperture=2,samples=100,ray=1<br />
Image:FocalBlur_a4.0_r1.png|FocalBlur aperture=4,samples=400,ray=1<br />
Image:FocalBlur_a4.0_r0.png|FocalBlur aperture=4,samples=400,ray=0<br />
Image:Focal_blur _ex6.png<br />
Image:Focal blur_ex_ap3.png<br />
Image:Focal blur_ex_ap3_mode1.png<br />
Image:Focal blur_ex_ap3_mode2.png<br />
Image:Focal blur_ex_ap3_mode3.png<br />
</gallery><br />
<br />
==Script==<br />
Load the script using the [[run]] command<br />
<br />
<source lang="python"><br />
from pymol import cmd<br />
from tempfile import mkdtemp<br />
from shutil import rmtree<br />
from math import sin,cos,pi,sqrt<br />
from PIL import Image<br />
<br />
def FocalBlur(aperture=2.0,samples=10,ray=0,width=0,height=0):<br />
'''<br />
DESCRIPTION<br />
<br />
Creates fancy figures by introducing a focal blur to the image. The object<br />
at the origin will be in focus. <br />
<br />
AUTHOR<br />
<br />
Jarl Underhaug<br />
University of Bergen<br />
jarl_dot_underhaug_at_gmail_dot_com<br />
<br />
Updates by Jason Vertrees and Thomas Holder<br />
<br />
USAGE<br />
<br />
FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int<br />
<br />
EXAMPELS<br />
<br />
FocalBlur aperture=1, samples=100<br />
FocalBlur aperture=2, samples=100, ray=1, width=600, height=400<br />
'''<br />
<br />
# Formalize the parameter types<br />
ray = (ray in ("True", "true", 1, "1"))<br />
aperture, samples = float(aperture), int(samples)<br />
width, height = int(width), int(height)<br />
<br />
# Create a temporary directory<br />
tmpdir = mkdtemp()<br />
<br />
# Get the orientation of the protein and the light<br />
light = cmd.get('light')[1:-1]<br />
light = [float(s) for s in light.split(',')]<br />
view = cmd.get_view()<br />
<br />
# Rotate the protein and the light in order to create the blur<br />
for frame in range(samples):<br />
# Angles to rotate protein and light<br />
# Populate angles as Fermat's spiral<br />
theta = frame * pi * 110.0/144.0<br />
radius = 0.5 * aperture * sqrt(frame/float(samples-1))<br />
x = cos(theta) * radius<br />
y = sin(theta) * radius<br />
xr = x/180.0*pi<br />
yr = y/180.0*pi<br />
<br />
# Rotate the protein<br />
cmd.turn('x',x)<br />
cmd.turn('y',y)<br />
<br />
# Rotate the light<br />
ly = light[1]*cos(xr)-light[2]*sin(xr)<br />
lz = light[2]*cos(xr)+light[1]*sin(xr)<br />
lx = light[0]*cos(yr)+lz*sin(yr)<br />
lz = lz*cos(yr)-lx*sin(yr)<br />
cmd.set('light',[lx,ly,lz])<br />
<br />
curFile = "%s/frame-%04d.png" % (tmpdir,frame)<br />
print "Created frame %i/%i (%0.0f%%)" % (frame+1,samples,100*(frame+1)/samples)<br />
<br />
# Save the image to temporary directory<br />
if ray:<br />
cmd.ray(width,height)<br />
cmd.png(curFile)<br />
else:<br />
cmd.png(curFile,quiet=1)<br />
<br />
# Create the average/blured image<br />
try:<br />
avg = Image.blend(avg,Image.open(curFile),1.0/(frame+1))<br />
except:<br />
avg = Image.open(curFile)<br />
<br />
# Return the protein and the light to the original orientation<br />
cmd.set('light',light)<br />
cmd.set_view(view)<br />
<br />
# Load the blured image<br />
avg.save('%s/avg.png' % (tmpdir))<br />
cmd.load('%s/avg.png' % (tmpdir))<br />
<br />
# Delete the temporary files<br />
rmtree(tmpdir)<br />
<br />
cmd.extend('FocalBlur', FocalBlur)<br />
<br />
</source><br />
<br />
<br />
[[Category:Script_Library]]</div>Inchoatehttps://pymolwiki.org/index.php?title=File:StylizedFocalBlur.png&diff=11166File:StylizedFocalBlur.png2013-04-17T14:55:08Z<p>Inchoate: </p>
<hr />
<div></div>Inchoatehttps://pymolwiki.org/index.php?title=Gallery&diff=11157Gallery2013-04-12T16:09:44Z<p>Inchoate: </p>
<hr />
<div>{| align="center"<br />
|+ style="font-size:190%; font-weight: bold; color:#038; padding-bottom: 15px;" |PyMOLWiki Gallery<br />
|- style="text-align:center; font-weight: bold; font-size:120%; color:#333;"<br />
| Cool PyMOL-generated Images and their Scripts.<br/><br/>''[[Talk:Gallery#Adding|Add Your Own]]''<br />
|-<br />
|}<br />
<br />
<br />
<br />
{{GalleryImage<br />
<!-- This creates a row entry for the Gallery section --><br />
|<!-- Image --><br />
image=BW_raytraced_complex_image.jpg|size=200px<br />
|<!-- Title above image --><br />
title=Complex B&W outline representation<br />
|<!-- 'Description' section (shows up below image)--><br />
description=Making a B&W outlined image with depth.<br />
|<!-- 'What to Type' section --><br />
cmdString=<source lang="python"><br />
# first load lipid model<br />
load lipids.pdb; <br />
# hide the initially loaded representation<br />
hide all; <br />
# set background color to white<br />
bg_color white; <br />
# show lipid model as sticks<br />
show sticks, lipids; <br />
# color the lipids model by element CHNOS #2 (carbon green)<br />
util.cbag lipids; <br />
<br />
# select all hydrogens and remove them from the model<br />
select hideme, hydro; <br />
hide everything, hideme; <br />
delete hideme;<br />
<br />
# create phosphate spheres<br />
create phos, elem p; <br />
hide everything, phos;<br />
show spheres, phos;<br />
<br />
# load helix model<br />
load helix.pdb; <br />
# hide the initially loaded representation<br />
hide everything, helix;<br />
# make the helical struct into a cartoon form<br />
show cartoon, helix; <br />
# style the cartoon form<br />
cartoon putty; <br />
<br />
# reposition the helix among the lipids using<br />
# the 3-Button Editing Mouse Mode<br />
# basically<br />
# Shift+Left Mouse to rotate the helix<br />
# Shift+Middle Mouse to move the helix<br />
# also, you may want to make liberal use of the<br />
# get_view and set_view commands.<br />
#<br />
# When you have the scene set like you want,<br />
# continue with...<br />
<br />
# move the model to find the view you want, <br />
# and use get_view to get the coordinate description<br />
get_view;<br />
<br />
# set ray_trace_mode to black and white outline<br />
set ray_trace_mode, 2;<br />
</source><br />
Now, you'll need to save multiple versions of your model. (use '''ray''', then '''png''' ''<filename>'' to save each version)<ol><br />
<li> Version A: with all the elements except for the helix. This will become the background.</li><br />
<li> Version B: with the 'front' elements, and the helix. Basically this is just a few 'layers' of lipid, with the helix among them. To do this:</li><ol type="a"><br />
<li>move the model around until you visually see the part to remove</li><br />
<li>switch your Mouse Mode to 3-button viewing, then use the +Box selection (Shift+Left mouse) to select the 'background' portion to hide.</li><br />
<li>choose Hide>Everything for the selection</li><br />
<li>use the code from get_view to go back to the original view</li><br />
</ol></ol><br />
Finally, you will need to compose the image in Photoshop (or Gimp, here I'll use Photoshop).<ol><br />
<li>Load the two versions.</li><br />
<li>Select the white background in Version B, then choose Select>Color Range...</li><br />
<li>Make sure 'Select' is set to 'Sampled Colors', and 'Fuzziness' is set to 150, then click okay.</li><br />
<li>delete the white selection, then choose Select>All</li><br />
<li>copy the picture, then switch to Version A and paste the selection (it should paste into its own layer as 'Layer 1')</li><br />
<li>Click on 'Layer 0' (which is Version A) and change its opacity to 30%</li><br />
<li>Create a new layer under 'Layer 0' which is filled with white only (or whatever background color you like)</li><br />
<li>Click on 'Layer 1' (which is Version B), and using the Move tool (and nudge), align the molecules in 'Layer 1' to 'Layer 0'</li><br />
<li>Some parts of 'Layer 1' are transparent and shouldn't be. Using the Paint Bucket tool fill in these areas with white (or whichever color you find appropriate).</li><br />
<li>Admire your handiwork; put it in a publication, presentation, or poster.</li></ol><br />
|<!-- 'See Also' section (shows up below image)--><br />
seeAlso=<br />
* [[Bg_Color|bg_color]]<br />
* [[Get_View|get_view]]<br />
* Mouse Modes (no good reference for this?)<br />
* [[png]]<br />
* [[Cartoon#Sausage_Representation|putty]]<br />
* [[ray]]<br />
* [[Ray#Modes|ray_trace_mode]]<br />
* [[set]]<br />
* [[Set_View|set_view]]<br />
* [[Single-word_Selectors |single word property selectors]]<br />
* [[Advanced_Coloring#Coloring_by_atom_type|util.cbag]]<br />
}}<br />
<br />
<br />
<br />
{{GalleryImage<br />
|image=Image_merged.png|size=200px|title=A "Sliced" Image|description=A more complex example of how to create an image of a slice.<br />
|cmdString=<source lang="python"><br />
# example script for creation of an image with a slice region<br />
load $PYMOL_PATH/test/dat/1tii.pdb<br />
orient<br />
<br />
# must disable depth cue and shadows<br />
unset depth_cue<br />
unset ray_shadows<br />
set ray_trace_mode, 0<br />
<br />
# this controls the z depth of the slice plane<br />
# (sets it halfway between the clipping planes)<br />
fraction = 0.42<br />
view = cmd.get_view()<br />
near_dist = fraction*(view[16]-view[15])<br />
far_dist = (view[16]-view[15]) - near_dist<br />
cmd.clip("near", -near_dist)<br />
<br />
# render opaque background image<br />
as surface<br />
set ray_interior_color, grey80<br />
set opaque_background<br />
set surface_color, white<br />
ray<br />
save image_back.png<br />
<br />
cmd.clip("near", near_dist)<br />
cmd.clip("far", far_dist)<br />
<br />
# render the foreground image<br />
as cartoon<br />
util.cbc<br />
unset opaque_background<br />
ray<br />
save image_front.png<br />
<br />
# now use Photoshop, Gimp, or ImageMagick to combine the images<br />
system composite image_front.png image_back.png image_merged.png<br />
system display image_merged.png<br />
</source><br />
|seeAlso=<br />
*[[load]]<br />
*[[orient]]<br />
*[[set]]<br />
*[[unset]]<br />
*[[depth_cue]]<br />
*[[ray_shadows]]<br />
*[[Ray#Modes|ray_trace_mode]]<br />
*[[Get_View]]<br />
*[[clip]]<br />
*[[as]]<br />
*[[surface]]<br />
*[[cartoon]]<br />
*[[ray_interior_color]]<br />
*[[color]]<br />
*[[ray]]<br />
*[[save]]<br />
*[[util.cbc]]<br />
*[[opaque_background]]<br />
*[[save]]<br />
*[[system]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
|image=Gm2.png|size=200px|title=Grid Mode|description=This image shows [[Grid mode|Grid Mode]] in action.<br />
|cmdString=<source lang="python"><br />
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;<br />
set grid_mode<br />
</source><br />
'''Hint:''' You may wish to execute the 'reset' command on the command line after running the above commands to get full molecules in view of window and centered in a more useable manner.<br />
|seeAlso=<br />
*[[Fetch]]<br />
*[[Set]]<br />
*[[grid_mode]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Fov60.png|size=200px|title=Cool Perspective|description=This image shows a perspective through [[Field_Of_View]].<br />
|cmdString=<source lang="python"><br />
load prot.pdb;<br />
zoom i. 46-49 and n. CA<br />
set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Ray]]<br />
*[[Zoom]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Pocket.png|size=200px|title=Representing a binding pocket|description=This image shows a nice way to show binding surfaces<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb, tmp<br />
extract lig, organic<br />
extract prot, polymer<br />
delete tmp<br />
<br />
set surface_carve_cutoff, 4.5<br />
set surface_carve_selection, lig<br />
set surface_carve_normal_cutoff, -0.1<br />
<br />
show surface, prot within 8 of lig<br />
set two_sided_lighting<br />
set transparency, 0.5<br />
show sticks, lig<br />
orient lig<br />
<br />
set surface_color, white<br />
set surface_type, 2 # mesh<br />
unset ray_shadows<br />
</source><br />
|seeAlso=<br />
*[[extract]]<br />
*[[delete]]<br />
*[[show]]<br />
*[[set]]<br />
*[[orient]]<br />
*[[surface_carve_cutoff]]<br />
*[[surface_carve_selection]]<br />
*[[surface_carve_normal_cutoff]]<br />
*[[surface_color]]<br />
*[[surface_type]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=QuteMolLike.png|size=400px|title=QuteMol Like|description=QuteMol like image--modern ''feel'' to it. Check out the [[Media:Depthmol.mpeg|movie]].<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb<br />
set_color oxygen, [1.0,0.4,0.4]<br />
set_color nitrogen, [0.5,0.5,1.0]<br />
remove solvent<br />
as spheres<br />
util.cbaw<br />
bg white<br />
set light_count,8<br />
set spec_count,1<br />
set shininess, 10<br />
set specular, 0.25<br />
set ambient,0<br />
set direct,0<br />
set reflect,1.5<br />
set ray_shadow_decay_factor, 0.1<br />
set ray_shadow_decay_range, 2<br />
unset depth_cue<br />
# for added coolness<br />
# set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Set_color]]<br />
*[[Remove]]<br />
*[[Solvent]]<br />
*[[As]]<br />
*[[Util]]<br />
*[[Util.cbaw]]<br />
*[[Bg]]<br />
*[[Light_Count]]<br />
*[[Spec_Count]]<br />
*[[Shininess]]<br />
*[[Specular]]<br />
*[[Ambient]]<br />
*[[Direct]]<br />
*[[Reflect]]<br />
*[[Ray_shadow_decay_factor]]<br />
*[[Ray_shadow_decay_range]]<br />
*[[Unset]]<br />
*[[depth_cue]]<br />
*[[Ray]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Tilt shift.png|size=500px|title=Simulating Tilt-shift|description=Tilt shift simulation<br />
|cmdString=<source lang="python"><br />
fetch 1wld<br />
as surface, poly<br />
as sticks, org<br />
h_add solvent<br />
color grey, poly<br />
orient org<br />
png img.png<br />
# now, go into Photoshop or the GIMP and apply a Gaussian or<br />
# Focus blur to the top and bottom portions of the image<br />
</source><br />
|seeAlso=<br />
*[[fetch]]<br />
*[[show_as]]<br />
*[[h_add]]<br />
*[[color]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
|image=Rnt.png|size=500px|title=Ray-normal-based transparency|description=Ray-normal-based transparency<br />
|cmdString=<source lang="python"><br />
# grey surface<br />
set surface_color, grey<br />
<br />
# cavity mode<br />
set surface_mode, 3<br />
<br />
# layered transparency mode<br />
set transparency_mode, 1<br />
<br />
# surface transparency<br />
set transparency, 0.5<br />
<br />
# oblique and contrast define the<br />
# look of the surface transparency:<br />
# if the normal vector is <br />
set ray_transparency_oblique<br />
set ray_transparency_oblique_power, 8<br />
set ray_transparency_contrast, 7<br />
<br />
# fetch a protein, with a <br />
# small molecule in a nice<br />
# hidden pocket<br />
fetch 1hpv, async=0<br />
<br />
hide<br />
<br />
# show the small molecule as surface<br />
show surface, org<br />
<br />
# arrange the view<br />
orient org<br />
<br />
# zoom back a little<br />
zoom org, 1<br />
<br />
# show the small molecule inside as sticks<br />
show sticks, org<br />
<br />
# show some nearby sidechains<br />
show lines, poly within 5 of org<br />
<br />
# enable frame caching for playback<br />
set cache_frames, 1<br />
<br />
set ray_trace_frames, 1<br />
<br />
mset 1x120<br />
<br />
movie.roll 1, 120, 1, x<br />
<br />
mplay<br />
<br />
# now sit back and wait 5 minutes...<br />
</source><br />
|seeAlso=<br />
* [[surface_color]]<br />
* [[surface_mode]]<br />
* [[transparency_mode]]<br />
* [[transparency]]<br />
* [[ray_transparency_oblique]]<br />
* [[ray_transparency_oblique_power]]<br />
* [[ray_transparency_contrast]]<br />
* [[fetch]]<br />
* [[orient]]<br />
* [[zoom]]<br />
* [[show]]<br />
* [[sticks]]<br />
* [[lines]]<br />
* [[cache_frames]]<br />
* [[mset]]<br />
* [[ray_trace_frames]]<br />
* [[movie.roll]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
| title=Blobby Main Chain<br />
| image=Gallery dark tube mc.png<br />
| description=Main chain as a darkened tube with special shading<br />
| seeAlso=<br />
* [[remove]]<br />
* [[alter]]<br />
* [[gaussian_resolution]]<br />
* [[map_new]]<br />
* [[spectrum]]<br />
* [[light_count]]<br />
* [[spec_count]]<br />
* [[shininess]]<br />
* [[reflect]]<br />
* [[direct]]<br />
* [[ambient]]<br />
* [[ray_shadow_decay_factor]]<br />
* [[ray_shadow_decay_range]]<br />
* [[fetch]]<br />
| cmdString=<source lang="python"><br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 3.5<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 0.5, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 3.0<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], [-1, -1, 0])<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
bg grey<br />
<br />
# soften out the image<br />
set light_count,8<br />
set spec_count,1<br />
set shininess, 10<br />
set specular, 0.075<br />
set ambient,0<br />
set direct,0<br />
set reflect, 0.85<br />
set ray_shadow_decay_factor, 0.1<br />
set ray_shadow_decay_range, 4<br />
<br />
unset depth_cue<br />
<br />
# ray trace the image<br />
orient<br />
ray<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Blobby Side Chains<br />
| image=Gallery blob sc.png<br />
| description=Main chain as tube with gaussian surfaced side chains<br />
| seeAlso=<br />
* [[cartoon]]<br />
* [[show_as]]<br />
* [[fetch]]<br />
* [[cartoon_tube_radius]]<br />
* [[cartoon_color]]<br />
* [[cartoon_side_chain_helper]]<br />
* [[alter]]<br />
* [[gaussian_resolution]]<br />
* [[map_new]]<br />
* [[isosurface]]<br />
* [[color]]<br />
* [[hide]]<br />
| cmdString=<source lang="python"><br />
# fetch a protein<br />
<br />
fetch 1rx1, async=0<br />
<br />
# setup the cartoon tubes<br />
<br />
as cartoon<br />
<br />
cartoon tube<br />
<br />
set cartoon_tube_radius, 0.7<br />
<br />
set cartoon_color, brown<br />
<br />
set cartoon_side_chain_helper, on<br />
<br />
show sticks, poly<br />
<br />
color yellow<br />
<br />
# README<br />
# stop here, or try this for "sloppy sticks"<br />
# beefy video card required!<br />
<br />
select rep sticks<br />
select sele and not n. C+O+N+CA<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 2.5 A map resolution<br />
<br />
set gaussian_resolution, 2.5<br />
<br />
# 0.2 A sampling; lower=smoother<br />
<br />
map_new map, gaussian, 0.2, sele, 5<br />
<br />
# create a surface from the map<br />
<br />
isosurface surf, map, 5.0<br />
<br />
color yellow, surf<br />
hide sticks<br />
<br />
# reconnect the main chain to the blobs<br />
show sticks, n. CA+CB<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Smooth surface with ligand<br />
| image=Abs surf.png<br />
| description=Gaussian abstracted surface colored by underlying b-factors and shown with ligand<br />
| seeAlso=<br />
* [[ramp_new]]<br />
* [[show_as]]<br />
* [[gaussian_resolution]]<br />
* [[fetch]]<br />
* [[isosurface]]<br />
* [[spectrum]]<br />
* [[set]]<br />
* [[alter]]<br />
* [[get_view]]<br />
* [[set_view]]<br />
| cmdString=<source lang="python"><br />
<br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 7.6<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 1, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 1.5<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the b-factors of the<br />
# underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
show sticks, org<br />
show spheres, org<br />
<br />
color magenta, org<br />
reinit<br />
<br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 7.6<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 1, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 1.5<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the b-factors of the<br />
# underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
show sticks, org<br />
show spheres, org<br />
<br />
color magenta, org<br />
set_bond stick_radius, 0.13, org<br />
set sphere_scale, 0.26, org<br />
<br />
set_bond stick_radius, 0.13, org<br />
set_bond stick_color, white, org<br />
set sphere_scale, 0.26, org<br />
set_view (\<br />
-0.877680123, 0.456324875, -0.146428943,\<br />
0.149618521, -0.029365506, -0.988305628,\<br />
-0.455291569, -0.889327347, -0.042500813,\<br />
-0.000035629, 0.000030629, -37.112102509,\<br />
-3.300258160, 6.586110592, 22.637466431,\<br />
8.231912613, 65.999290466, -50.000000000 )<br />
<br />
# ray trace the image<br />
ray<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Complex Stylized Protein<br />
| image=Cool.png<br />
| description=A Cool, Stylized Rendering<br />
| seeAlso=<br />
* [[field_of_view]]<br />
* [[set]]<br />
* [[light_count]]<br />
* [[ambient]]<br />
* [[ramp_new]]<br />
* [[color]]<br />
* [[surface_quality]]<br />
* [[transparency]]<br />
* [[ambient_occlusion_mode]]<br />
* [[spec_reflect]]<br />
* [[spec_direct]]<br />
* [[disable]]<br />
* [[ray_shadows]]<br />
* [[ray_opaque_background]]<br />
* [[ray_transparency_oblique]]<br />
* [[ray_transparency_oblique_power]]<br />
* [[ray_transparency_contrast]]<br />
| cmdString=<source lang="python"><br />
fetch 1eaz, async=0<br />
<br />
extract oo, org<br />
<br />
hide everything, solvent<br />
<br />
set field_of_view, 50<br />
<br />
preset.ball_and_stick("oo")<br />
<br />
set_bond stick_color, 0xffff44, oo<br />
<br />
set_bond stick_transparency, 0.35, oo<br />
<br />
color grey, oo and e. C<br />
<br />
set valence, 1, oo<br />
<br />
ramp_new pRamp, oo, selection=poly, range=[5,30], color=rainbow<br />
<br />
set surface_color, pRamp, poly<br />
<br />
show spheres, poly<br />
<br />
color white, poly<br />
<br />
color grey30, poly and e. C<br />
<br />
set sphere_scale, 0.99, poly<br />
<br />
set ray_transparency_contrast, 0.20<br />
<br />
set ray_transparency_oblique, 1.0<br />
<br />
set ray_transparency_oblique_power, 20<br />
<br />
show surface, poly<br />
<br />
set surface_quality, 2<br />
<br />
set light_count, 5<br />
<br />
set ambient_occlusion_mode, 1<br />
<br />
set ambient_occlusion_scale, 50<br />
<br />
set ambient, 0.40<br />
<br />
set transparency, 0.50<br />
<br />
disable pRamp<br />
<br />
set spec_power, 1200<br />
<br />
set spec_reflect, 0.20<br />
<br />
set ray_opaque_background, 0<br />
<br />
set ray_shadow, 0<br />
<br />
ray<br />
</source><br />
}}<br />
<br />
<br />
{{GalleryImage<br />
| title=Goodsell-like<br />
| image=Goodsell_like2.png<br />
| description=Create Goodsell-like images in PyMOL<br />
| seeAlso=<br />
* [[set]]<br />
* [[light_count]]<br />
* [[color]]<br />
* [[ray_shadows]]<br />
* [[ray_trace_mode]]<br />
* [[specular]]<br />
* [[orient]]<br />
* [[ray_trace_gain]]<br />
* [[depth_cue]]<br />
| cmdString=<source lang="python"><br />
# fetch the protein<br />
<br />
fetch 1rx1, async=0<br />
<br />
# show it as blue/magenta spheres<br />
<br />
as spheres<br />
<br />
color lightblue, not org<br />
<br />
color magenta, org<br />
<br />
remove solvent<br />
<br />
# set the view<br />
<br />
orient all within 8 of org<br />
<br />
# set the lights, ray tracing setttings<br />
# to get the Goodsell-like rendering<br />
<br />
unset specular<br />
<br />
set ray_trace_gain, 0<br />
<br />
set ray_trace_mode, 3<br />
<br />
bg_color white<br />
<br />
set ray_trace_color, black<br />
<br />
unset depth_cue<br />
<br />
ray<br />
</source><br />
}}<br />
<br />
<br />
{{GalleryImage<br />
| title=Stylized Ball and Stick<br />
| image=Stylized bns.png<br />
| description=Stylized Ball and Sticks<br />
| seeAlso=<br />
| cmdString=<source lang="python"><br />
hide everything<br />
show sticks<br />
show spheres<br />
set stick_radius, .07<br />
set sphere_scale, .18<br />
set sphere_scale, .13, elem H<br />
set bg_rgb=[1, 1, 1]<br />
set stick_quality, 50<br />
set sphere_quality, 4<br />
color gray85, elem C<br />
color red, elem O<br />
color slate, elem N<br />
color gray98, elem H<br />
set stick_color, black<br />
set ray_trace_mode, 1<br />
set ray_texture, 2<br />
set antialias, 3<br />
set ambient, 0.5<br />
set spec_count, 5<br />
set shininess, 50<br />
set specular, 1<br />
set reflect, .1<br />
set dash_gap, 0<br />
set dash_color, black<br />
set dash_gap, .15<br />
set dash_length, .05<br />
set dash_round_ends, 0<br />
set dash_radius, .05<br />
python<br />
preset.ball_and_stick("vis")<br />
python end<br />
fetch 1rx1, async=0<br />
remove not org<br />
orient org<br />
ray<br />
</source><br />
}}</div>Inchoatehttps://pymolwiki.org/index.php?title=File:Stylized_bns.png&diff=11156File:Stylized bns.png2013-04-12T16:07:37Z<p>Inchoate: Stylized ball and sticks</p>
<hr />
<div>Stylized ball and sticks</div>Inchoatehttps://pymolwiki.org/index.php?title=Dehydron&diff=11152Dehydron2013-03-27T20:58:38Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/dehydron.py<br />
|author = [[User:OsvaldoMartin|Osvaldo Martin]]<br />
|license = GPL<br />
}}<br />
== Introduction ==<br />
A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure.<br />
<br />
A dehydron is a protein main chain hydrogen bond incompletely shielded from water attack. Dehydrons are sticky, since they promote the removal of surrounding water through protein associations or ligand binding. Dehydrons are less conserved than other structural motifs, hence identification of dehydrons could help to increase specificity during the rational drug design process.<br />
<br />
For a brief introduction to the dehydron concept, please read [http://en.wikipedia.org/wiki/Dehydron wikipedia].<br />
<br />
== Installation ==<br />
=== Linux ===<br />
This plugin is ready "out-of-box" for Linux users through the project [[git_intro | Pymol-script-repo]]<br />
<br />
=== Windows ===<br />
This plugin is ready "out-of-box" for Windows users through the project [[git_intro | Pymol-script-repo]]<br />
<br />
=== Mac OsX ===<br />
This plugin have not been tested on a Mac OsX machine, but it should work.<br />
<br />
== Usage ==<br />
The plugin can be accessed using the following command:<br />
<br />
<source lang="python"><br />
dehydron [ selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]<br />
</source><br />
<br />
[[Image:Dehydrons.png|580px|thumb|Dehydrons calculated and displayed in PyMOL.]]<br />
<br />
<br />
Or using a graphical environment (see accompanying figure)<br />
<br />
<br />
There are five parameters the user can change:<br />
<br />
Two of them control the hydrogen bonds detection.<br />
<br />
* Angle range: deviation in degrees from the optimal hydrogen bond angle (C=0 N-H).<br />
* Max distance: maximum donor-acceptor distance.<br />
<br />
Another two control the dehydron detection.<br />
<br />
* Desolvatation sphere radius: this parameter controls the radius of the two spheres centered at the Cα carbon of the donor and acceptor residues. A dehydron is defined by the number of "wrappers" inside this two spheres.<br><br />
* Min wrappers: a hydrogen bond surrounded with less "wrappers" than "min_wrappers" is a dehydron. Setting this parameter to a "high" value, something like 100, will return all main chain hydrogen bonds (according to the angle range and max distance parameters).<br />
<br />
A wrapper is defined as a carbon atom not bonded directly to an oxygen or nitrogen atom, i.e. a non-polar carbon atom. The plugin count as wrappers any non-polar carbon from any protein chain, organic ligand or other type of molecule, if the atoms belong "selection" (see below). This means that if you have, for example, a dimeric protein you will probably get different results for the dimer and for the isolated monomers. Instead, if you upload two (or more) different files the results will be independent because the plugin does not count atoms from other objects<br />
<br />
* Selection: This parameter allows the user to select which part of system is used to calculate dehydrons. This parameter is useful, for example, to calculate dehydronds for different objects independently or to easily calculate dehydrons with and without an organic ligand. The default selection is "all".<br />
<br />
<br />
== Acknowledgement ==<br />
The H-bond detection code is based on the list_mc_hbonds.py script from Robert L. Campbell http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/<br />
<br />
== Changelog ==<br />
<br />
* 2012-01-14 (Version 1.0)<br />
*# First public version was released and put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].<br />
<br />
*2012-01-28 (Version 1.1) <br />
*# Minor changes in the code most of them not visible for the end-user.<br />
<br />
*2012-02-28 (Version 1.5) <br />
*# The code was cleaned (e.g. remove global variables and other ugly stuff)<br />
*# The code was made available as a PyMOL command<br />
*# Better support for multiple objects<br />
All features in this version and most of the code was provided by [[User:Speleo3|Thomas Holder]], thanks Thomas! :-)<br />
<br />
*2012-03-14 (Version 1.6)<br />
*# Representation is not changed to "cartoon" after each calculation<br />
*# Total control over the selection from which dehydrons are calculated<br />
<br />
*2013-03-26 (Version 1.7)<br />
*# Wrappers were not correctly counted for structures with hydrogen atoms. <br />
Thanks Shafqat Rasool for reporting the bug.<br />
<br />
== References ==<br />
Citation for Dehydrons:<br><br />
Fernández A. and Scott R.; "Adherence of packing defects in soluble proteins", Phys. Rev. Lett. 91, 018102 (2003).<br />
<br />
Fernández A., Rogale K., Scott R. and Scheraga H.A.; "Inhibitor design by wrapping packing defects in HIV-1 proteins", PNAS, 101, 11640-45 (2004).<br />
<br />
Fernández A. "Transformative Concepts for Drug Design: Target Wrapping" (ISBN 978-3642117916), Springer-Verlag, Berlin, Heidelberg (2010).<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Inertia_tensor&diff=11131Inertia tensor2013-03-08T01:55:12Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = Python Module<br />
|filename = inertia_tensor.py<br />
|author = [http://www.mattmaciejewski.com Mateusz Maciejewski]<br />
|license = MIT<br />
}}<br />
<br />
[[Image:It.png|300px|right]]<br />
<br />
This script will draw the eigenvectors of the inertia tensor of the selected part of the molecule.<br />
<br />
== Usage ==<br />
<br />
tensor selection, name, model<br />
<br />
== Examples ==<br />
<br />
To draw the inertia tensor of the first model in PDB file 4B2R do:<br />
<br />
<source lang="python"><br />
fetch 4b2r, async=0<br />
hide lines<br />
show cartoon<br />
run inertia_tensor.py<br />
tensor 4b2r & n. n+ca+c & i. 569-623, tensor_dom11, 1<br />
</source><br />
<br />
== Reference ==<br />
<br />
A figure generated using this script can be seen in the following reference:<br />
<br />
* ''Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings''. Maciejewski M, Tjandra N, Barlow PN. '''Biochemistry'''. 50(38) 2011, p. 8138-49, fig. 1 [http://dx.doi.org/10.1021/bi200575b doi:10.1021/bi200575b]<br />
<br />
[[Category:Script_Library]]<br />
[[Category:UI_Scripts]]</div>Inchoatehttps://pymolwiki.org/index.php?title=File:It.png&diff=11130File:It.png2013-03-08T01:54:27Z<p>Inchoate: inertia tensor</p>
<hr />
<div>inertia tensor</div>Inchoatehttps://pymolwiki.org/index.php?title=Inertia_tensor&diff=11128Inertia tensor2013-03-06T01:19:41Z<p>Inchoate: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = Python Module<br />
|filename = inertia_tensor.py<br />
|author = [http://www.mattmaciejewski.com Mateusz Maciejewski]<br />
|license = MIT<br />
}}<br />
<br />
This script will draw the eigenvectors of the inertia tensor of the selected part of the molecule.<br />
<br />
== Usage ==<br />
<br />
tensor selection, name, model<br />
<br />
== Examples ==<br />
<br />
To draw the inertia tensor of the first model in PDB file 4B2R do:<br />
<br />
<source lang="python"><br />
fetch 4b2r, async=0<br />
hide lines<br />
show cartoon<br />
run inertia_tensor.py<br />
tensor 4b2r & n. n+ca+c & i. 569-611, tensor_dom11, 1<br />
</source><br />
<br />
== Reference ==<br />
<br />
A figure generated using this script can be seen in the following reference:<br />
<br />
* ''Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings''. Maciejewski M, Tjandra N, Barlow PN. '''Biochemistry'''. 50(38) 2011, p. 8138-49, fig. 1 [http://dx.doi.org/10.1021/bi200575b doi:10.1021/bi200575b]<br />
<br />
[[Category:Script_Library]]<br />
[[Category:UI_Scripts]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Gallery&diff=11020Gallery2013-02-28T20:35:32Z<p>Inchoate: </p>
<hr />
<div>{| align="center"<br />
|+ style="font-size:190%; font-weight: bold; color:#038; padding-bottom: 15px;" |PyMOLWiki Gallery<br />
|- style="text-align:center; font-weight: bold; font-size:120%; color:#333;"<br />
| Cool PyMOL-generated Images and their Scripts.<br/><br/>''[[Talk:Gallery#Adding|Add Your Own]]''<br />
|-<br />
|}<br />
<br />
<br />
<br />
{{GalleryImage<br />
<!-- This creates a row entry for the Gallery section --><br />
|<!-- Image --><br />
image=BW_raytraced_complex_image.jpg|size=200px<br />
|<!-- Title above image --><br />
title=Complex B&W outline representation<br />
|<!-- 'Description' section (shows up below image)--><br />
description=Making a B&W outlined image with depth.<br />
|<!-- 'What to Type' section --><br />
cmdString=<source lang="python"><br />
# first load lipid model<br />
load lipids.pdb; <br />
# hide the initially loaded representation<br />
hide all; <br />
# set background color to white<br />
bg_color white; <br />
# show lipid model as sticks<br />
show sticks, lipids; <br />
# color the lipids model by element CHNOS #2 (carbon green)<br />
util.cbag lipids; <br />
<br />
# select all hydrogens and remove them from the model<br />
select hideme, hydro; <br />
hide everything, hideme; <br />
delete hideme;<br />
<br />
# create phosphate spheres<br />
create phos, elem p; <br />
hide everything, phos;<br />
show spheres, phos;<br />
<br />
# load helix model<br />
load helix.pdb; <br />
# hide the initially loaded representation<br />
hide everything, helix;<br />
# make the helical struct into a cartoon form<br />
show cartoon, helix; <br />
# style the cartoon form<br />
cartoon putty; <br />
<br />
# reposition the helix among the lipids using<br />
# the 3-Button Editing Mouse Mode<br />
# basically<br />
# Shift+Left Mouse to rotate the helix<br />
# Shift+Middle Mouse to move the helix<br />
# also, you may want to make liberal use of the<br />
# get_view and set_view commands.<br />
#<br />
# When you have the scene set like you want,<br />
# continue with...<br />
<br />
# move the model to find the view you want, <br />
# and use get_view to get the coordinate description<br />
get_view;<br />
<br />
# set ray_trace_mode to black and white outline<br />
set ray_trace_mode, 2;<br />
</source><br />
Now, you'll need to save multiple versions of your model. (use '''ray''', then '''png''' ''<filename>'' to save each version)<ol><br />
<li> Version A: with all the elements except for the helix. This will become the background.</li><br />
<li> Version B: with the 'front' elements, and the helix. Basically this is just a few 'layers' of lipid, with the helix among them. To do this:</li><ol type="a"><br />
<li>move the model around until you visually see the part to remove</li><br />
<li>switch your Mouse Mode to 3-button viewing, then use the +Box selection (Shift+Left mouse) to select the 'background' portion to hide.</li><br />
<li>choose Hide>Everything for the selection</li><br />
<li>use the code from get_view to go back to the original view</li><br />
</ol></ol><br />
Finally, you will need to compose the image in Photoshop (or Gimp, here I'll use Photoshop).<ol><br />
<li>Load the two versions.</li><br />
<li>Select the white background in Version B, then choose Select>Color Range...</li><br />
<li>Make sure 'Select' is set to 'Sampled Colors', and 'Fuzziness' is set to 150, then click okay.</li><br />
<li>delete the white selection, then choose Select>All</li><br />
<li>copy the picture, then switch to Version A and paste the selection (it should paste into its own layer as 'Layer 1')</li><br />
<li>Click on 'Layer 0' (which is Version A) and change its opacity to 30%</li><br />
<li>Create a new layer under 'Layer 0' which is filled with white only (or whatever background color you like)</li><br />
<li>Click on 'Layer 1' (which is Version B), and using the Move tool (and nudge), align the molecules in 'Layer 1' to 'Layer 0'</li><br />
<li>Some parts of 'Layer 1' are transparent and shouldn't be. Using the Paint Bucket tool fill in these areas with white (or whichever color you find appropriate).</li><br />
<li>Admire your handiwork; put it in a publication, presentation, or poster.</li></ol><br />
|<!-- 'See Also' section (shows up below image)--><br />
seeAlso=<br />
* [[Bg_Color|bg_color]]<br />
* [[Get_View|get_view]]<br />
* Mouse Modes (no good reference for this?)<br />
* [[png]]<br />
* [[Cartoon#Sausage_Representation|putty]]<br />
* [[ray]]<br />
* [[Ray#Modes|ray_trace_mode]]<br />
* [[set]]<br />
* [[Set_View|set_view]]<br />
* [[Single-word_Selectors |single word property selectors]]<br />
* [[Advanced_Coloring#Coloring_by_atom_type|util.cbag]]<br />
}}<br />
<br />
<br />
<br />
{{GalleryImage<br />
|image=Image_merged.png|size=200px|title=A "Sliced" Image|description=A more complex example of how to create an image of a slice.<br />
|cmdString=<source lang="python"><br />
# example script for creation of an image with a slice region<br />
load $PYMOL_PATH/test/dat/1tii.pdb<br />
orient<br />
<br />
# must disable depth cue and shadows<br />
unset depth_cue<br />
unset ray_shadows<br />
set ray_trace_mode, 0<br />
<br />
# this controls the z depth of the slice plane<br />
# (sets it halfway between the clipping planes)<br />
fraction = 0.42<br />
view = cmd.get_view()<br />
near_dist = fraction*(view[16]-view[15])<br />
far_dist = (view[16]-view[15]) - near_dist<br />
cmd.clip("near", -near_dist)<br />
<br />
# render opaque background image<br />
as surface<br />
set ray_interior_color, grey80<br />
set opaque_background<br />
set surface_color, white<br />
ray<br />
save image_back.png<br />
<br />
cmd.clip("near", near_dist)<br />
cmd.clip("far", far_dist)<br />
<br />
# render the foreground image<br />
as cartoon<br />
util.cbc<br />
unset opaque_background<br />
ray<br />
save image_front.png<br />
<br />
# now use Photoshop, Gimp, or ImageMagick to combine the images<br />
system composite image_front.png image_back.png image_merged.png<br />
system display image_merged.png<br />
</source><br />
|seeAlso=<br />
*[[load]]<br />
*[[orient]]<br />
*[[set]]<br />
*[[unset]]<br />
*[[depth_cue]]<br />
*[[ray_shadows]]<br />
*[[Ray#Modes|ray_trace_mode]]<br />
*[[Get_View]]<br />
*[[clip]]<br />
*[[as]]<br />
*[[surface]]<br />
*[[cartoon]]<br />
*[[ray_interior_color]]<br />
*[[color]]<br />
*[[ray]]<br />
*[[save]]<br />
*[[util.cbc]]<br />
*[[opaque_background]]<br />
*[[save]]<br />
*[[system]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
|image=Gm2.png|size=200px|title=Grid Mode|description=This image shows [[Grid mode|Grid Mode]] in action.<br />
|cmdString=<source lang="python"><br />
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;<br />
set grid_mode<br />
</source><br />
'''Hint:''' You may wish to execute the 'reset' command on the command line after running the above commands to get full molecules in view of window and centered in a more useable manner.<br />
|seeAlso=<br />
*[[Fetch]]<br />
*[[Set]]<br />
*[[grid_mode]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Fov60.png|size=200px|title=Cool Perspective|description=This image shows a perspective through [[Field_Of_View]].<br />
|cmdString=<source lang="python"><br />
load prot.pdb;<br />
zoom i. 46-49 and n. CA<br />
set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Ray]]<br />
*[[Zoom]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Pocket.png|size=200px|title=Representing a binding pocket|description=This image shows a nice way to show binding surfaces<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb, tmp<br />
extract lig, organic<br />
extract prot, polymer<br />
delete tmp<br />
<br />
set surface_carve_cutoff, 4.5<br />
set surface_carve_selection, lig<br />
set surface_carve_normal_cutoff, -0.1<br />
<br />
show surface, prot within 8 of lig<br />
set two_sided_lighting<br />
set transparency, 0.5<br />
show sticks, lig<br />
orient lig<br />
<br />
set surface_color, white<br />
set surface_type, 2 # mesh<br />
unset ray_shadows<br />
</source><br />
|seeAlso=<br />
*[[extract]]<br />
*[[delete]]<br />
*[[show]]<br />
*[[set]]<br />
*[[orient]]<br />
*[[surface_carve_cutoff]]<br />
*[[surface_carve_selection]]<br />
*[[surface_carve_normal_cutoff]]<br />
*[[surface_color]]<br />
*[[surface_type]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=QuteMolLike.png|size=400px|title=QuteMol Like|description=QuteMol like image--modern ''feel'' to it. Check out the [[Media:Depthmol.mpeg|movie]].<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb<br />
set_color oxygen, [1.0,0.4,0.4]<br />
set_color nitrogen, [0.5,0.5,1.0]<br />
remove solvent<br />
as spheres<br />
util.cbaw<br />
bg white<br />
set light_count,8<br />
set spec_count,1<br />
set shininess, 10<br />
set specular, 0.25<br />
set ambient,0<br />
set direct,0<br />
set reflect,1.5<br />
set ray_shadow_decay_factor, 0.1<br />
set ray_shadow_decay_range, 2<br />
unset depth_cue<br />
# for added coolness<br />
# set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Set_color]]<br />
*[[Remove]]<br />
*[[Solvent]]<br />
*[[As]]<br />
*[[Util]]<br />
*[[Util.cbaw]]<br />
*[[Bg]]<br />
*[[Light_Count]]<br />
*[[Spec_Count]]<br />
*[[Shininess]]<br />
*[[Specular]]<br />
*[[Ambient]]<br />
*[[Direct]]<br />
*[[Reflect]]<br />
*[[Ray_shadow_decay_factor]]<br />
*[[Ray_shadow_decay_range]]<br />
*[[Unset]]<br />
*[[depth_cue]]<br />
*[[Ray]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Tilt shift.png|size=500px|title=Simulating Tilt-shift|description=Tilt shift simulation<br />
|cmdString=<source lang="python"><br />
fetch 1wld<br />
as surface, poly<br />
as sticks, org<br />
h_add solvent<br />
color grey, poly<br />
orient org<br />
png img.png<br />
# now, go into Photoshop or the GIMP and apply a Gaussian or<br />
# Focus blur to the top and bottom portions of the image<br />
</source><br />
|seeAlso=<br />
*[[fetch]]<br />
*[[show_as]]<br />
*[[h_add]]<br />
*[[color]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
|image=Rnt.png|size=500px|title=Ray-normal-based transparency|description=Ray-normal-based transparency<br />
|cmdString=<source lang="python"><br />
# grey surface<br />
set surface_color, grey<br />
<br />
# cavity mode<br />
set surface_mode, 3<br />
<br />
# layered transparency mode<br />
set transparency_mode, 1<br />
<br />
# surface transparency<br />
set transparency, 0.5<br />
<br />
# oblique and contrast define the<br />
# look of the surface transparency:<br />
# if the normal vector is <br />
set ray_transparency_oblique<br />
set ray_transparency_oblique_power, 8<br />
set ray_transparency_contrast, 7<br />
<br />
# fetch a protein, with a <br />
# small molecule in a nice<br />
# hidden pocket<br />
fetch 1hpv, async=0<br />
<br />
hide<br />
<br />
# show the small molecule as surface<br />
show surface, org<br />
<br />
# arrange the view<br />
orient org<br />
<br />
# zoom back a little<br />
zoom org, 1<br />
<br />
# show the small molecule inside as sticks<br />
show sticks, org<br />
<br />
# show some nearby sidechains<br />
show lines, poly within 5 of org<br />
<br />
# enable frame caching for playback<br />
set cache_frames, 1<br />
<br />
set ray_trace_frames, 1<br />
<br />
mset 1x120<br />
<br />
movie.roll 1, 120, 1, x<br />
<br />
mplay<br />
<br />
# now sit back and wait 5 minutes...<br />
</source><br />
|seeAlso=<br />
* [[surface_color]]<br />
* [[surface_mode]]<br />
* [[transparency_mode]]<br />
* [[transparency]]<br />
* [[ray_transparency_oblique]]<br />
* [[ray_transparency_oblique_power]]<br />
* [[ray_transparency_contrast]]<br />
* [[fetch]]<br />
* [[orient]]<br />
* [[zoom]]<br />
* [[show]]<br />
* [[sticks]]<br />
* [[lines]]<br />
* [[cache_frames]]<br />
* [[mset]]<br />
* [[ray_trace_frames]]<br />
* [[movie.roll]]<br />
}}<br />
<br />
<br />
{{GalleryImage<br />
| title=Blobby Main Chain<br />
| image=Gallery dark tube mc.png<br />
| description=Main chain as a darkened tube with special shading<br />
| seeAlso=<br />
* [[remove]]<br />
* [[alter]]<br />
* [[gaussian_resolution]]<br />
* [[map_new]]<br />
* [[spectrum]]<br />
* [[light_count]]<br />
* [[spec_count]]<br />
* [[shininess]]<br />
* [[reflect]]<br />
* [[direct]]<br />
* [[ambient]]<br />
* [[ray_shadow_decay_factor]]<br />
* [[ray_shadow_decay_range]]<br />
* [[fetch]]<br />
| cmdString=<source lang="python"><br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 3.5<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 0.5, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 3.0<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], [-1, -1, 0])<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
bg grey<br />
<br />
# soften out the image<br />
set light_count,8<br />
set spec_count,1<br />
set shininess, 10<br />
set specular, 0.075<br />
set ambient,0<br />
set direct,0<br />
set reflect, 0.85<br />
set ray_shadow_decay_factor, 0.1<br />
set ray_shadow_decay_range, 4<br />
<br />
unset depth_cue<br />
<br />
# ray trace the image<br />
orient<br />
ray<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Blobby Side Chains<br />
| image=Gallery blob sc.png<br />
| description=Main chain as tube with gaussian surfaced side chains<br />
| seeAlso=<br />
* [[cartoon]]<br />
* [[show_as]]<br />
* [[fetch]]<br />
* [[cartoon_tube_radius]]<br />
* [[cartoon_color]]<br />
* [[cartoon_side_chain_helper]]<br />
* [[alter]]<br />
* [[gaussian_resolution]]<br />
* [[map_new]]<br />
* [[isosurface]]<br />
* [[color]]<br />
* [[hide]]<br />
| cmdString=<source lang="python"><br />
# fetch a protein<br />
<br />
fetch 1rx1, async=0<br />
<br />
# setup the cartoon tubes<br />
<br />
as cartoon<br />
<br />
cartoon tube<br />
<br />
set cartoon_tube_radius, 0.7<br />
<br />
set cartoon_color, brown<br />
<br />
set cartoon_side_chain_helper, on<br />
<br />
show sticks, poly<br />
<br />
color yellow<br />
<br />
# README<br />
# stop here, or try this for "sloppy sticks"<br />
# beefy video card required!<br />
<br />
select rep sticks<br />
select sele and not n. C+O+N+CA<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 2.5 A map resolution<br />
<br />
set gaussian_resolution, 2.5<br />
<br />
# 0.2 A sampling; lower=smoother<br />
<br />
map_new map, gaussian, 0.2, sele, 5<br />
<br />
# create a surface from the map<br />
<br />
isosurface surf, map, 5.0<br />
<br />
color yellow, surf<br />
hide sticks<br />
<br />
# reconnect the main chain to the blobs<br />
show sticks, n. CA+CB<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Smooth surface with ligand<br />
| image=Abs surf.png<br />
| description=Gaussian abstracted surface colored by underlying b-factors and shown with ligand<br />
| seeAlso=<br />
* [[ramp_new]]<br />
* [[show_as]]<br />
* [[gaussian_resolution]]<br />
* [[fetch]]<br />
* [[isosurface]]<br />
* [[spectrum]]<br />
* [[set]]<br />
* [[alter]]<br />
* [[get_view]]<br />
* [[set_view]]<br />
| cmdString=<source lang="python"><br />
<br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 7.6<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 1, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 1.5<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the b-factors of the<br />
# underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
show sticks, org<br />
show spheres, org<br />
<br />
color magenta, org<br />
reinit<br />
<br />
fetch 3uex, struct, async=0<br />
<br />
remove solvent<br />
<br />
# set the B-factors nice and high for smoothness<br />
alter all, b=10<br />
alter all, q=1<br />
<br />
# 3.5 A map resolution<br />
set gaussian_resolution, 7.6<br />
<br />
# new gaussian map w/resolution=0.5 Ang<br />
# on just the main chain<br />
map_new map, gaussian, 1, n. C+O+N+CA, 5<br />
<br />
# create a surface from the map<br />
isosurface surf, map, 1.5<br />
<br />
# color the protein by number<br />
spectrum count, rainbow, struct<br />
<br />
# now color the map based on the b-factors of the<br />
# underlying protein<br />
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")<br />
<br />
# set the surface color<br />
cmd.set("surface_color", "ramp", "surf")<br />
<br />
# hide the ramp and lines<br />
disable ramp<br />
hide lines<br />
<br />
show sticks, org<br />
show spheres, org<br />
<br />
color magenta, org<br />
set_bond stick_radius, 0.13, org<br />
set sphere_scale, 0.26, org<br />
<br />
set_bond stick_radius, 0.13, org<br />
set_bond stick_color, white, org<br />
set sphere_scale, 0.26, org<br />
set_view (\<br />
-0.877680123, 0.456324875, -0.146428943,\<br />
0.149618521, -0.029365506, -0.988305628,\<br />
-0.455291569, -0.889327347, -0.042500813,\<br />
-0.000035629, 0.000030629, -37.112102509,\<br />
-3.300258160, 6.586110592, 22.637466431,\<br />
8.231912613, 65.999290466, -50.000000000 )<br />
<br />
# ray trace the image<br />
ray<br />
</source><br />
}}<br />
<br />
{{GalleryImage<br />
| title=Complex Stylized Protein<br />
| image=Cool.png<br />
| description=A Cool, Stylized Rendering<br />
| seeAlso=<br />
* [[field_of_view]]<br />
* [[set]]<br />
* [[light_count]]<br />
* [[ambient]]<br />
* [[ramp_new]]<br />
* [[color]]<br />
* [[surface_quality]]<br />
* [[transparency]]<br />
* [[ambient_occlusion_mode]]<br />
* [[spec_reflect]]<br />
* [[spec_direct]]<br />
* [[disable]]<br />
* [[ray_shadows]]<br />
* [[ray_opaque_background]]<br />
* [[ray_transparency_oblique]]<br />
* [[ray_transparency_oblique_power]]<br />
* [[ray_transparency_contrast]]<br />
| cmdString=<source lang="python"><br />
fetch 1eaz, async=0<br />
<br />
extract oo, org<br />
<br />
hide everything, solvent<br />
<br />
set field_of_view, 50<br />
<br />
preset.ball_and_stick("oo")<br />
<br />
set_bond stick_color, 0xffff44, oo<br />
<br />
set_bond stick_transparency, 0.35, oo<br />
<br />
color grey, oo and e. C<br />
<br />
set valence, 1, oo<br />
<br />
ramp_new pRamp, oo, selection=poly, range=[5,30], color=rainbow<br />
<br />
set surface_color, pRamp, poly<br />
<br />
show spheres, poly<br />
<br />
color white, poly<br />
<br />
color grey30, poly and e. C<br />
<br />
set sphere_scale, 0.99, poly<br />
<br />
set ray_transparency_contrast, 0.20<br />
<br />
set ray_transparency_oblique, 1.0<br />
<br />
set ray_transparency_oblique_power, 20<br />
<br />
show surface, poly<br />
<br />
set surface_quality, 2<br />
<br />
set light_count, 5<br />
<br />
set ambient_occlusion_mode, 1<br />
<br />
set ambient_occlusion_scale, 50<br />
<br />
set ambient, 0.40<br />
<br />
set transparency, 0.50<br />
<br />
disable pRamp<br />
<br />
set spec_power, 1200<br />
<br />
set spec_reflect, 0.20<br />
<br />
set ray_opaque_background, 0<br />
<br />
set ray_shadow, 0<br />
<br />
ray<br />
</source><br />
}}<br />
<br />
<br />
{{GalleryImage<br />
| title=Goodsell-like<br />
| image=Goodsell_like2.png<br />
| description=Create Goodsell-like images in PyMOL<br />
| seeAlso=<br />
* [[set]]<br />
* [[light_count]]<br />
* [[color]]<br />
* [[ray_shadows]]<br />
* [[ray_trace_mode]]<br />
* [[specular]]<br />
* [[orient]]<br />
* [[ray_trace_gain]]<br />
* [[depth_cue]]<br />
| cmdString=<source lang="python"><br />
# fetch the protein<br />
<br />
fetch 1rx1, async=0<br />
<br />
# show it as blue/magenta spheres<br />
<br />
as spheres<br />
<br />
color lightblue, not org<br />
<br />
color magenta, org<br />
<br />
remove solvent<br />
<br />
# set the view<br />
<br />
orient all within 8 of org<br />
<br />
# set the lights, ray tracing setttings<br />
# to get the Goodsell-like rendering<br />
<br />
unset specular<br />
<br />
set ray_trace_gain, 0<br />
<br />
set ray_trace_mode, 3<br />
<br />
bg_color white<br />
<br />
set ray_trace_color, black<br />
<br />
unset depth_cue<br />
<br />
ray<br />
</source><br />
}}</div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=10987Main Page2013-02-14T19:20:26Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Script<br />
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.<br />
|-<br />
! New Script<br />
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.<br />
|-<br />
! New Script<br />
| [[DistancesRH|Distances RH]]<br />
|-<br />
! PyMOL on the iPad<br />
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
|-<br />
! OS X Compatibility<br />
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
|-<br />
! New Script<br />
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
|-<br />
! New Script<br />
| [[b2transparency]] can set surface transparency based on atom b-factor<br />
|-<br />
! New Extension<br />
| [[psico]] is a python module which extends PyMOL with many commands<br />
|-<br />
! New Script<br />
| [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
|-<br />
! New Plugin<br />
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
|-<br />
! New Script<br />
| [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
|-<br />
! New Script<br />
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
|-<br />
! New Script<br />
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
|-<br />
! New Script<br />
| [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
|-<br />
! New Plugin<br />
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map<br />
|-<br />
! New Script<br />
| [[spectrum_states]] colors states of multi-state object<br />
|-<br />
! New Script<br />
| [[TMalign]] is a wrapper for the TMalign program<br />
|-<br />
! Gallery Updates<br />
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
|-<br />
! New Script<br />
| [[save_settings]] can dump all changed settings to a file<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
|-<br />
! Wiki Update<br />
| Wiki has been updated. Please report any problems to the sysops.<br />
|-<br />
! New Scripts<br />
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
|-<br />
! New Script<br />
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
|-<br />
! New Script<br />
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
|-<br />
! New Script<br />
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=450<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Covers&diff=10920Covers2013-01-03T05:15:11Z<p>Inchoate: </p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:ParM.gif|'''End-on view of the atomic model of the bacterial actinlike ParM protein double-helical filament, generated from an electron microscopic reconstruction.''' [http://www.sciencemag.org/content/338/6112.toc A Bipolar Spindle of Antiparallel ParM Filaments Drives Bacterial Plasmid Segregation].<br />
Image:Proteins_08010_c1_sp_Ob.png|'''A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES''' [http://dx.doi.org/10.1002/prot.24113 Proteins, Volume 80, Issue 10, 2012].<br />
Image:PNASCover.gif|Image of two short stretches of double-stranded DNA linked by a ruthenium 'light-switch complex', October 25, 2011; 108 (43) [[http://www.pnas.org/content/108/43.cover-expansion]]<br />
Image:Goldenberg cover.jpg|'''Protein Science''', Vol. 20, No. 12, Dec 2011<br />
Image:Polymer_physics_cover.png|'''Journal of Polymer Science''', Nov 15 2011<br />
Image:Biophysical_cover.png|'''Biophysical Journal''', Aug 3 2011<br />
Image:Science 2011 16.jpg|'''Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing''', [[http://www.sciencemag.org/content/333/6049.toc Science, Sept. 16, 2011]].<br />
Image:JExpBiol-214-4.jpg|'''Deconstructing honeybee vitellogenin''' [http://dx.doi.org/10.1242/jeb.048314 J. Exp. Biol., Volume 214, Issue 4, 2011].<br />
Image:FEBS-585-8.png|'''Binding of 14-3-3g to membranes''' [http://dx.doi.org/10.1016/j.febslet.2011.03.027 FEBS lett., Volume 585, Issue 8, 2011].<br />
Image:MolecularCell011.jpg|'''FLT3 Activation by an Oncogenic Insertion''' Molecular Cell, Volume 13 Number 2, January 30, 2004.<br />
Image:Cen.jpg|'''PI3K Inhibitors''' C&EN, April 11, 2011.<br />
Image:Salam.jpg|'''Microbiology of article entitled "Genetic mapping of the interface between the ArsD metallochaperone and the ArsA ATPase.''' Volume 79, Feb, 2011, [http://onlinelibrary.wiley.com/doi/10.1111/mmi.2011.79.issue-4/issuetoc ''Molecular Microbiology'']<br />
Image:101209Nature.jpg|'''X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor''' [http://www.nature.com/nature/journal/v462/n7274/full/nature08624.html ''Nature'']<br />
Image:biochem_010110_cover.jpg|'''Crystal Structure of the Class D beta-lactamase OXA-1 in complex with doripenem''' [http://www.ncbi.nlm.nih.gov/pubmed/19919101 ''Biochemistry'']<br />
Image:MMcoverMay2009.png|'''Impact of rRNA methylations on ribosome recycling and fidelity of initiation in ''Escherichia coli''.''' [http://www.ncbi.nlm.nih.gov/pubmed/19400784 ''Molecular Microbiology'']<br />
Image:jbc_mchu.jpeg|'''Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125'''. Chu ML, Chavas LM, Douglas KT, Eyers PA, Tabernero L. ''[http://www.ncbi.nlm.nih.gov/pubmed/18480048 J Biol Chem.'' 2008 Aug 1;283(31):21495-500]. Epub 2008 May 14.<br />
Image:JBC_Apr18_2008.jpg|'''Allosteric motions in structures of yeast NAD-specific isocitrate dehydrogenase.''' [http://www.ncbi.nlm.nih.gov/pubmed/18256028?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''J. Biol. Chem.'']<br />
Image:ACR_Jun_2007.jpg|'''Shall we dance? How a multicopper oxidase chooses its electron transfer partner.''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17425282&query_hl=1&itool=pubmed_docsum ''Acc. Chem. Res.'']<br />
Image:ABB_May1_2007.jpg|'''Crystal structure of the yeast nicotinamidase Pnc1p.''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17382284&query_hl=1&itool=pubmed_docsum ''Arch. Biochem. Biophys.'']<br />
Image:Cover_royal_soc_small.png |[http://pymolwiki.org/index.php/File:Cover_royal_soc_small.png Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009 ]<br />
Image:Image_large.png |[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]<br />
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]<br />
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]<br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:Jbc_20070413.gif|<b>''Mycobacterium tuberculosis'' PknD dimerization</b> [http://www.jbc.org/content/282/15 JBC], April 13 2007 Cover, Vol. 282, Issue 15.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
<br />
Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:apr2003_ProtSci.png|<b>''Pae'' SmAP1</b> 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.<br />
Image:Iapp.gif|<b>Cross-Beta Spine of IAPP</b>, [http://www3.interscience.wiley.com/journal/121603721/issue ''Protein Science'', September 2008].<br />
Image:JBC 080406 no31 proof.png|<b>Calcium Sensor</b>, [http://www.jbc.org/content/281/31 ''JBC'', August 4, 2006].<br />
Image:AngewChemIntEd_Comm_Cover_R_Cighetti.jpg |[http://pymolwiki.org/index.php/File:AngewChemIntEd_Comm_Cover_R_Cighetti.jpg, <b>LPS coated nanoparticle</b>, ''Angew.Chem.Int.Ed.'', January 17, 2011]<br />
Image:Structure_cover_Dec2010.jpg|<b>DAXX helical bundle (DHB) and DHB/Rassf1C structures</b>, [http://www.cell.com/structure/issue?pii=S0969-2126%2810%29X0013-2 ''Structure'', December 2010].<br />
</gallery></div>Inchoatehttps://pymolwiki.org/index.php?title=File:ParM.gif&diff=10919File:ParM.gif2013-01-03T05:13:29Z<p>Inchoate: </p>
<hr />
<div></div>Inchoatehttps://pymolwiki.org/index.php?title=Main_Page&diff=10918Main Page2013-01-02T22:59:53Z<p>Inchoate: </p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Script<br />
| [[DistancesRH|Distances RH]]<br />
|-<br />
! PyMOL on the iPad<br />
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
|-<br />
! OS X Compatibility<br />
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
|-<br />
! New Script<br />
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
|-<br />
! New Script<br />
| [[b2transparency]] can set surface transparency based on atom b-factor<br />
|-<br />
! New Extension<br />
| [[psico]] is a python module which extends PyMOL with many commands<br />
|-<br />
! New Script<br />
| [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
|-<br />
! New Plugin<br />
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
|-<br />
! New Script<br />
| [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
|-<br />
! New Script<br />
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
|-<br />
! New Script<br />
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
|-<br />
! New Script<br />
| [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
|-<br />
! New Plugin<br />
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map<br />
|-<br />
! New Script<br />
| [[spectrum_states]] colors states of multi-state object<br />
|-<br />
! New Script<br />
| [[TMalign]] is a wrapper for the TMalign program<br />
|-<br />
! Gallery Updates<br />
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
|-<br />
! New Script<br />
| [[save_settings]] can dump all changed settings to a file<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
|-<br />
! Wiki Update<br />
| Wiki has been updated. Please report any problems to the sysops.<br />
|-<br />
! New Scripts<br />
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
|-<br />
! New Script<br />
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
|-<br />
! New Script<br />
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
|-<br />
! New Script<br />
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=450<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
</DPL><br />
<br />
|}</div>Inchoatehttps://pymolwiki.org/index.php?title=Stick_ball&diff=10909Stick ball2012-12-20T16:32:13Z<p>Inchoate: </p>
<hr />
<div>== Overview ==<br />
<br />
'''This setting is deprecated in v1.5 and later as it is always enabled.'''<br />
<br />
The setting "stick_ball" controls whether bonded atoms are shown simply as joined sticks (set stick_ball, off) or as traditional "ball-and-stick" representation (set stick_ball, on). Note that simply setting stick_ball on will result in balls with the same radius as the sticks and so will appear only slightly different (the joins will be smoother).<br />
<br />
== Settings ==<br />
<source lang="python"><br />
set stick_ball, on # displays atoms as balls joined by sticks<br />
set stick_ball, off # displays only connected sticks<br />
<br />
set stick_ball_ratio, 1.7 # change the radius of the balls<br />
</source><br />
<br />
== Examples ==<br />
Open the images to actually see the details!<br />
<gallery><br />
Image:stick_ball_off.png|stick_ball, off<br />
Image:stick_ball_on.png|stick_ball, on<br />
Image:Stick_ball_ratio_1.5.png|stick_ball "on" with stick_ball_ratio at 1.5<br />
</gallery><br />
<br />
[[Category:Settings|Stick ball]]<br />
[[Category:Sticks]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Stick_ball&diff=10908Stick ball2012-12-20T16:31:52Z<p>Inchoate: </p>
<hr />
<div>== Overview ==<br />
<br />
***This setting is deprecated in v1.5 and later as it is always enabled.***<br />
<br />
The setting "stick_ball" controls whether bonded atoms are shown simply as joined sticks (set stick_ball, off) or as traditional "ball-and-stick" representation (set stick_ball, on). Note that simply setting stick_ball on will result in balls with the same radius as the sticks and so will appear only slightly different (the joins will be smoother).<br />
<br />
== Settings ==<br />
<source lang="python"><br />
set stick_ball, on # displays atoms as balls joined by sticks<br />
set stick_ball, off # displays only connected sticks<br />
<br />
set stick_ball_ratio, 1.7 # change the radius of the balls<br />
</source><br />
<br />
== Examples ==<br />
Open the images to actually see the details!<br />
<gallery><br />
Image:stick_ball_off.png|stick_ball, off<br />
Image:stick_ball_on.png|stick_ball, on<br />
Image:Stick_ball_ratio_1.5.png|stick_ball "on" with stick_ball_ratio at 1.5<br />
</gallery><br />
<br />
[[Category:Settings|Stick ball]]<br />
[[Category:Sticks]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Volume&diff=10904Volume2012-12-05T14:56:24Z<p>Inchoate: </p>
<hr />
<div>[[Volume]] creates a new volume object from a map object. The data (3D scalar fields) are shown as a true 3D object using coloring and transparencies defined by the user to illustrate the data values.<br />
<br />
This technique supports single and multiple isosurfaces.<br />
<br />
= Usage =<br />
<br />
= Examples =<br />
* [http://www.youtube.com/watch?v=tuAo_8-_HIc Silent demo movie] showing the basics of loading and using a volume in PyMOL. There are more capabilities, but this is the basic functionality.<br />
<br />
= See Also =<br />
[[Map_new]] [[Isomesh]] [[Isosurface]]<br />
<br />
[[Category:Commands]] [[Category:Volume]] [[Category:Representations]]</div>Inchoatehttps://pymolwiki.org/index.php?title=MovieSchool_1&diff=10903MovieSchool 12012-12-04T18:56:59Z<p>Inchoate: </p>
<hr />
<div>== Movie Making ==<br />
While PyMOL's capability to produce static images is quite powerful, there are some stories that are better told through movies, than static images alone. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL.<br />
<br />
== Your First Movie ==<br />
Movies can be very simple, for example, animating an NMR ensemble:<br />
<source lang="python"><br />
# Your first movie.<br />
fetch 1nmr<br />
mplay<br />
<br />
# to stop the movie when you're ready<br />
# type 'mstop'.<br />
</source><br />
<br />
What PyMOL did here was to [[fetch]] the file from the PDB and load it into an object with 20 states. Somewhere between then and issuing [[mplay]] PyMOL created 20 frames for your object and assigned one state to each frame. This created the animated effect as we scroll through the frames.<br />
<br />
== Movie Making for the Impatient ==<br />
If you don't have time to or care to make more complex movies and want a movie ''now'' then read this section. It mostly involves the GUI for making movies, so get your mouse ready.<br />
<br />
=== Simple Camera Motions ===<br />
==== Simple 360 Scene Rotation ====<br />
To make a movie that simply rotates around your scene 360 degrees, in the menu click on:<br />
:: '''Movie->Program->Camera->X-Roll->N Seconds'''<br />
for an N-second movie rolling over the X-axis. Chose <br />
:: '''Movie->Program->Camera->Y-Roll->N Seconds'''<br />
for the Y-axis roll.<br />
<br />
Done! Press '''play'''.<br />
<br />
==== Simple 30, 60, 90, 120, 180, Scene Rocking ====<br />
This will show up to a 30, 60, 90, 120 or 180 rocking 'wedge' of the scene. If you don't want to rotate all the way around, use this.<br />
:: '''Movie->Program->Camera->X-Rock->X-Degrees over N-Seconds'''<br />
<br />
Done! Press '''play'''.<br />
<br />
==== Nutate ====<br />
Nutating is like a wiggle-rock; try it and see.<br />
:: '''Movie->Program->Camera->X-Rock->X-Degrees over N-Seconds'''<br />
<br />
Done! Press '''play'''.<br />
<br />
==== Zooming Around an Object ====<br />
This is also known as camera movement. Let's make a simple program that just zooms in and out on a some atom.<br />
:: '''Build->Residue->Tryptophan'''<br />
:: '''Scene->Store->F1'''<br />
:: ''Click any atom and zoom on it''<br />
:: '''Scene-Store->F2'''<br />
:: '''Movie->Program->Scene Loop->''' and if you want to nutate while at the scene choose '''Nutate''' otherwise choose '''Y-Rock'''.<br />
<br />
Done! Press '''play'''.<br />
<br />
* ''Hint'': Make multiple scenes, making sure to store each one. Then use the Scene Loop to automatically program a movie for you!<br />
<br />
==== Real-world Example ====<br />
First load the tutorial PDB:<br />
<source lang="python"><br />
load $TUT/1hpv.pdb<br />
</source><br />
:: '''Action->Preset->Technical''' (on the object in the viewer gui)<br />
:: '''Scene->Store->F1'''<br />
:: Type ''zoom i. 200'' to zoom on the ligand<br />
:: '''Scene->Store->F2'''<br />
:: '''Movie->Program->Scene Loop->Y-Rock->4 Seconds Each'''<br />
<br />
Done! Press '''play'''.<br />
<br />
[[MovieSchool| &larr; MovieSchool Home]] [[MovieSchool_2| Next Lesson &rarr;]]<br />
<br />
[[Category:Movies]]<br />
[[Category:Tutorials]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Connect_mode&diff=10899Connect mode2012-12-03T23:34:43Z<p>Inchoate: </p>
<hr />
<div>= Overview =<br />
Sets how bonds are made when loading a file.<br />
<br />
Values:<br />
* 0 = distance-based and CONECT records<br />
* 1 = CONECT records<br />
* 2 = distance-based, ignores CONECT records<br />
* 3 = CONECT records and distance <br />
<br />
= Syntax =<br />
<source lang="python"><br />
# ignore CONECT records<br />
set connect_mode, 2<br />
<br />
</source><br />
<br />
= See Also =<br />
[[Load]], [[Connect_cutoff]], [[Connect_bonded]]<br />
<br />
[[Category:Settings]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Dump2CGO&diff=10882Dump2CGO2012-10-25T12:56:29Z<p>Inchoate: </p>
<hr />
<div>= Overview =<br />
Dumps a PyMOL object to a CGO object.<br />
<br />
= The Code =<br />
<source lang="python"><br />
from pymol import cmd<br />
from pymol.cgo import *<br />
<br />
def dump2surfaceCGO():<br />
CGOobj = []<br />
dumpedFile = open("dump.tmp").read()<br />
for block in dumpedFile.split('\n\n'):<br />
CGOobj.append(BEGIN)<br />
CGOobj.append(TRIANGLES)<br />
<br />
for line in block.split('\n'):<br />
if line == '':<br />
continue<br />
<br />
vals = line.split()<br />
CGOobj.append(NORMAL)<br />
CGOobj.append(float(vals[3]))<br />
CGOobj.append(float(vals[4]))<br />
CGOobj.append(float(vals[5]))<br />
CGOobj.append(VERTEX)<br />
CGOobj.append(float(vals[0]))<br />
CGOobj.append(float(vals[1]))<br />
CGOobj.append(float(vals[2]))<br />
<br />
CGOobj.append(END)<br />
return CGOobj<br />
<br />
def dump2meshCGO():<br />
CGOobj = []<br />
dumpedFile = open("dump.tmp").read()<br />
for block in dumpedFile.split('\n\n'):<br />
CGOobj.append(BEGIN)<br />
CGOobj.append(LINE_STRIP)<br />
<br />
for line in block.split('\n'):<br />
if line == '':<br />
continue<br />
<br />
CGOobj.append(VERTEX)<br />
vals = line.split()<br />
<br />
CGOobj.append(float(vals[0]))<br />
CGOobj.append(float(vals[1]))<br />
CGOobj.append(float(vals[2]))<br />
<br />
CGOobj.append(END)<br />
return CGOobj<br />
<br />
def getType(objname):<br />
session = cmd.get_session()['names']<br />
for obj in session:<br />
if obj == None:<br />
continue<br />
if obj[0] != objname:<br />
continue<br />
return obj[4]<br />
return -1<br />
<br />
<br />
def dump2CGO(obj):<br />
cmd.dump("dump.tmp", obj)<br />
type = getType(obj)<br />
cgo = []<br />
if (type == 3): # Mesh<br />
cgo = dump2meshCGO()<br />
elif (type == 7): #Surface<br />
cgo = dump2surfaceCGO()<br />
else:<br />
print "Unknown type"<br />
return<br />
<br />
cmd.load_cgo(cgo, "CGO " + obj)<br />
<br />
cmd.extend('dump2CGO', dump2CGO)<br />
cmd.auto_arg[0]['dump2CGO'] = [cmd.object_sc, 'object', '']<br />
</source><br />
<br />
[[Category:Script_Library]] [[Category:Math_Scripts]]<br />
[[Category:CGO]]</div>Inchoatehttps://pymolwiki.org/index.php?title=CgoCircle&diff=10881CgoCircle2012-10-25T12:56:06Z<p>Inchoate: </p>
<hr />
<div>= Overview =<br />
This script will create a CGO circle with the origin at the specified X,Y,Z coordinates. Also, you can specify the radius and the colors. See the examples.<br />
<br />
If you want to draw a circle around an object or selection, use '''circleSelection'''. If you want pure flexibility over your circle then use '''cgoCircle'''.<br />
<br />
<br />
'''There are two functions here:'''<br />
<br />
'''cgoCircle'''<br />
::&mdash; creates a CGO circle at some user-specified location<br />
'''circleSelection'''<br />
::&mdash;creates a circle around the named object or selection.<br />
<br />
<br />
<br />
<gallery heights=200px widths=300px perrow=3><br />
Image:Circle1.png|Drawn circle.<br />
Image:Circle2.png|CGO circle.<br />
Image:Circle3.png|Circles of specified radius.<br />
Image:CircleR.png|Circle with specified width.<br />
Image:CircleR2.png|Circle with a line width of 150. Pores anyone?<br />
</gallery><br />
<br />
= Usage =<br />
<source lang="python"><br />
import math<br />
import pymol<br />
from pymol.cgo import *<br />
import random<br />
<br />
def cgoCircle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):<br />
"""<br />
Create a CGO circle<br />
<br />
PARAMS<br />
x, y, z<br />
X, Y and Z coordinates of the origin<br />
<br />
r<br />
Radius of the circle<br />
<br />
cr, cg, cb<br />
Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].<br />
<br />
w<br />
Line width of the circle<br />
<br />
RETURNS<br />
the CGO object (it also loads it into PyMOL, too).<br />
<br />
"""<br />
x = float(x)<br />
y = float(y)<br />
z = float(z)<br />
r = abs(float(r))<br />
cr = abs(float(cr))<br />
cg = abs(float(cg))<br />
cb = abs(float(cb))<br />
w = float(w)<br />
<br />
obj = [ BEGIN, LINES, COLOR, cr, cg, cb ]<br />
for i in range(180):<br />
obj.append( VERTEX )<br />
obj.append(r*math.cos(i) + x )<br />
obj.append(r*math.sin(i) + y )<br />
obj.append(z)<br />
obj.append( VERTEX )<br />
obj.append(r*math.cos(i+0.1) + x )<br />
obj.append(r*math.sin(i+0.1) + y )<br />
obj.append(z)<br />
obj.append(END)<br />
<br />
cName = cmd.get_unused_name("circle_")<br />
cmd.load_cgo( obj, cName )<br />
cmd.set("cgo_line_width", w, cName )<br />
return obj<br />
<br />
<br />
def circleSelection( selName, r=None, cr=1.0, cg=0.4, cb=0.8, w=2.0 ):<br />
"""<br />
circleSelection -- draws a cgo circle around a given selection or object<br />
<br />
PARAMS<br />
selName<br />
Name of the thing to encircle.<br />
<br />
r<br />
Radius of circle.<br />
DEFAULT: This cript automatically defines the radius for you. If<br />
you select one atom and the resultant circle is too small, then<br />
you can override the script's calculation of r and specify your own.<br />
<br />
cr, cg, cb<br />
red, green and blue coloring, each a value in the range [0.0, 1.0]<br />
<br />
RETURNS<br />
The circle object.<br />
<br />
"""<br />
((minX, minY, minZ), (maxX, maxY, maxZ)) = cmd.get_extent(selName)<br />
<br />
if r==None:<br />
r = max( [maxX-minX, maxY-minY, maxZ-minZ] )<br />
<br />
stored.coords = []<br />
cmd.iterate_state(1, selName, "stored.coords.append([x,y,z])")<br />
l = len(stored.coords)<br />
<br />
centerX = sum(map(lambda x: x[0], stored.coords)) / l<br />
centerY = sum(map(lambda x: x[1], stored.coords)) / l<br />
centerZ = sum(map(lambda x: x[2], stored.coords)) / l<br />
<br />
return cgoCircle( centerX, centerY, centerZ, r, cr, cg, cb, w )<br />
<br />
<br />
cmd.extend( "cgoCircle", cgoCircle )<br />
cmd.extend( "circleSelection", circleSelection )<br />
</source><br />
<br />
= Updates =<br />
* Line width option<br />
* better circle naming<br />
<br />
[[Category:Script_Library]]<br />
[[Category:Math_Scripts]]<br />
[[Category:CGO]]</div>Inchoatehttps://pymolwiki.org/index.php?title=Plane_Wizard&diff=10880Plane Wizard2012-10-25T12:55:51Z<p>Inchoate: </p>
<hr />
<div>This wizard has a simple purpose - to draw a cgo plane that passes through three points picked by the user. Most of the wizard itself was copied from the measure wizard.<br />
<br />
To use, put it in the same directory as the other wizards. This is not quality code, and there may be bugs, but it seems to work okay.<br />
<br />
<source lang="python"><br />
import pymol<br />
from pymol import cmd<br />
from pymol.wizard import Wizard<br />
from chempy import cpv<br />
from pymol.cgo import *<br />
<br />
def makePrimitive(cgo, name):<br />
cmd.set('auto_zoom', 0, quiet=1)<br />
cmd.load_cgo(cgo, name)<br />
cmd.set('auto_zoom', 1, quiet=1)<br />
<br />
def point(p):<br />
x, y, z = p<br />
return [COLOR, 1, 1, 1, SPHERE, float(x), float(y), float(z), 0.5]<br />
<br />
def line(p1, p2):<br />
x1, y1, z1 = p1<br />
x2, y2, z2 = p2<br />
return [CYLINDER, float(x1), float(y1), float(z1), float(x2), float(y2), float(z2), 0.25, 1, 1, 1, 1, 1, 1]<br />
<br />
def plane(corner1, corner2, corner3, corner4, normal):<br />
planeObj = []<br />
planeObj.extend(point(corner1))<br />
planeObj.extend(point(corner2))<br />
planeObj.extend(point(corner3))<br />
planeObj.extend(point(corner4))<br />
planeObj.extend(line(corner1, corner2))<br />
planeObj.extend(line(corner2, corner3))<br />
planeObj.extend(line(corner3, corner4))<br />
planeObj.extend(line(corner4, corner1))<br />
<br />
planeObj.extend([COLOR, 0.8, 0.8, 0.8])<br />
planeObj.extend([BEGIN, TRIANGLE_STRIP])<br />
planeObj.append(NORMAL)<br />
planeObj.extend(normal)<br />
for corner in [corner1, corner2, corner3, corner4, corner1]:<br />
planeObj.append(VERTEX)<br />
planeObj.extend(corner)<br />
planeObj.append(END)<br />
return planeObj<br />
<br />
def planeFromPoints(point1, point2, point3, facetSize):<br />
v1 = cpv.normalize(cpv.sub(point2, point1))<br />
v2 = cpv.normalize(cpv.sub(point3, point1))<br />
normal = cpv.cross_product(v1, v2)<br />
v2 = cpv.cross_product(normal, v1)<br />
x = cpv.scale(v1, facetSize)<br />
y = cpv.scale(v2, facetSize)<br />
center = point2<br />
corner1 = cpv.add(cpv.add(center, x), y)<br />
corner2 = cpv.sub(cpv.add(center, x), y)<br />
corner3 = cpv.sub(cpv.sub(center, x), y)<br />
corner4 = cpv.add(cpv.sub(center, x), y)<br />
return plane(corner1, corner2, corner3, corner4, normal)<br />
<br />
<br />
class PlaneWizard(Wizard):<br />
<br />
def __init__(self):<br />
Wizard.__init__(self)<br />
<br />
# some attributes to do with picking<br />
self.pick_count = 0<br />
self.object_count = 0<br />
self.object_prefix = "pw"<br />
<br />
# the plane facet size (the 'radius' of the section of plane we show)<br />
self.facetSize = 5<br />
<br />
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")<br />
cmd.set("mouse_selection_mode",0) # set selection mode to atomic<br />
cmd.deselect()<br />
<br />
def reset(self):<br />
cmd.delete(self.object_prefix + "*")<br />
cmd.delete("sele*")<br />
cmd.delete("_indicate*")<br />
cmd.unpick()<br />
cmd.refresh_wizard()<br />
<br />
def delete_all(self):<br />
cmd.delete("plane*")<br />
<br />
def cleanup(self):<br />
cmd.set("mouse_selection_mode",self.selection_mode) # restore selection mode<br />
self.reset()<br />
self.delete_all()<br />
<br />
def get_prompt(self):<br />
self.prompt = None<br />
if self.pick_count == 0:<br />
self.prompt = [ 'Please click on the first atom...']<br />
elif self.pick_count == 1:<br />
self.prompt = [ 'Please click on the second atom...' ]<br />
elif self.pick_count == 2:<br />
self.prompt = [ 'Please click on the third atom...' ]<br />
return self.prompt<br />
<br />
def do_select(self, name):<br />
# "edit" only this atom, and not others with the object prefix<br />
try:<br />
cmd.edit("%s and not %s*" % (name, self.object_prefix))<br />
self.do_pick(0)<br />
except pymol.CmdException, pmce:<br />
print pmce<br />
<br />
def pickNextAtom(self, atom_name):<br />
# transfer the click selection to a named selection<br />
cmd.select(atom_name, "(pk1)")<br />
<br />
# delete the click selection<br />
cmd.unpick()<br />
<br />
# using the magic of indicate, highlight stuff<br />
indicate_selection = "_indicate" + self.object_prefix<br />
cmd.select(indicate_selection, atom_name)<br />
cmd.enable(indicate_selection)<br />
<br />
self.pick_count += 1<br />
self.error = None<br />
<br />
# necessary to force update of the prompt<br />
cmd.refresh_wizard()<br />
<br />
def do_pick(self, picked_bond):<br />
<br />
# this shouldn't actually happen if going through the "do_select"<br />
if picked_bond:<br />
self.error = "Error: please select bonds, not atoms"<br />
print self.error<br />
return<br />
<br />
atom_name = self.object_prefix + str(self.pick_count)<br />
if self.pick_count < 2:<br />
self.pickNextAtom(atom_name)<br />
else:<br />
self.pickNextAtom(atom_name)<br />
<br />
point1 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "0"))<br />
point2 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "1"))<br />
point3 = cmd.get_atom_coords("(%s%s)" % (self.object_prefix, "2"))<br />
plane = planeFromPoints(point1, point2, point3, self.facetSize)<br />
<br />
planeName = "plane-%02d" % self.object_count<br />
self.object_count += 1<br />
makePrimitive(plane, planeName)<br />
cmd.show("cgo", "plane*")<br />
<br />
self.pick_count = 0<br />
self.reset()<br />
<br />
def get_panel(self):<br />
return [<br />
[ 1, 'Plane Wizard',''],<br />
[ 2, 'Reset','cmd.get_wizard().reset()'],<br />
[ 2, 'Delete All Planes' , 'cmd.get_wizard().delete_all()'],<br />
[ 2, 'Done','cmd.set_wizard()'],<br />
]<br />
<br />
# create an instance<br />
<br />
wiz = PlaneWizard()<br />
<br />
# make this the active wizard<br />
<br />
cmd.set_wizard(wiz)<br />
</source><br />
[[Category:Script_Library|Plane Wizard]]<br />
[[Category:Math_Scripts]]<br />
[[Category:CGO]]</div>Inchoate