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| | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" | | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" |
| | | The community-run support site for the [http://pymol.org PyMOL] molecular viewer. | | | The community-run support site for the [http://pymol.org PyMOL] molecular viewer. |
| − | | | + | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" |
| | + | | New accounts: email jason (dot) vertrees (@) gmail dot com |
| | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" | | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" |
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| | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates | | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates |
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| − | ! Wiki Update | + | ! Official Release |
| − | | Wiki has been updated. Please report any problems to the sysops. | + | | [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014. |
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| − | ! New Scripts | + | ! Official Release |
| − | | Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]] | + | | [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014. |
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| − | ! New Script | + | ! New Plugin |
| − | | [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. | + | | [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds. |
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| − | ! New Script
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| − | | [[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]].
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| − | ! New Script
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| − | | [[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.
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| − | ! New Script
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| − | | [[PluginDirectory]]: How to set up a personal plugin directory
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| − | ! New Script
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| − | | Add focal blur to images [[FocalBlur]].
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| − | ! New Script
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| − | | Visualize VDW clashes with [[show bumps]]
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| | ! New Plugin | | ! New Plugin |
| − | | Color by [[DSSP]] or [[Stride]] secondary structure assignment | + | | [[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. |
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| − | ! New Script
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| − | | There is a new script to calculate the [[Radius of gyration]]
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| − | ! New Command
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| − | | [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.
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| − | ! New Script
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| − | | [[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. | |
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| − | ! New Script
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| − | | [[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.
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| | |- | | |- |
| − | ! New Script | + | ! 3D using Geforce |
| − | | Two new scripts: [[AAindex]] and [[Sidechaincenters]] | + | | 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. |
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| | ! New Plugin | | ! New Plugin |
| − | | [[CAVER_2.0]] update to the CAVER plugin. | + | | [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS. |
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| − | ! New Script
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| − | | [[AngleBetweenHelices]] calculates the angle between two helices.
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| − | |-
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| − | ! Search
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| − | | [[GoogleSearch]] widget fixed.
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| − | |-
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| − | ! New Script
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| − | | [[Spectrumany]] creates color gradients with arbitrary color sequences.
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| − | |-
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| − | ! New Script
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| − | | [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
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| − | |-
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| − | ! New Script
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| − | | [[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).
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| − | |-
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| − | ! New Script
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| − | | [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
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| − | |-
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| − | ! New Scripts
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| − | | [[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.
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| − | |-
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| − | ! New Script
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| − | | See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
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| − | |-
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| − | ! New Script
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| − | | See [[Supercell]], the new script for making XxYxZ supercells.
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| − | ! New Script | + | ! New Software |
| − | | 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. | + | | [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL. |
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| | ! New Script | | ! New Script |
| − | | See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models. | + | | [[cgo_arrow]] draws an arrow between two picked atoms. |
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| − | ! Server updates
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| − | | 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.
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| − | |-
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| − | ! fetch_host setting
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| − | | [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
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| − | |-
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| − | ! Fetch
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| − | | [[Fetch]] has been updated to also load electron density maps.
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| − | ! Schrodinger Buys PyMOL
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| − | | Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
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| − | |-
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| − | ! User Movie
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| − | | One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
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| − | |-
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| − | ! New setting
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| − | | [[surface_cavity_mode]] to change how PyMOL displays cavities.
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| − | |-
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| − | ! Search fixed.
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| − | | Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
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| − | |-
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| − | ! New Command
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| − | | [[Cache]]—stores information on structures, so we don't have to recompute them.
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| | |- | | |- |
| − | ! Warren | + | ! Tips & Tricks |
| − | | News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]]. | + | | Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL. |
| | |- | | |- |
| − | ! Setting | + | ! Older News |
| − | | [[Fetch_Path]]—Sets the default path for the [[fetch]] command. | + | | See [[Older_News|Older News]]. |
| − | |-
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| − | ! New Script
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| − | | [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box. | |
| | |} | | |} |
| | |style="vertical-align: top; width: 40%"| | | |style="vertical-align: top; width: 40%"| |
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| | category=Commands|Plugins|Script_Library|Settings | | category=Commands|Plugins|Script_Library|Settings |
| | includepage=* | | includepage=* |
| − | includemaxlength=450 | + | includemaxlength=1050 |
| | escapelinks=false | | escapelinks=false |
| | resultsheader=__NOTOC__ __NOEDITSECTION__ | | resultsheader=__NOTOC__ __NOEDITSECTION__ |
