Difference between revisions of "TOPTOC"
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− | == | + | *'''See Also: [[OLD_TOPTOC|Old Table of Contents]]''' |
− | + | *'''Warning: This page is new and needs more updating.''' | |
+ | {| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;" | ||
+ | |- | ||
+ | | align="left" valign="top" | | ||
+ | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
+ | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Installation, Configuration & Learning | ||
+ | |- | ||
+ | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
+ | # '''[[:Category:Installation|Installation]]''' | ||
+ | ## [[Linux_Install|Linux]] | ||
+ | ## [[MAC_Install|MAC]] | ||
+ | ## [[Windows_Install|Windows]] | ||
+ | # '''[[:Category:Stereo 3D Display|Stereo 3D Display]]''' | ||
+ | ## [[Linux XFree86 Configuration]] | ||
− | + | ||
− | + | [[Image:0903_1_1.jpg|center|85px]] | |
− | # | + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| |
− | + | # '''[[:Category:Using Pymol|Using PyMol]]''' | |
− | + | ## '''[[:Category:Launching|Launching]]''' | |
− | + | ### [[Launching PyMOL|Launching PyMOL]] | |
− | # [[:Category: | + | ### [[Command_Line_Options|Command Line Options]] |
− | ## [[:Category: | + | ### [[Launching_From_a_Script|Launching From a Script]] |
− | ### [[ | + | ## [[Mouse_Controls|Mouse Controls]] |
− | ### [[ | + | ## '''[[:Category:Objects and Selections|Objects and Selections]]''' |
− | ### [[ | + | ### '''[[:Category:Working with Objects|Working with Objects]]''' |
− | + | ### '''[[:Category:Working with Selections|Working with Selections]]''' | |
− | # | + | ### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]''' |
− | |||
− | # [[ | ||
− | ## | ||
− | |||
− | ### [[:Category:Working with Objects|Working with Objects]] | ||
− | ### [[:Category:Working with Selections|Working with Selections]] | ||
− | ### [[:Category:Selector_Quick_Reference|Selector Quick Reference]] | ||
#### [[Single-word Selectors|Single-word Selectors]] | #### [[Single-word Selectors|Single-word Selectors]] | ||
#### [[Property Selectors|Property Selectors]] | #### [[Property Selectors|Property Selectors]] | ||
#### [[Selection Algebra|Selection Algebra]] | #### [[Selection Algebra|Selection Algebra]] | ||
#### [[Selection Macros|Selection Macros]] | #### [[Selection Macros|Selection Macros]] | ||
− | ### [[:Category:Representations|Representations]] | + | |} |
− | + | | align="left" valign="top" | | |
− | + | {| style="color:#CC9752; padding: 10px; background: transparent;" | |
− | #### [[Cartoon|Cartoon]] | + | !style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;" colspan="2" | Commands, Representations & Settings |
− | + | |- | |
− | + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | |
− | + | # '''[[:Category:Commands|PyMOL Commands]]''' | |
− | + | # '''[[:Category:Settings|Settings (Documented)]]''' | |
− | # | + | ## [[Settings|All]] |
− | + | ||
− | ## [[:Category: | + | |
− | + | [[Image:050429science.pdf.jpg|85px|center]] | |
− | + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | |
− | + | # '''[[:Category:Representations|Representations]]''' | |
− | + | ## [[Lines|Lines]] | |
− | ## [[ | + | ## [[Sticks|Sticks]] |
− | + | ## [[Ball_and_Stick|Ball and Sticks]] | |
− | + | ## [[Cartoon|Cartoon]] | |
− | + | ## [[Surface|Surface]] | |
− | + | ## [[Mesh|Mesh]] | |
− | + | ## [[Spheres|Spheres]] | |
− | # | + | ## [[Dots|Dots]] |
− | + | # '''[[:Category:Coloring|Coloring]]''' | |
− | + | ## [[Color|Color]] | |
− | + | |} | |
− | + | |- | |
− | ## [[:Category:Image Manipulation|Image Manipulation]] | + | | align="left" valign="top" | |
− | + | {| style="color:#CC9752; padding: 10px; background: transparent;" | |
− | + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling | |
− | + | |- | |
− | + | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | |
− | # [[:Category:Scripting|Scripting]] | + | # '''[[:Category:Biochemical_Properties|Biochemical Properties]]''' |
+ | ## [[Displaying Biochemical Properties|Displaying biochemical properties]] | ||
+ | ## [[Surfaces_and_Voids|Surfaces and Voids]] | ||
+ | |||
+ | |||
+ | [[Image:Ribbon_hh1.png|center|85px]] | ||
+ | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
+ | # [[Modeling_and_Editing_Structures|Modeling and editing structures]] | ||
+ | ## [[Editing atoms|Editing Atoms]] | ||
+ | ## [[Molecular Sculpting|Molecular sculpting]] | ||
+ | ## [[Homology Modeling|Homology modeling]] | ||
+ | |} | ||
+ | | align="left" valign="top" | | ||
+ | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
+ | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2" | Images & Movies | ||
+ | |- | ||
+ | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
+ | # '''[[:Category:Image Manipulation|Image Manipulation]]''' | ||
+ | ## [[Label|Labels]] | ||
+ | ## Photoshop/GIMP | ||
+ | ## [[Stereo_Ray|Stereo Figures]] | ||
+ | ## [[Publication Quality Images|Publication-quality images]] | ||
+ | ## [[PovRay|PovRay]] | ||
+ | | | ||
+ | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
+ | # [[Making_Movies|Making Movies]] | ||
+ | ## [[Software_Codecs|Codecs]] | ||
+ | |||
+ | |||
+ | [[Image:070816nature.pdf.jpg|center|85px]] | ||
+ | |} | ||
+ | |- | ||
+ | | align="left" valign="top" | | ||
+ | {| style="color:#CC9752; padding: 10px; background: transparent;" | ||
+ | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Extending, Embedding & Scripting | ||
+ | |- | ||
+ | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
+ | # [[:Category:Development|PyMOL Development]] | ||
+ | # [[Scripting|Scripting]] | ||
## [[Example Scripts|Example Scripts]] | ## [[Example Scripts|Example Scripts]] | ||
− | ## [[:Category:Script Library|Script Library]] | + | ## '''[[:Category:Script Library|Script Library]]''' |
− | # [[:Category:Plugins|Plugins]] | + | # '''[[:Category:Plugins|Plugins]]''' |
− | ## [[:Category:Electrostatics|Electrostatics and energy minimization.]] | + | ## '''[[:Category:Electrostatics|Electrostatics and energy minimization.]]''' |
### [[APBS|APBS Plugin]] | ### [[APBS|APBS Plugin]] | ||
− | ## rtools | + | ### [[Protein_contact_potential]] |
− | ## [[ | + | ## [http://www.rubor.de/bioinf/pymol_extensions.html rtools] |
− | # | + | ## [[Plugins_Tutorial|Tutorial on writing plugins]] |
+ | | | ||
+ | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
# High-Level Applications | # High-Level Applications | ||
## Crystallography Applications | ## Crystallography Applications | ||
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## NMR Applications | ## NMR Applications | ||
### Working with Structure Families | ### Working with Structure Families | ||
− | ## | + | ## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]''' |
### NMR Restraints and Analysis | ### NMR Restraints and Analysis | ||
− | # | + | |} |
− | + | | align="left" valign="top" | | |
− | + | {| style="color:#CC9752; padding: 10px; background: transparent;" | |
− | # | + | ! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2"| Third Party Applications |
− | # [[ | + | |- |
− | # [[:Category:PyMol_Integration|PyMol_Integration]] | + | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| |
+ | # [[O]] | ||
+ | # [[SURFNET]] | ||
+ | |||
+ | |||
+ | [[Image:080602cnen.pdf.jpg|center|85px]] | ||
+ | | | ||
+ | | style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"| | ||
+ | # [[Python_Integration|Python Integration]] | ||
+ | # '''[[:Category:PyMol_Integration|PyMol_Integration]]''' | ||
## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension | ## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension | ||
## [[CASTp|CASTp]] -- Binding and Active site prediction | ## [[CASTp|CASTp]] -- Binding and Active site prediction | ||
## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox | ## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox | ||
− | ## [[ | + | ## [[ProMOL]] |
− | # [[ | + | ## [[S2S]] |
− | + | ## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]''' | |
− | [[ | + | |} |
− | + | |} |
Latest revision as of 07:03, 9 September 2010
- See Also: Old Table of Contents
- Warning: This page is new and needs more updating.
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