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== | *'''See Also: [[OLD_TOPTOC|Old Table of Contents]]''' | ||
*'''Warning: This page is new and needs more updating.''' | |||
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{| style="color:#CC9752; padding: 10px; background: transparent;" | |||
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Installation, Configuration & Learning | |||
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# '''[[: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]] | |||
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# | # '''[[:Category:Using Pymol|Using PyMol]]''' | ||
## '''[[:Category:Launching|Launching]]''' | |||
# | ### [[Launching PyMOL|Launching PyMOL]] | ||
### [[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]]''' | |||
# [[Launching PyMOL|Launching PyMOL]] | ### '''[[:Category:Working with Selections|Working with Selections]]''' | ||
## [[ | ### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]''' | ||
## [[ | |||
## [[ | |||
## [[:Category:Objects and Selections|Objects and Selections]] | |||
### [[:Category: | |||
### [[:Category: | |||
### [[: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: | |} | ||
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{| style="color:#CC9752; padding: 10px; background: transparent;" | |||
## | !style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;" colspan="2" | Commands, Representations & Settings | ||
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# '''[[:Category:Commands|PyMOL Commands]]''' | |||
# '''[[:Category:Settings|Settings (Documented)]]''' | |||
## [[Settings|All]] | |||
## [[ | |||
## [[ | [[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: | |- | ||
## [[ | | 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:Biochemical_Properties|Biochemical Properties]]''' | |||
## [[Displaying Biochemical Properties|Displaying biochemical properties]] | |||
## | ## [[Surfaces_and_Voids|Surfaces and Voids]] | ||
# [[ | |||
## [[ | [[Image:Ribbon_hh1.png|center|85px]] | ||
## [[:Category: | | style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"| | ||
# [[:Category:Plugins|Plugins]] | # [[Modeling_and_Editing_Structures|Modeling and editing structures]] | ||
## [[:Category: | ## [[Editing atoms|Editing Atoms]] | ||
### [[ | ## [[Molecular Sculpting|Molecular sculpting]] | ||
## [[: | ## [[Homology Modeling|Homology modeling]] | ||
## [[ | |} | ||
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# | {| 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]] | ||
# [[:Category:PyMol_Integration|PyMol_Integration]] | ## [[Software_Codecs|Codecs]] | ||
## [[ | |||
## [[ | |||
# [[ | [[Image:070816nature.pdf.jpg|center|85px]] | ||
|} | |||
[[ | |- | ||
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{| style="color:#CC9752; padding: 10px; background: transparent;" | |||
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Extending, Embedding & Scripting | |||
|- | |||
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# [[:Category:Development|PyMOL Development]] | |||
# [[Scripting|Scripting]] | |||
## [[Example Scripts|Example Scripts]] | |||
## '''[[:Category:Script Library|Script Library]]''' | |||
# '''[[:Category:Plugins|Plugins]]''' | |||
## '''[[:Category:Electrostatics|Electrostatics and energy minimization.]]''' | |||
### [[APBS|APBS Plugin]] | |||
### [[Protein_contact_potential]] | |||
## [http://www.rubor.de/bioinf/pymol_extensions.html rtools] | |||
## [[Plugins_Tutorial|Tutorial on writing plugins]] | |||
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# High-Level Applications | |||
## Crystallography Applications | |||
### Symmetry|Symmetry | |||
### Electron Density | |||
## NMR Applications | |||
### Working with Structure Families | |||
## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]''' | |||
### NMR Restraints and Analysis | |||
|} | |||
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{| 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 | |||
|- | |||
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# [[O]] | |||
# [[SURFNET]] | |||
[[Image:080602cnen.pdf.jpg|center|85px]] | |||
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# [[Python_Integration|Python Integration]] | |||
# '''[[:Category:PyMol_Integration|PyMol_Integration]]''' | |||
## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension | |||
## [[CASTp|CASTp]] -- Binding and Active site prediction | |||
## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox | |||
## [[ProMOL]] | |||
## [[S2S]] | |||
## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]''' | |||
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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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