PyMOL Wiki - User contributions [en]

Main Page

2014-03-28T23:43:58Z

Pyadmin:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- 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.
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| New accounts: email thomas (dot) holder (@) schrodinger dot com
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
|}
{| 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;"
|+ 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
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| 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]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')

|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
|-
! New Plugin
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
|-
! New Plugin
| [[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.
|-
! 3D using Geforce
| 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.
|-
! New Plugin
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
|-
! New Software
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
|-
! New Script
| [[cgo_arrow]] draws an arrow between two picked atoms.
|-
! Tips & Tricks
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 60%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
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|style="vertical-align: top; width: 18%"|

|}

PyMOL Wiki:About

2014-03-28T22:31:43Z

Pyadmin: Created page with "==About== Reading the PyMol list for years, we users noticed a trend: person A would ask a question, person B would answer and then two months later person C would ask th..."

==About==

Reading the [[PyMol list]] for years, we users noticed a trend: person A would ask a question, person B would answer and then two months later person C would ask the same question again, but now to get the answer everyone had to search for it. We have a growing corpus of knowledge; it's now time to organize it.

This site came from acknowledging that.

TOPTOC

2014-03-28T21:17:19Z

Pyadmin:

*'''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]]
### [[Command_Line_Options|Command Line Options]]
### [[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]]'''
#### [[Single-word Selectors|Single-word Selectors]]
#### [[Property Selectors|Property Selectors]]
#### [[Selection Algebra|Selection Algebra]]
#### [[Selection Macros|Selection Macros]]
|}
| align="left" valign="top" |
{| 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
|-
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# '''[[: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]]
|}
|-
| 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]]
| 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]]
## '''[[: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]]
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# 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
|}
| 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
|-
| 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
## [[CASTp|CASTp]] -- Binding and Active site prediction
## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox
## [[ProMOL]]
## [[S2S]]
## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]'''
|}
|}

File:File.xyz.tar

2014-03-28T19:31:44Z

Pyadmin: Pyadmin uploaded "File:File.xyz.tar"

xyz-coordinatinates of the Produkt in the Dublett-states obtained from

http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja991878x

File:Long movie ray.mpg

2014-03-28T19:31:26Z

Pyadmin: Pyadmin uploaded "File:Long movie ray.mpg"

Long movie, showing camera motions, object motions and scenes. This took longer to render than it did to make. :-)

File:Motions movie.mpg

2014-03-28T19:31:25Z

Pyadmin: Pyadmin uploaded "File:Motions movie.mpg"

Movie combining motions and representations.

File:PyMOLreferenceCard-test.zip

2014-03-28T19:30:47Z

Pyadmin: Pyadmin uploaded "File:PyMOLreferenceCard-test.zip"

test

File:PyMOLreferenceCard.zip

2014-03-28T19:30:47Z

Pyadmin: Pyadmin uploaded "File:PyMOLreferenceCard.zip"

PyMOL Cheat Sheet Code

File:Cealign-0.9.zip

2014-03-28T19:30:13Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.9.zip"

Untested CEalign 0.9.

File:Cealign-0.8-RBS.zip

2014-03-28T19:30:13Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.8-RBS.zip"

File:Cealign-0.6.zip

2014-03-28T19:30:12Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.6.zip"

File:Cealign-0.5.zip

2014-03-28T19:30:11Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.5.zip"

File:Cealign-0.4.zip

2014-03-28T19:30:10Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.4.zip"

More bugs.

File:Cealign-0.3.zip

2014-03-28T19:29:29Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.3.zip"

Fixed a minute bug.

File:Cealign-0.2.zip

2014-03-28T19:29:28Z

Pyadmin: Pyadmin uploaded a new version of "File:Cealign-0.2.zip"

CE Align v0.2 zipfile

File:Cealign-0.1.zip

2014-03-28T19:29:28Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.1.zip"

File:Script.pml.tar

2014-03-28T19:28:48Z

Pyadmin: Pyadmin uploaded a new version of "File:Script.pml.tar"

File:Torus.zip

2014-03-28T19:28:33Z

Pyadmin: Pyadmin uploaded a new version of "File:Torus.zip"

File:Cealign-0.7.zip

2014-03-28T19:28:17Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.7.zip"

File:Script.pml.tar

2014-03-28T19:26:45Z

Pyadmin: Pyadmin uploaded "File:Script.pml.tar"

File:Torus.zip

2014-03-28T19:26:45Z

Pyadmin: Pyadmin uploaded "File:Torus.zip"

File:Traj movie.mpg

2014-03-28T19:26:23Z

Pyadmin: Pyadmin uploaded "File:Traj movie.mpg"

A snippet of an MD movie, made using PyMOL.

File:Cealign-0.2.zip

2014-03-28T19:25:35Z

Pyadmin: Pyadmin uploaded "File:Cealign-0.2.zip"

CE Align v0.2 zipfile

File:X3dna r3d pymol.png

2014-03-28T19:22:52Z

Pyadmin: Pyadmin uploaded "File:X3dna r3d pymol.png"

File:Wrappers histogram.png

2014-03-28T19:22:51Z

Pyadmin: Pyadmin uploaded "File:Wrappers histogram.png"

Histogram of the number of wrappers per hydrongen bond for a set of high-quality X-ray protein structures.

File:Wow grid mode.png

2014-03-28T19:22:50Z

Pyadmin: Pyadmin uploaded "File:Wow grid mode.png"

159 proteins loaded in grid mode! I thought PyMOL would crash upon doing this many, but it handled it with ease.

File:Wood.png

2014-03-28T19:22:50Z

Pyadmin: Pyadmin uploaded "File:Wood.png"

Wooden like rendering.

File:Warren.jpg

2014-03-28T19:21:39Z

Pyadmin: Pyadmin uploaded "File:Warren.jpg"

Photograph of Warren.

File:Viewer guide.png

2014-03-28T19:21:38Z

Pyadmin: Pyadmin uploaded "File:Viewer guide.png"

A labeled legend of the PyMol interface.

File:Valence1.png

2014-03-28T19:21:37Z

Pyadmin: Pyadmin uploaded "File:Valence1.png"

Valence On (double bonds shown, too)

File:Valence0.png