Main Page: Difference between revisions

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.editing

Revision as of 09:57, 11 September 2015

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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Script Library	Plugins	FAQ
Gallery \| Covers	PyMOL Cheat Sheet (PDF)	GoogleSearch

News & Updates
PyMOL Open-Source Fellowship	Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release	PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin	PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin	Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin	MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce	PyMOL can now be 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.
Older News	See Older News.

Did you know...

Dssp

dssp is a wrapper for the popular DSSP program, which computes secondary structure. The command updates PyMOL's ss atom property.

Installation

The dssp command is available from the psico package and requires the dssp binary (or mkdssp, dsspcmbi, dssp-2).

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c salilab -c speleo3 dssp

Usage

dssp [ selection [, exe [, raw [, state ]]]]

Arguments

selection = str: atom selection {default: all}
exe = str: path to dssp binary {default: search $PATH for dsspcmbi, dssp, dssp-2, mkdssp}
raw = str: atom property to assign the dssp secondary structure type to. This type will also be translated to PyMOL's H/S/L types and assiged to the ss property {default: }
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A Random PyMOL-generated Cover. See Covers.

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 {| class="jtable" style="float: left; width: 90%;"
 |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
-|-
-! Official Release
-| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 3, 2014.
-|-
-! New Plugin
-| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 |-
 ! PyMOL Open-Source Fellowship
@@ Line 35: / Line 29: @@
 |-
 ! Official Release
-| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
+| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 |-
-! Official Release
+! New Plugin
-| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
+| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 |-
 ! New Plugin
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 ! 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