Difference between revisions of "Main Page"

Type	Python Module
Download	colorbyrmsd.py
Author(s)	Shivender Shandilya, Jason Vertrees, Thomas Holder
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

Revision as of 11:18, 11 February 2019

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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org

Quick Links
Tutorials	Table of Contents	Commands
Script Library	Plugins	FAQ
Gallery \| Covers	PyMOL Cheat Sheet (PDF)	Getting Help

News & Updates
Official Release	PyMOL v2.3 has been released on February 11, 2019.
POSF	New PyMOL fellows announced for 2018-2019
Tutorial	Plugins Tutorial updated for PyQt5
New Plugin	ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Selection keywords	New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update	MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script	dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News	See Older News.

Did you know...

ColorByRMSD

Introduction

This script allows you to color two structures by Root Mean Square Deviation (RMSD). The distances between aligned C-alpha atom pairs are stored as B-factors of these residues, which are colored by a color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Unaligned residues are colored gray.

Usage

colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]

Arguments

mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
doAlign = 0 or 1: Superpose selections before calculating distances {default: 1}
doPretty = 0 or 1: Show nice representation and colors {default: 1}
guide = 0 or 1: Only use C-alpha atoms {default: 1}
method = align or ..→

A Random PyMOL-generated Cover. See Covers.

@@ Line 28: / Line 28: @@
 {| 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
+| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
+|-
+! POSF
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
+|-
+! Tutorial
+| [[Plugins Tutorial]] updated for PyQt5
+|-
+! New Plugin
+| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 |-
 ! Selection keywords
 | New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
-|-
-! Official Release
-| [https://pymol.org PyMOL v2.0 has been released] on September 20, 2017.
 |-
 ! Plugin Update
 | [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
-|-
-! Official Release
-| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
-|-
-! Official Release
-| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
 |-
 ! New Script
 | [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
-|-
-! New Plugin
-| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
-|-
-! Official Release
-| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
-|-
-! PyMOL Open-Source Fellowship
-| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
-|-
-! Official Release
-| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
-|-
-! New Plugin
-| [[PyANM|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: 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.
 |-
 ! Older News