Difference between revisions of "Main Page"

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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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! Official Release
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| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
 
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! New Plugin
 
! New Plugin
 
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
 
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
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! Official Release
 
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| [https://pymol.org PyMOL v2.1 has been released] on March 13, 2018.
 
 
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! Selection keywords
 
! Selection keywords
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! New Script
 
! New Script
 
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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! New Plugin
 
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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
 
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! New Plugin
 
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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
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! New Plugin
 
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
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! New Plugin
 
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| [[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.
 
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! 3D using Geforce
 
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| 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.
 
 
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! Older News
 
! Older News

Revision as of 05:27, 19 February 2019

hosted by SBGridlogo2.jpg
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
Python 3 New Python 3 compatibility guide for scripts and plugins
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...

Contact Surface

= Overview =

This script calculates individual or global contact areas between a receptor molecule and a (multimodel) bundle of docked ligand structures. The exact contact surface area values (in Angstrom^2) are printed to the screen and also appended to a file called contactareas.txt. If only a single global contact surface is calculated, a selection named "contact" is created that includes all receptor atoms within 3.9A of any ligand atom to illustrate the approximate contact surface.


The parameters are:

receptor (string)

The name of the selection/object representing the receptor protein

ligand (string)

The name of the selection/object representing the ligand
Note that this may be another protein!

states (integer), default:0

Calculate contact surface between the receptor and the first n states of the ligand.
If states = 0, the script calculates a global contact surface which takes all possible ligand states into account.


Usage

<source lang="python"> contact_surface ..→

A Random PyMOL-generated Cover. See Covers.


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