Main Page

From PyMOLWiki
Revision as of 04:49, 24 July 2018 by Speleo3 (talk | contribs) (PyMOL v2.2 release)
Jump to: navigation, search
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
Official Release PyMOL v2.2 has been released on July 24, 2018.
POSF PyMOL Open-Source Fellowship program accepting applications for 2018-2019
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
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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...

Movie fade

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

This script will help fade in and out settings in a movie. Just specify the setting, it's initial value at an initial frame and it's ending value and frame.

Usage

movie_fade setting, startFrame, startVal, endFrame, endVal [, selection ]

Examples

To fade in sticks from fully transparent to fully opaque across 60 frames do:

mset 1x60
movie_fade stick_transparency, 1, 1., 60, 0.

More complex example which involves camera motion:

fetch 1rx1, async=0
as cartoon
show surface
mset 1x80
movie.roll
movie_fade transparency,  1, 0., 40, 1.
movie_fade transparency, 41, 1., 80, 0.

Example file:

Result

<source lang="python"> import movie_fade

fetch 1hpv, async=0 orient

  1. format

bg black show_as cartoon color marine, ss s color ..→

A Random PyMOL-generated Cover. See Covers.