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! Official Release
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 2, 2014.
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 3, 2014.
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! New Plugin
! New Plugin

Revision as of 23:42, 3 December 2014

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 3, 2014.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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 v1.7.2 have all been released on August 4, 2014.
Official Release PyMOL, AxPyMOL, and JyMOL 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 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.
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 generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...
= Overview =

This script will aid you in making publication quality figures for the currently displayed scene. It understands a variety of preset "modes" and sizes.


Usage

make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]

The parameters are:

filename : The name of the resulting image file.

The extension .png is added automatically.


NOTE: if no further arguments are given, the script generates quick figures for general use:

  • figures are not ray-traced
  • TWO figures at 300 x 300 px, 72 dpi
  • views are rotated 180° about y (front and back view)
  • _front_quick and _back_quick are appended to the filename


mode : Type of figure desired. Possible values are as follows:


single = "single view"
  • one ray-traced 300 dpi figure of the current view


fb = "front and back view"
  • TWO ray-traced 300 dpi figures
  • views are rotated 180° about y
  • _front and _back are appended to the filename


sides ..→
A Random PyMOL-generated Cover. See Covers.