Main Page

From PyMOLWiki
Jump to: navigation, search
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
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
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...

Plane Wizard

This wizard has a simple purpose - to draw a cgo plane that passes through three points picked by the user. Most of the wizard itself was copied from the measure wizard.

To use, put it in the same directory as the other wizards. This is not quality code, and there may be bugs, but it seems to work okay.

import pymol
from pymol import cmd
from pymol.wizard import Wizard
from chempy import cpv
from pymol.cgo import *
def makePrimitive(cgo, name):
    cmd.set('auto_zoom', 0, quiet=1)
    cmd.load_cgo(cgo, name)
    cmd.set('auto_zoom', 1, quiet=1)
def point(p):
    x, y, z = p
    return [COLOR, 1, 1, 1, SPHERE, float(x), float(y), float(z), 0.5]
def line(p1, p2):
    x1, y1, z1 = p1
    x2, y2, z2 = p2
    return [CYLINDER, float(x1), float(y1), float(z1), float(x2), float(y2), float(z2), 0.25, 1, 1, 1, 1, 1, 1]
def plane(corner1, corner2, corner3, corner4, normal):
    planeObj = []
    planeObj.extend [[Plane Wizard|..→]]
A Random PyMOL-generated Cover. See Covers.

Personal tools