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! Official Release
! Official Release
| [[PyMOL, AxPyMOL, and JyMO v1.7 have all been released|http://pymol.org]] today, January 14, 2014.
| [[http://pymol.org|PyMOL, AxPyMOL, and JyMO v1.7 have all been released]] today, January 14, 2014.
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! New Plugin
! New Plugin

Revision as of 15:38, 14 January 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 [AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
New Plugin Bondpack is a 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...

Isomesh

isomesh creates a mesh isosurface object from a map object.

Usage

isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]] 
  • name = str: the name for the new mesh isosurface object.
  • map = str: the name of the map object to use for computing the mesh.
  • level = float: the contour level (in sigma units) {default: 1.0}
  • selection = str: an atom selection about which to display the mesh with an additional "buffer" (if provided).
  • buffer = float: (see selection)
  • state = int: the state into which the object should be loaded (default=1) (set state=0 to append new mesh as a new state) {default: 1}
  • carve = float: a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.

Example

<source lang="python"> fetch 6sps fetch 6sps, type=2fofc

  1. mesh for entire map object

isomesh mesh_all, 6sps_2fofc

  1. mesh within bounding box of ligand, enlarged by 2 Angstrom

isomesh mesh_ligand, 6sps_2fofc, selection=(resn LR5), buffer=2

  1. mesh only ..→
A Random PyMOL-generated Cover. See Covers.