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(News update)
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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
|-
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 3, 2014.
|-
! New Plugin
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
|-
|-
! PyMOL Open-Source Fellowship
! PyMOL Open-Source Fellowship
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|-
|-
! Official Release
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
|-
|-
! Official Release
! New Plugin
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
|-
|-
! New Plugin
! New Plugin
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! 3D using Geforce
! 3D using Geforce
| 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.
| 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.
|-
! 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.
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! New Script
| [[cgo_arrow]] draws an arrow between two picked atoms.
|-
! Tips & Tricks
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
|-
|-
! Older News
! Older News

Revision as of 09:57, 11 September 2015

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
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 v1.7.6 have all been released on May 4, 2015.
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...

Save

save writes selected atoms to a file.

Details

  • The file format is autodetected if the extension is .pdb, .pqr, .mol, .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw, .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2.
  • If the file extension is ".pse" (PyMOL Session), the complete PyMOL state is always saved to the file (the selection and state parameters are thus ignored).
  • CLUSTALW formatted alignments can be written by PyMOL as well. Once you perform an alignment like the following,
align proteinA, proteinB, object=A_on_B
the alignment can be written using:
save A_aligned_with_B.aln, A_on_B

USAGE

save file [,(selection) [,state [,format]] ]

EXAMPLES

# save only the alpha carbons
save onlyCAs.pdb, n. CA

# save my MD trajectory file to disk
save myTraj.pdb, myMDTrajectory, state=0

# save a PyMOL session
save thisSession.pse

===PYMOL ..→

A Random PyMOL-generated Cover. See Covers.


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