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 [1].
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.
PyMOL is now available on the iPad as a free download from the AppStore. See pymol.org/mobile for more info.
OS X Compatibility
Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here X11 Libraries.
New Script
select_sites can set author/paper selections according to SITE annotation in pdb file
New Script
b2transparency can set surface transparency based on atom b-factor
New Extension
psico is a python module which extends PyMOL with many commands
New Script
uniprot_features makes named selections for sequence annotations from uniprot
New Plugin
Gyration_tensor Calculates chain-wise gyration tensor of a protein.
New Script
set_phipsi can set phi/psi angles for all residues in a selection
New Script
dehydron A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
New Script
pymol2glmol is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
New Script
cyspka is an experimental surface cysteine pKa predictor.
Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
New Script
Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See DisplacementMap.
New Script
propka: Fetches the pka values for your protein from the propka server. propka generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
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,
alignproteinA,proteinB,object=A_on_B
the alignment can be written using:
saveA_aligned_with_B.aln,A_on_B
USAGE
savefile[,(selection)[,state[,format]]]
EXAMPLES
# save only the alpha carbonssaveonlyCAs.pdb,n.CA# save my MD trajectory file to disksavemyTraj.pdb,myMDTrajectory,state=0# save a PyMOL sessionsavethisSession.pse
