[PyMOL] Pymol scripts for visualizing the location of post-translationally modified residues

We have added a subroutine to the structure viewer window of PhosphoSitePlus® (PSP)
 (http://www.phosphosite.org) that generates downloadable scripts that label and color amino acids  that are known to be post-translationally modified.

Only the reactive groups on each amino acid are colored, e.g. -OH on Ser, Thr or Tyr.

For example, go to the PKACa page on PSP (http://www.phosphosite.org/proteinAction.do?id=637&showAllSites=true), select 2GUB, and open the viewer. By clicking on "Get PyMOL Script", a rendering script will be downloaded onto your desktop which can be opened in PyMOL.

The intent of this routine is to allow users to determine if known modification sites might lie within known functional regions of the protein (e.g., protein-protein or protein-DNAcontact surfaces), or if modification sites that are separated by many residues in the primary structure might lie close to each other in the tertiary structure, suggesting possible mechanism for cross-talk between modification sites.

Please let colleagues that may be interested in this feature and who use Pymol know about this feature.

I would welcome feedback on this implementation might be improved.

Peter


Peter Hornbeck, Ph.D.
Senior Scientist, Director of PhosphoSitePlus®
http://www.phosphosite.org
Cell Signaling Technology
3 Trask Lane
Danvers, MA 01923
Phone: (978) 867-2368