Hi Eric, On Wed, Mar 2, 2011 at 1:41 PM, Eric Schreiter <eric_...@mit.edu> wrote: > I'm looking for a quick way to color two superimposed structures such that > SSEs for which there is an equivalent in both structures are colored and the > non-matching SSEs and loops are grey. Also, the colored SSEs would be > rainbow (e.g. the first matching SSE colored blue, second colored green, > etc.). Any ideas how to do this?
Interesting idea. I think PyMOL is well suited for this task. Here's an example: # grab two similar proteins fetch 1cll 1ggz, async=0 # align them align 1cll, 1ggz, object=aln # select atoms of similar SS select similarSS, (1ggz or 1cll) in aln and (ss 'H' or ss 'S') # color by rainbow util.rainbow similarSS and 1ggz util.rainbow similarSS and 1cll # now color everything else grey color grey70, not (similarSS) # update the representation as cartoon # hide indicators select none That's cool enough to be it's own script. I'll add that to the PyMOLWiki if I find the time. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
