> Message: 6 > Date: Sat, 11 Jul 2009 23:34:01 -0700 > From: Donnie Berkholz <dberkh...@gentoo.org> > Subject: [PyMOL] Comparing B-factors of aligned residues > To: pymol-users@lists.sourceforge.net > Message-ID: <20090712063401.ga10...@comet> > Content-Type: text/plain; charset=us-ascii > > Hi all, > > I'm trying to compare the B-factors in two homologous proteins I aligned > using 'super'. I can create an alignment object mapping residue pairs > together, so I think what I want to do should be possible. I'd like to > somehow use that to map the *difference* between the two CA B's onto one > of the structures, then color it by B-factor and color unaligned > residues gray. > > I can't even figure out how to get at the alignment object or what's in > it, much less how to do this. Could anyone help me? > > -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State > University
Donnie, you can find something similar in the interfaceResidues script on the PyMOLWiki: http://pymolwiki.org/index.php/InterfaceResidues It shows you how to load something into the B-factors and calculate the difference using the q field. Don't forget you can do super protein1, protein2, object=foo and foo will be the alignment differences shown as CGO. If you could extract the values of the lengths of those CGO lines you'd be done. -- J -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ 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
