On 10:11 Sun 12 Jul , Jason Vertrees wrote: > Donnie Berkholz wrote: > > 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? > > > 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.
Yeah, that's a nice use of the occupancy field. The problem is that I can't even figure out which subtractions to do without some way to access the residue mapping between the two nonidentical sequences that I know is calculated during alignment. In my original email, I mentioned that I'd discovered how to create that alignment object, I just can't figure out how to iterate over the residue numbers it's connecting. I might have to do something annoying like threading one of the sequences onto the other structure so I can hack around this residue-mapping problem. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University ------------------------------------------------------------------------------ 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
