On Nov 19, 2010, at 4:00 PM, Srivastava, Dhiraj wrote:
Hi All
does anyone know any software that can calculate and print out
RMSD of every residue (c alpha will be good) for homologous
structures which has only 30-40 % sequence similarity? I looked on
the web but all the software that I found require the sequence to be
the same for both structure.
You can use the MatchMaker tool in UCSF Chimera to generate a sequence
alignment of the two structures. That alignment will have an "RMSD"
header. If you use the alignment's Headers->Save menu item to save
the RMSD header then the RMSD value for each column in the alignment
will be saved to a file. Furthermore, if you don't like some of the
residue correspondences in the MatchMaker-generated alignment, the
alignment can be edited to rectify the problems. Alternatively, if
you had an alignment file of your own, you could open that in Chimera
along with the two structures (Chimera will figure out the
correspondence between the structures and alignment sequences
automatically) and then show and save the RMSD header of that alignment.
--Eric
pertinent URLs:
Chimera home page: http://www.cgl.ucsf.edu/chimera/
MatchMaker tool:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html
alignment editing:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing
