On Feb 21, 2012, at 4:00 PM, sreetama das wrote:
Is there any software which will print the RMSDs (residue wise, and not chain wise) for more-than-2 chains (having similar/ same sequences) superposed together?
In UCSF Chimera you can use the Match->Align tool to create a structure-based sequence alignment (or you can open an alignment file if you already have one). The the alignment will show per-residue RMSD as a bar chart across the top of the alignment (if you opened your own alignment file you'd have to use the Headers->RMSD menu entry to show the bar chart). You can save the numeric RMSD values to a file with Headers->Save.
Also, Match->Align will report a couple of additional normalized RMSD scores, namely Structural Distance Measure and Q-score.
Chimera home page: www.cgl.ucsf.edu/chimera Match->Align page: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchalign/matchalign.html sequence aignment viewer: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html --Eric Eric Pettersen http://www.cgl.ucsf.edu/home/pett "And isn't sanity really just a one trick pony anyway? I mean all you get is one trick, rational thinking, but when you're good and crazy, oooh oooh oooh, the sky is the limit!"-The Tick
