residuewise rmsd for multiple chain superposition

From: sreetama das
Date: 21 February 2012 09:33

Dear all,

           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?

Thanks in advance,

sreetama

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From: Thomas Holder


Dear Sreetama,

theseus can superpose multiple structures and reports RMSD per residue.

http://www.theseus3d.org/

If your sequences are not identical and you want least squares superposition, run it like this:

theseus_align -l -f *.pdb

This will produce several output files. The file "theseus_variances.txt" contains the RMSD per residue.

Cheers,
 Thomas

-- 

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From: Eric Pettersen

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

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From: Avinash Punekar


Dear Sreetama,

ProFit (http://www.bioinf.org.uk/software/profit/) does the RMS-by-residue calculation for multiple chain superposition.

Avinash Punekar