[Chimera-users] Way to compute residue wise RMSD using python script in chimera:

Kamalesh Damodaran kamaleshdams at gmail.com
Sat Aug 31 07:20:10 PDT 2019

Dear sir/madam,

I would like to superimpose the two structures and compute the residue wise
RMSD values. With Gui support in chimera, I opened the two structures and
used Matchmaker to superimpose two structures. In Matchmaker, I checked the
box 'Show pairwise alignment(s)' and click Apply, subsequently it displays
MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone -->
Save --> filenamegiven. This process would give me residue wise RMSD score
only for backbone atoms in .hdr format.

I wants to write python script to do the same, so that I will compare large
number of structures, and my script is able to perform till the procedure
of superimposition using matchmaker and display MultAlignViewer dialogue
box. I don't know the way to store the RMSD : backbone and RMSD : calpha in
.hdr format using python script through chimera.

Can some one please help me in this. The reason why I specifically want to
do in this approach is, because among the two structures, some residues of
one structure is missing. Since this approach will compute RMSD only for
the matching residues, I am interested in this.

Hope my question is not confusing. Thanks in advance.

Best regards,
Kamalesh D.
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