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

[Kamalesh Damodaran]

Hi Eric,

Thank you so much for your guidance and the python script. I got everything
what I was looking for.

Thanks and regards,
Kamalesh D.

On Wed, 4 Sep 2019 at 04:54, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Kamalesh,
> If you are familiar with Python, there is a script attached to this
> previous mailing-list message:  [Chimera-users] Writing alignment and
> RMSD out
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002090.html> that
> would be easy to modify to do what you want.  You would just remove the
> parts the parts that used Multalign Viewer to write the sequence
> alignment.  The RMSD that the MatchMaker.match() function returns is a
> carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more
> work.  Let me know and I can offer guidance on that.  Also, match() returns
> the overall RMSD of the match.  To get the per-residue RMSD you would loop
> over the atom lists returned by the match() function and for corresponding
> pairs get the distance (== RMSD for two atoms) with:
>  atom1.xformCoord().distance(atom2.xformCoord()).  For output purposes you
> can get a string representation of an atom’s residue with str(atom.residue).
> Also, unfortunately the attachment to the message has a “.bin” suffix
> despite being from a Python file that had a “.py” suffix, so if that’s a
> problem let me know and I can send you the .py file directly.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
> On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran <kamaleshdams at gmail.com>
> wrote:
>
> 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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