[Chimera-users] using CHIMERA to measure RMSD for large number of short peptides against a template structure

[Elaine Meng]

On Oct 21, 2009, at 6:45 AM, Sumitro Harjanto wrote:
>
> Background:
> Basically I would like to compare peptide to peptide and obtain the  
> RMSD between the two peptides using CHIMERA. These peptides may  
> have different lengths (eg 9-mer vs 10-mer) and they are not  
> conserved at all, in fact, they can be quite different in sequence.  
> They however have similar structures.
>
> Problem:
> I have a dilemma in choosing which alignment method to use. If I  
> use matchmaker, which is based on sequence alignment, only selected  
> amino acid pairs will be measured (since the peptides are not  
> conserved); if I use match instead, the peptides have to be of  
> equal length, but they are not. Is there way to get around this  
> dilemma..?
> I need the RMSD value to be exported from CHIMERA. I understand  
> that CHIMERA kept a log (replylog) for each session. Is there a way  
> for me to extract the content of this file? Or is there any other  
> way to keep a record of the RMSD values (since I would need to  
> automate this process to calculate RMSD for many pairs of peptides.
> Thanks,
> Sumitro

Hi Sumitro,
Matchmaker does not require the sequences to be identical, but  
generally it is intended for homologous proteins with at least partly  
conserved sequences and secondary structures.  If you are working  
with short peptides, I agree that matchmaker will probably not give  
the matches that you want, so "match" would be the way to go.

The "match" command does not require that the overall structures have  
the same number of atoms, only that you tell it to use equal numbers  
of atoms from the two models.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
For example, model 0 could be some protein with residues 1-500 in  
chain A and residues 1-250 in chain B, while model 1 is your peptide  
that only has 10 residues.  In the match command you just say exactly  
which atoms and residues should be used.  When the residues are of  
different types, you would normally just use their backbone atoms  
instead of the whole residues, which could have different numbers of  
atoms.  Examples:

match #1:1-10 at ca  #0:1-10.a at ca
match #1:1-10 at n,ca,c,o #0:425-434.b at n,ca,c,o
match #1:2-9 at ca #0:4.a,6-9.a,8-10.b at ca

The RMSD values will be reported in the Reply Log (under Favorites  
menu).  You can copy the text in  it and paste to a file. Or, if you  
are running Chimera in "nogui" mode, this information can be  
redirected to a file as described in this previous post:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/ 
003064.html>

For more about scripting to process multiple structures, see previous  
posts such as:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 
003261.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 
003262.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco