[Chimera-users] matching peptides with altenate locations

Sumitro Harjanto u0601918 at nus.edu.sg
Thu Dec 31 02:12:14 PST 2009

Hi elaine, 

I was experimenting with the "match" command and I found that when
alternate locations are involved, sometimes the best alignment is not

For example I had 3FQW as #0 and 3FQX as #1; I was comparing the Chain C
(9-mer peptide) of the two models. 
#0 had alternate location in the 7th residue while
#1 had the alternate locations in the 2nd and 4th residue. 
They were essentially identical in sequence except for the 4th residue. 

When I matched the 6 residues, which did not have any alternate
locations, by the command:

match #0:1.c,3.c,5.c,6.c,8.c,9.c at ca #1:1.c,3.c,5.c,6.c,8.c,9.c at ca 

the RMSD returned is 0.080, which was reasonable judging from the high
conservation of the sequences.

but when I matched all the residues, and designate the .b alternate
location to be excluded by the command:

match #0:.c at ca&~@.b #1:.c at ca&~@.b

The RMSD returned was 8.730, which was unreasonably high. It was also
clear by visual inspection that the alignment was way off the best. I
would expect that the RMSD returned by the first and second command to
be roughly equal; because the alternate locations of the residues do not
alter the C-alpha position by much, it was the side-chain positions that
were more extensively varied.

Please advise. Thanks! =]


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 16 December 2009 3:23 AM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] matching peptides with altenate locations

Hi Sumitro,
OK, I have 1akj as model 0 and 2gtz as model 1.  The second command  
you gave will work if you remove the spaces before and after "|":

match #0:1-5.c at ca #1:1-3.c at ca|#1:4-5.c at ca.a

The space is used to separate the two sets of atoms.  The first  
command you gave wouldn't work because only some of the residues in #1  
have alternate locations.

If you want to use all nine residues, here is one possibility:

match #0:1-9.c at ca #1:1-9.c at ca&~@.b

meaning ...and not alternate location B.  If there were more alternate  
locations (C,D,...) you would also need to exclude those.  I hope this  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 14, 2009, at 11:23 AM, Sumitro Harjanto wrote:

> Hi,
> I would like to match two peptides; one with alternate conformations  
> in residue 4 and 5. I have tried:
> match   #0:1-9.c at ca   #1:1-9.c at ca.a
> match   #0:1-5.c at ca   #1:1-3.c at ca   |   #1:4-5.c at ca.a
> but both don't work and give me the "unequal number of atom chosen"  
> error message.
> I tried changing match to sel in the latter case and I can get 10  
> atoms; 5 from each model, which is what I intended.
> How should I deal with this?
> Thanks,
> Sumitro

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