[Chimera-users] matching peptides with altenate locations

[Sumitro Harjanto]

Hi elaine, 

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

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! =]

Cheers,
Sumitro

-----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  
helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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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