[Chimera-users] mmaker - superposing two structures based on a subset of a chain

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 21 11:03:16 PDT 2009

Hi Andrea,
If you already know what numbers are supposed to go together, just use  
the "match" command, e.g.:

match #0:1-100.h at ca #2:1-100.h at ca

However, maybe you meant you don't know exactly which numbers should  
pair but you only want it to consider those segments.  Currently that  
cannot be done.  However...

In many cases, specifying a subset of a chain is not necessary to  
exclude flexible parts because by default the fit is iterated.  In  
other words, only the parts that do fit in space will end up being  
used in the final match, because the far-apart pairs (even though  
aligned in the sequence alignment) will be pruned.  If you use "show  
true" with "mmaker" it will show the sequence alignment with orange  
boxes around the parts that are actually used in the final fit.

One problem with the command you sent is that you need to include  
"pair ss" to use those chains.  Perhaps it is not even using the H  

If with "pair ss" and "show true" you see that the initial matchmaker  
fit is still using parts you didn't want it to use, you can drag a box  
in the sequence alignment and only use the positions inside that box  
(of course, that part of the alignment must be correct).  To do that,  
choose from the sequence alignment window "Structure... Match" and  
turn on "Match active region only."

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

On Jul 21, 2009, at 10:43 AM, Andrea Rossi wrote:

> Dear Chimera Team,
> I was wondering if it is possible to superpose two structures based  
> on a subset of a chain (a domain for example). I tried the command:
> mmaker #0:1-100.H #2:1-100.h
> but Chimera doesn't seem to take into account the residue selection.
> Superposing according to a subset of a chain is particularly useful  
> when the chain is formed by two or more domains and the domains are  
> connected by a flexible linker (as in the case of antibodies). I can  
> provide more specific examples if needed.
> Andrea

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