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

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 21 16:13:04 PDT 2009

Hi Andrea,
Most of my previous suggestions are for the command line, except the  
very last part about drawing a box on the alignment and using  
"Structure... Match" from the sequence alignment window.   
Unfortunately, we do not have commands to draw a box on an alignment,  
or to match structures using that box.  Sorry about that,

On Jul 21, 2009, at 3:53 PM, Andrea Rossi wrote:

> Hi Elaine,
> The method you recommend works very well. I wonder if there is any  
> equivalent from command line.
> Thanks!
> Andrea
> On Tue, Jul 21, 2009 at 11:03 AM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> 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  
> chains.
> 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
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> 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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