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

Andrea Rossi aredze at gmail.com
Tue Jul 21 15:53:51 PDT 2009

Hi Elaine,

The method you recommend works very well. I wonder if there is any
equivalent from command line.


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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