[Chimera-users] mmaker - superposing two structures based on a subset of a chain
meng at cgl.ucsf.edu
Tue Jul 21 16:13:04 PDT 2009
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.
> On Tue, Jul 21, 2009 at 11:03 AM, Elaine Meng <meng at cgl.ucsf.edu>
> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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