mmaker - superposing two structures based on a subset of a chain
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
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@ca #2:1-100.h@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
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@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@ca #2:1-100.h@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
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, Elaine 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@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@ca #2:1-100.h@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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participants (2)
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Andrea Rossi -
Elaine Meng