[Chimera-users] MatchMaker

Tom Goddard goddard at sonic.net
Tue Feb 5 12:13:38 PST 2013


Hi Sebastian,

   If you want to align dimer AB with another dimer CD and you want to 
rigidly move one dimer without changing the relative positions of the 
two monomers, and you want to align using just one monomer (A and C 
say), then a command to do that is

     match #1 #3 move #1,2

where the monomers A,B,C,D are models #1,2,3,4 in Chimera.  This command 
says align monomer A with monomer C (#1 to #3) and move both A and B (#1 
and #2) as a rigid unit.  This will only work if A and C contain exactly 
the same set of atoms, since that is a requirement of the "match" 
command.  The approach Elaine described using Match Maker handles 
aligning with different residue sequences by computing a sequence 
alignment for you.  But the match maker command (mmaker) does not have 
the "move" option that the match command has which is why you need to 
use "combine" for that approach. If your monomers have the same sequence 
but not all atoms are the same (e.g. point mutation) you could align 
using just carbon alpha atoms:

     match #1 at CA #3 at CA move #1,2

or some other subset of atoms that both monomers have in common.

   http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

Tom


-------- Original Message --------
Subject: Re: [Chimera-users] MatchMaker
From: Elaine Meng
To: Mock, Sebastian
Date: 2/5/13 9:47 AM
> Hi Sebastian,
> I think I understand.
>
> If you need the dimer relationship to remain EXACTLY the same, you could combine models (e.g. Model Panel function "copy/combine") so that each group in which you want to retain the relative positions is made into a single model.  That will probably require chain ID reassignment, which is an option in the combination dialog.  Then in MatchMaker you could use the chain pairing option "specific chain(s) in reference structure with specific chain(s) in match structure" and explicitly say which chain in the first dimer you want matched to which chain in the second dimer.  I mentioned the option in the GUI, but there is a corresponding option of the matchmaker command.  There is also a "combine" command, but the GUI called from the Model Panel as mentioned above may be easier to use (you don't have to look up the command options and syntax).
>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
>
> Otherwise you could just match first subunit with first subunit and second with second, but as you said, that would change the relationship between first and second subunits that moved during the match process.
>
> 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
>
> On Feb 5, 2013, at 5:58 AM, Mock, Sebastian wrote:
>
>> Hi,
>> I am facing a problem with Matching!
>>   
>> Is there any possibility to match two structures, without losing the coordinates of e.g. a dimer unit.
>> In this case, I want to match a homo-dimer to another similar structure. When I match all of the above mentioned dimers (chains), Chimera will match it all at the same place, so I will have two identical positions. In this case I am losing the steric information about the assembly of the homo-dimer.
>>   
>> Is there any method, to treat the dimer as one molecule, which cannot be splitted and can be matched on another structure without losing the biological assembly?
>>   
>> It is hard to explain, I hope you get me.
>>   
>> Thanks in advance
>> Sebastian
>
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