[Chimera-users] Match command question

Yann STERCKX Yann.Sterckx at vub.be
Tue Nov 21 05:40:06 PST 2017


Dear Elaine,

my apologies if my explanations were not clear enough. But you got exactly what I wanted to say. Each liganded state is a tetramer and there is one pivot point in each monomer. The goal was to superpose all structures on the monomer pivot points (e.g. superpose the 4 pivot points of the unliganded state onto the 4 pivot points of the liganded state).

The problem was indeed related to the chain IDs and providing more elaborate atom specification works perfectly now.

Many thanks for your help,

Yann

On 17 Nov 2017, at 19:39, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Yann,
> I don’t understand the situation well.  So each state (unliganded, and in complex with each different ligand) is a tetramer?  And there is one pivot point in each monomer of the tetramer?  I.e. something like chains A-D, with :430-433 occurring in each chain?
> 
> Your match command is trying to match all the pivot points of all four tetramers at once with a single rigid-body movement. It won’t move the monomers separately.  To do that, you’d have to split each tetramer into separate models for each monomer and then match the monomers individually.
> 
> However, if you do intend to match all the pivot points of all four tetramers at once with a single rigid-body movement, my only idea is that maybe the chain IDs or ordering are different for some of the liganded tetramers than the others.  In that case you may have to give a more elaborate atom specification in the commandor edit the files (e.g. change chain IDs) to get the correct pairing.  You can mouse over the structures to see if the chain IDs are for the corresponding chains (using the balloon information that appears when you pause over the structure).  This is really just a guess but all I can think of based on the description.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Nov 17, 2017, at 2:31 AM, Yann STERCKX <Yann.Sterckx at vub.be> wrote:
>> 
>> Dear Chimera users,
>> I've been struggling with the match command and was hoping you could help me out.
>> 
>> I'm working a tetrameric enzyme. When the enzyme binds ligands, its domains rotate over a pivot point in the monomer. What I would like to do is superpose different liganded structures of the enzyme on the four monomer pivot points. Here's what I've done so far:
>> 
>> * Each liganded state of the tetrameric enzyme is a single model
>> * I use the match command to superpose the structures on the monomer pivot points (residues 430-433 in the structure). I used the following command
>> 
>> match #model1:430-433 #model2:430-433
>> 
>> What is strange is that I obtain exactly what I want for 2 out of 4 models. Using this command I get an rmsd of 0.77A. But for the other 2 models, match does not seem to work as I obtain an RMSD of 27A and the superposition is clearly off. Including the iterate option does not alleviate the problem. I don't want to use matchmaker because this feature will, at least in my understanding, try to optimally fit two chains (or selections within two chains) on top of each other. If I do that, I do not get to see how the enzyme rotates around the monomer pivot points.
>> 
>> How come match works really well for 2 out of 4 structures, but fails to perform the same task for the rest? Any pointers on what I might be doing wrong?
>> 
>> Many thanks and kind regards,
>> 
>> Yann
>> 
>> PS: I've browsed through the archive, but could not really find a thread related to this problem (unless I overlooked it).
>> 
>> 
>> 
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