[Chimera-users] Match command question

Yann STERCKX Yann.Sterckx at vub.be
Fri Nov 17 02:31:51 PST 2017


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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