[Chimera-users] structure matching

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 4 09:05:10 PST 2009

Hello Bala,

(1) I can't tell what happened without seeing the data.  It sounds  
like what you did would work, but perhaps in editing the prot1 file  
you would also need to renumber the residues (if chain A and chain B  
both had residue 10, if you don't renumber there will be two residues  
number 10, which could cause a problem) and remove "TER" lines to make  
sure it is really interpreted as a single chain.

(2) After you open everything you can just use "Actions... Focus" in  
the menu to make everything visible (or command "focus" or "window").   
This will zoom out.  It will not put each molecule in the center,  
because it will still use the coordinates that are in the files.  The  
only way to put the molecules in the center is to focus on the  
reference structure and then match the others onto it, such as with  
MatchMaker or "match."

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 4, 2009, at 8:08 AM, Bala subramanian wrote:

> Hello all,
> 1) I have to superimpose two protein structures based on sequence  
> matching say prot1 and prot2. Precisely matchmaker.
> My prot1 is a cryo electron microscopy structure, the structure is  
> not continuous, it has missing residues and hence its pdb contains 3  
> Chains.
> My prot2 is a crystal structure, having one chain. I need your  
> suggestion in superimposing these two structure wherever the  
> sequences are matching.
> What i tried:
> I opened pro1 pdb and changed all chain names as A ( it contains  
> chain A,B,C). Then i tried to superimpose with prot2, but matchmaker  
> doesn work.
> 2) when i open molecules one by one, i need all the molecules appear  
> in the center of the chimera window. How to set this in chimera.  
> After opening the first pdb, when i open the second one, it is  
> invisible.
> Thanks,
> Bala

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