[Chimera-users] Octamer to dimer

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 16 14:14:48 PDT 2009

Hi John,
You could select them with Ctrl-click or Ctrl-drag in the graphics  
window, but that can be somewhat tedious.  I usually just use commands  
with some kind of distance criterion.  For example, if the protein  
chains that form the dimer are A and B, I might use commands:

sel :.a-b z>5
delete sel

You could do it in a single command and not bother selecting, but with  
the above you can verify what is selected before nuking it!  Also,  
there are many possible variations, such as different distances, or  
only residues with a particular name, and referring to the dimer as  
"protein" (assuming you don't have other proteins around).  If the  
bleomycins were named BLE (I'm just making this up), additional  
possibilities would be something like

sel :ble & :.a-b z>4.5
delete sel

-- OR --

sel :ble & protein z>3.8
delete sel

All the distance calculations in the zone spec can make command  
execution a little slow.
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 16, 2009, at 1:43 PM, John Lowenstein wrote:

> Dear Folks,
> 	In PDB 1ewj the structure comes up as an octamer.  The  
> physiological entity, in which I
> am interested, is a dimer.  I can eliminate three of the for dimers,  
> but I have not found
> a way to eliminate the six extra ligands (bleomycin) associated with  
> the three eliminated
> dimers.  (I want the dimer with two ligands.) Any suggestions?   
> Thanks.
> 	Sincerely,
> 	John Lowenstein

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