[Chimera-users] Axis Of Symmetry

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 6 13:33:42 PDT 2017


Hi Catherine,
(Cc’ing chimera-users at cgl.ucsf.edu which is the recommended address for Chimera questions)

As the message suggests, your models #0 and #1 are not rotated from each other. I’m guessing that you opened the same dimer structure twice and then matched it to itself.  For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees).  You have to make sure that the matching is A to B and B to A.  To do this with the “mm” command, for example, you would have to specify the chains AND use the “pair ss” option.

There is a specific example of commands for structure 5hvp in this previous post. 
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi Eric,
> I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error:
> 
> <image.png>
> 
> I am using chimera version 1.11.2. Can you please help me with this?
> Thanks,
> Catherine




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