[Chimera-users] Axis Of Symmetry

[Elaine Meng]

Hi Catherine,
Please send Chimera questions to chimera-users at cgl.ucsf (CC’d here) to ensure a response.

This "measure rotation” command does not use any atoms, it merely reports how a model is currently rotated and translated relative to the another model.  The rotating/translating is done by the matching command before that measurement.  From our previous emails I see you were using the “matchmaker”  command (same as “mmaker”) which, as described in the manual, uses only CA atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>

If you want to use other atoms in the fitting, you have to instead use the “match” command with the specific atoms given in the command.  See the manual:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>

See also the page on “Superimposing Structures”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

and for a specific example, the “Matching” section in the Glycoside Hydrolases tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.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 9, 2017, at 12:02 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi Elaine,
> 
> Can you tell me how Axis is configured? after using the command measure rotation, it gives me the reply log with information like axis, axis point, rotation angle etc., But I want to know specifically if Axis is calculated by just using the CA atoms of the chains or All atoms? Is there a way to find axis only using CA/All atoms.
> 
> Thanks,
> Catherine
> 
> On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
> 
>