Hi Catherine, Please send Chimera questions to chimera-users@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@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@cgl.ucsf.edu> wrote: Hi Catherine, (Cc’ing chimera-users@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

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On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen@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:

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I am using chimera version 1.11.2. Can you please help me with this? Thanks, Catherine