[Chimera-users] Copy protein orientation

[Elaine Meng]

Hello Kenneth,
Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.

However, given the situation you have now, maybe:
(1) in session 1, use "matrixget  <file-pathname>" to save file with transformation of protein A. See:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>

(2) in session 2, use "matrixset  <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1.  However, that will probably ignore protein B, so you may need step 3.

(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1"
See: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>

I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance.  Also you may need to adjust the command if you have different model numbers.

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

> On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Kenneth,
> 
> Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files.
> Then work on the problem from there on. This seems like a possible direction to try? 
> 
> Sincerely,
> David 
> 
>> On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
>> 
>> 1) Identify orientation of protein A in session 1
>> 2) Copy that orientation
>> 3) Apply that orientation to protein A in session 2
>> 4) Have protein B in session 2 remain aligned to protein A despite the new orientation
>> 
>> Thank you,
>> Kenneth Sandoval
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