[Chimera-users] calculating orientation parameters between two asymmetric units

[Sen, Anindito]

HI Elaine,

what will be a typical command for the job with 2 asymmetric units in Chimera and ChimeraX. I will try both.

Thanks for the help.




Stay safe & Regards


Anindito Sen. Ph.D


Microscopy and Imaging Center
Texas A&M University

301 Old Main Dr

College Station, TX 77843-2257



Office: ILSB Room 1133
<http://microscopy.tamu.edu/>Tel. 979-458-9881
fax: 979-847-8933

http://microscopy.tamu.edu<http://microscopy.tamu.edu/>



________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, February 4, 2022 10:39 AM
To: Sen, Anindito <andysen at tamu.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] calculating orientation parameters between two asymmetric units

Hi Anindito, If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies. ZjQcmQRYFpfptBannerStart
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Hi Anindito,
If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies.
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html*rotation__;Iw!!KwNVnqRv!S8vHmW1YIUzSiFWfwcHNB6HiJ0QEPfT9v12A_cm_vgrc52uYaka7P-EIeK0wsVM$ >

If you currently have only the map and not the fitted atomic structures, then you could try "measure symmetry" but it only works on certain cases and I don't know if it would work on yours.
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html*symmetry__;Iw!!KwNVnqRv!S8vHmW1YIUzSiFWfwcHNB6HiJ0QEPfT9v12A_cm_vgrc52uYaka7P-EIxU-JJQU$ >

If you're interested in maybe switching from Chimera to ChimeraX, ChimeraX also has these measure command options (although syntax may be slightly different).  ChimeraX measure:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html__;!!KwNVnqRv!S8vHmW1YIUzSiFWfwcHNB6HiJ0QEPfT9v12A_cm_vgrc52uYaka7P-EIurUiirg$ >

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

> On Feb 3, 2022, at 8:42 PM, Sen, Anindito via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
>
> Dear All,
> How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical).


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