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

[Elaine Meng]

Hi Anindito,
Well if you had two copies of the same atomic structure as models #2,3 already fitted into the two different parts of map #1, then the command could be something like

Chimera:  
measure rotation #2 #3
ChimeraX: 
measure rotation #2 toModel #3

Or to try to figure it out from map alone, maybe a command something like (same in both programs):

measure symmetry #1

However, you should still take a look at the help links I sent before, because you might want or even need to use some of the other command options.
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 4, 2022, at 3:44 PM, Sen, Anindito via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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
> Tel. 979-458-9881
> fax: 979-847-8933
> 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
>  
> This Message Is From an External Sender 
> This message came from outside your organization. 
> 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).