You want

sym #3 H,8,120,10,-5

as indicated in the documentation

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html

  Tom

On Oct 9, 2024, at 2:50 PM, Hernando J Sosa <hernando.sosa@einsteinmed.edu> wrote:

 Also when tryng to give the symetry explicitly I get an error. Perhaps I am using the wrong syntax (??)

sym #3 sym-type H,8,120,10,-5
Expected a keyword

Thanks


H.


___________________________________
Hernando Sosa, PhD.                                                          
Dept. of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone (718) 430-3456
___________________________________



From: Hernando J Sosa <hernando.sosa@einsteinmed.edu>
Sent: Wednesday, October 9, 2024 5:41 PM
To: Tom Goddard <goddard@sonic.net>
Subject: Re: [Chimera-users] Center and Orient
 
I need to explicitly  give the symmetry  (helical) because the command


measure symmetry #1 set true  (#1 is my map)

reports:

No symmetry found for my_map.mrc


H.



From: Tom Goddard <goddard@sonic.net>
Sent: Wednesday, October 9, 2024 12:32 PM
To: Hernando J Sosa <hernando.sosa@einsteinmed.edu>
Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Center and Orient
 
CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.
Hi Hernando,

  Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX.  First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model.  Here is an example

open 8ofx
open 16862 from emdb
measure symmetry #2 set true
sym #1 symmetry #2

  Tom

8ofx.png

On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thanks Elaine,

I will try to do this with ChimeraX. What I am trying to to do is to generate  symetry related copies of a model  fitted into a density map using the sym command. I noticed that  the only way to define the center of  symetry to be centered on the density volume was using the option center #n (where n is the id of the  voume density) but only  after doing center and orient by pressing the buttons in the volume viewer.

Although chimeraX is much more prowerful I still find hard to  find the the equivalent  in ChimeraX  of some operations  that I use often in Chimera. 😉

Thanks again,

Best

H.

_
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Tuesday, October 8, 2024 5:04 PM
To: Hernando J Sosa <hernando.sosa@einsteinmed.edu>
Cc: chimera-users <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Center and Orient
 
CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.

In Chimera, there may not be commands that do exactly the same thing as some button.  You might look at  "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons.

That's one reason ChimeraX is way better than Chimera!  You can use the GUI and it shows the command that it used in the Log.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Dear Chimera,
>
> What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer  menu tab?
>
> Thanks
>
> H.

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