[Chimera-users] on point-group symmetry used for the 3-D calculation

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 25 09:45:26 PDT 2015


Dear Smith,
Map symmetry can be used in the “sym” command and “fitmap” symmetric fitting command calculations, but most map file formats don’t include this information.  So depending on how you read in the map, the symmetry is probably not known automatically by Chimera.  In that case you would have to specify the symmetry yourself manually using the “group” option if you are using the “sym” command, or with the “symmetry” option of the “volume” command, or try to have Chimera figure it out using “measure symmetry”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#symmetry>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>

Then to save the symmetry in the map file, you would have to save it in the Chimera map format, for example with the “save” option of the “volume” command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#save>

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

> On Aug 24, 2015, at 6:46 PM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear All,
> By chimera, can we know the point-group symmetry used for the 3-D calculation?
> Best regards.
> Smith




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