[Chimera-users] generating symmetry mates of a surface model created with shape command

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 1 09:26:30 PDT 2015


Hi Carmen,
Sorry, the “sym” command only works on molecule models (atomic coordinates).  The “shape” command creates surface models, not atomic coordinates.
 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

If your shape could instead be approximated by the molecular surface around some set of atoms, you could then use “sym” on those atoms, surface them, and try using the resulting surface(s) as a mask.  However, even if you did have such a set of atoms, this would probably be very difficult, since you would still need to specify the symmetry information needed to make copies in the “sym” command (center of symmetry, axis, etc.).

Best,
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 Jul 1, 2015, at 2:49 AM, Carmen San Martin <carmen at cnb.csic.es> wrote:

> Dear all,
> is it possible to generate symmetry-related copies of a surface model created by the shape command? I am interested in masking out certain map regions related by symmetry. I got the right shape at the right place but now cannot figure out how to create the shape symmetry mates. The sym command followed by the model number of my shape complaints that no molecules are specified.
> Thanks,
>                Carmen 
> 




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