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

Carmen San Martin carmen at cnb.csic.es
Wed Jul 1 09:41:09 PDT 2015

Thanks Elaine. I do have the symmetry parameters but not the atoms, alas.
How about saving the shape surface model as an mrc map so that I could use
an external program to apply the symmetry? Would that be possible?



  Carmen San Martín, Ph. D.
  Centro Nacional de Biotecnología (CNB-CSIC)
  Darwin, 3
  28049-Madrid (SPAIN)
  Email:  carmen at cnb.csic.es
  Phone:  34-91-5855450
  Fax:     34-91-5854506

On Wed, Jul 1, 2015 at 6:26 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> >
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150701/cd48679e/attachment.html>

More information about the Chimera-users mailing list