generating symmetry mates of a surface model created with shape command
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 ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen@cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 http://www.cnb.csic.es/ http://tinyurl.com/carmensanmartinlab http://orcid.org/0000-0001-9799-175X ------------------------------------------------------------
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@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
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? Regards, Carmen ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen@cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 http://www.cnb.csic.es/ http://tinyurl.com/carmensanmartinlab http://orcid.org/0000-0001-9799-175X ------------------------------------------------------------ On Wed, Jul 1, 2015 at 6:26 PM, Elaine Meng <meng@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@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
Hi Carmen, The shape surface is only a surface, not a density map. Maybe you could do something more elaborate, like use the surface from “shape” as a mask on some other map with the “mask” command (maybe not important which map, as long as you can display an isosurface of the desired shape?) to create a new map, then save the new map as a file, and use some external program to apply the symmetry to that map. Then read the processed new map with symmetry copies, show isosurfaces now with symmetry copies, and THEN finally do the masking you had wanted to do in the first place. I don’t know if that would work, and it may be more trouble than it’s worth! 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 9:41 AM, Carmen San Martin <carmen@cnb.csic.es> wrote:
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? Regards, Carmen
participants (2)
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Carmen San Martin -
Elaine Meng