Hi Dmitry, I doubt that the "sym" command is what you need. It does not write matrices. There are other commands that write matrices, but not for the complete symmetry operations needed to generate a multimer from the monomer, and also they may not be of the format required for a PDB deposition. I don't know what program or procedure is normally used to generate such matrices.

The "sym" command's main function is to build multimer atomic coordinates from a monomer atomic structure. Thus the error is from specifying the map #0: the command would instead take an atomic model, e.g. #1 if that were the monomer, to build the 14-mer using the symmetry information that you gave.

https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html

If the symmetry of a map is unknown, Chimera has a "measure symmetry" command to guess, but it is limited to certain symmetry types and other conditions: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry

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

On May 19, 2023, at 8:37 AM, Dmitry A. Semchonok via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Dear colleagues,

I have 14-homo oligomer and such as GroEL. I want to deposit a monomer to PDB with a correspondent rotation matrix for the biological unit.

For that, I tried to do a rotation matrix file by UCSF Chimera.

Using this command sym #0 group d7 center 147.4,147.4,147.4

where the #0 is a map model is #1

But I got an error – «No molecules specified».

Could you please tell me what is wrong and how to do that?

Another question – if the symmetry type is unknown, how can the rotation matrix be indexed?

Many thanks for considering my request.

Sincerely, Dmitry