[Chimera-users] How to build symmetry in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 1 09:06:20 PDT 2016


Hi Ana,
You can specify the symmetry directly in the “sym” command with its “group” option.  However, it does not accept the Hermann-Mauguin symbols such as P 61.  It can take some of the simple Schoenflies notations like C6, but you would also need to specify other things like the center and axis coordinates.   “center” and “axis” are additional options of the “sym” command, but it may be difficult to figure out what values are correct for your data.

sym command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

Or, you could try manually editing the PDB file to add a CRYST1 line with the necessary information and then use the Unit Cell tool (in Chimera menu under Tools… Higher-Order Structure).  Again it could be difficult to figure out the correct values, though.

Unit Cell tool:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>

CRYST1 line contents and format:
<http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#CRYST1>

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 Jun 1, 2016, at 2:05 AM, Ana Ramos <aramosve85 at gmail.com> wrote:

> To whom it may concern,
> I am working with a protein with P61 symmetry, and I would like to build symmetry mates; however in the pdb, the symmetry is not stated. How can I build in chimera symmetry mates with a P61 symmetry?
> Best,
> Ana




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