[Chimera-users] How to build symmetry in Chimera

Tom Goddard goddard at sonic.net
Wed Jun 1 12:15:13 PDT 2016


Hi Ana,

  Putting a CRYST1 record into your PDB file as Elaine suggested is the solution.  To use spacegroup (P61) symmetry you need the unit cell size and cell angles which are specified in the PDB CRYST1 record.  You can copy the CRYST1 line from another PDB file and adjust the cell size and angle values and group name to the correct values, making sure to keep the values in the same columns since PDB format requires values in specific columns.

	Tom


> On Jun 1, 2016, at 9:06 AM, Elaine Meng  wrote:
> 
> 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 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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