[Chimera-users] build a homotetramer based on crystallographic symmetry

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 30 10:26:06 PDT 2016


Hi Sharon,
Chimera has lots of different ways for building multimers using crystallographic symmetry information.  If the symmetry information is already in the file, it is quite easy.  Otherwise, you would have to specify the symmetry yourself in a command.

Possibilities include:

“sym” command (which also allows you to enter the symmetry yourself if needed)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

… and two graphical interfaces,
Unit Cell tool
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>
Multiscale Models tool
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

I would probably try “sym” first just to see what happens, i.e. if your dimer is open as model #0 and you think the input file has the symmetry information in it already as BIOMT matrices, try:

sym #0

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

P.S. you can also fetch predicted biounit from PDB, see menu: File… Fetch by ID

On Sep 29, 2016, at 8:05 PM, Shuanghong Huo <SHuo at clarku.edu> wrote:

> Dear All,
> Can UCSF Chimera build a homotetramer from a dimer based on crystallographic symmetry?
> Thanks,
> Sharon Huo
> Clark University




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