[Chimera-users] Symmetry operation calculations for multimeric fibrillar assemblies

[Elaine Meng]

Dear Einav,
In my opinion, it is difficult to try to back-calculate symmetry relationships between copies of a structure in Chimera, and the results are not exact truth especially when you have hand-placed those copies.  I doubt it would be suitable for deposition purposes.

For example Chimera instructions, see this recent post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014625.html>

There is also a “measure symmetry” command to guess the symmetry of a density map (not atomic structures), but it only looks for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>

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

> On Jun 12, 2018, at 1:47 PM, Einav Tayeb-Fligelman <einavt at gmail.com> wrote:
> 
> Dear Chimera support team,
> 
> I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that.
> I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure.
> I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt.
> 
> Thank you in advance,
> Einav