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

[Einav Tayeb-Fligelman]

Dear Elaine,

Thank you for your reply. I am not sure what you mean by hand placing the
copies. I place the copies by increasing the number of unit cells in a
certain direction in the higher order tab, and therefore I thought that The
symmetry operations could be extracted... If this information changes your
answer somehow please let me know.

Best,
Einav




On Wed, Jun 13, 2018 at 3:34 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
> --
Einav Tayeb-Fligelman, PhD
The Landau lab
Faculty of Biology
Technion, Israel Institute of Technology
Haifa, Israel
E-mail :einavtf at campus.technion.ac.il
Tel at the lab:+972-77-8871964 <javascript:void(0);>
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