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

[Einav Tayeb-Fligelman]

Thank you very much Elaine, I will give it a try now!

Einav

On Wed, Jun 13, 2018 at 8:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Einav,
> Sorry for my misinterpretation… ignore what I said about hand placement.
>
> The instructions in that previous post would still be one way to get the
> symmetry relationship between copies of a protein, but the process is
> rather long and complicated.  Since then, I was reminded of a less arduous
> approach:
>
> To get the transformation between atomic structures that are similar but
> displaced from one another (without actually superimposing them), use the
> “match" command with “move false" and "showMatrix true":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>
> I’m still not completely sure if it will suffice for what is needed to
> submit the structure, but you can try this and see what you think.  I hope
> this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jun 12, 2018, at 10:16 PM, Einav Tayeb-Fligelman <einavt at gmail.com>
> wrote:
> >
> > 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
> > _______________________________________________
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>
> --
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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