[Chimera-users] Constructing a biological assembly in Chimera

Ahmad Khalifa underoath006 at gmail.com
Mon Apr 8 10:14:47 PDT 2019

Thanks Elaine. I've been looking into this and found some info about BIOMT
records and the sym command. However, I couldn't get it to work.

I think what can solve my problem is if I can copy/combine and fit monomers
from the "main" monomer then use the sym command to generate a BIOMT record
of all these fitted structure into the main monomer. That way any
modifications I make to that "main monomer" will be present in the new
structures that I generate using the biological unit function in Chimera.

 How can I do that using the sym command?

On Mon, Apr 8, 2019 at 12:12 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Ahmad,
> There is no feature to automatically apply any changes in one monomer to
> all the other monomers.  As far as I know, you would need to first modify
> the monomer and then create the biological assembly of the modified monomer.
> If you already have the biological assembly of the unmodified monomer,
> another possibility is to open several copies of modified one and match
> them onto the unmodified ones (possibly by writing your own script to do it
> since I imagine it would be a lot of repetitious commands), and then close
> the unmodified ones.  However, that might be more work than just using the
> modified monomer to make the assembly in the first place, and might give a
> slightly different result.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 7, 2019, at 6:07 AM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> >
> > Hello,
> > I'm working with a lattice made of a tubulin monomer that I modeled and
> refined in Coot.
> >
> > I have fitted other units of the monomer along the length and to the
> side of my monomer in a cryo-EM map to study tubulin interactions with non
> tubulin proteins.
> >
> > Instead, I wonder if I can construct a biological assembly of just one
> unit, to have any modifications or changes in that unit reflected in the
> entire biological assembly.
> >
> > Any other help or suggestions would be appreciated.
> > Regards.
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