[Chimera-users] Constructing a biological assembly in Chimera

[Ahmad Khalifa]

Thank you, is there any other program that can make BIOMT? I know I can get
the rotation and translation matrix of the BIOMT record if I do: measure
rotation #spec1 #spec2. I wonder how I can iterate over a lot of #spec2
models and how to get the output matrices in a row text format?

I intend to write a script that can write that information to my pdb BIOMT
record.

On Mon, Apr 8, 2019 at 5:19 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Ahmad,
> The sym command does not create BIOMT matrices.  It adds symmetry copies
> of the atomic structure based on:
>
> (1) BIOMT matrices that are already included in the structure file (for
> example, use a text-editor to view the PDB file for 1FAV)
> - OR -
> (2) other symmetry specified manually on the command line
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>
>
> There is no tool in Chimera for creating the BIOMT matrices or identifying
> symmetry from your fitted atomic copies that could be used in the “sym”
> command, sorry.  There is a “measure symmetry” command for maps, but it has
> limitations and can only guess helical symmetries if you give it
> approximate rise and angle values.
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry
> >
>
> Elaine
>
> > On Apr 8, 2019, at 10:14 AM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> >
> > 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.
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190408/06933bd3/attachment.html>