[Chimera-users] Constructing a biological assembly in Chimera
meng at cgl.ucsf.edu
Tue Apr 9 08:19:32 PDT 2019
Sorry, I don’t know of a program to do it, but maybe other users on this list will have suggestions.
> On Apr 8, 2019, at 6:22 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 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
> 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.
> > 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.
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