[Chimera-users] BIOMT matrix in Chimera?

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 25 11:39:36 PDT 2008

Hi Francesco,
It might work to put the matrices from the template into the homology  
model PDB file.  Just be aware that the resulting multimer would be  
approximate and might have atoms from different monomers clashing  
with each other.  You can see how it turns out and use your judgement  
as to whether it is good enough, and of course say what you had done  
if you were describing the work in a paper.

After putting the matrix information in the homology model file, you  
would then proceed as with the original template structure to build  
the multimer in Chimera.  Depending on the structure, you might want  
not only BIOMT, but also MTRIX, SMTRY and CRYST1 lines.  Also be  
aware that it is fairly common for such information in a PDB file to  
be wrong, or only set to "identity" (regenerates the same coordinates  
already present in the file).  However, if generating a multimer  
already worked for the template structure, that is not a concern.

As mentioned in this previous mail to you, multimers can be built  
from symmetry information using "Unit Cell" or "Multiscale Models":

Yet another way is with the command "sym":

"Unit Cell" does not use BIOMT, but the other two methods can handle  
that type of information.

Other than using Chimera, you might want to see whether Modeller can  
just build the multimer in the first place, given a multimer template.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 25, 2008, at 10:32 AM, Francesco Pietra wrote:

>> From a homotrimer pdb template I have created (with Modeler) a
> homology model, with very good score, using a single subunit. Is it
> possible with Chimera to create the homology homotrimer, as this is
> what I need? To this concern, the original pdb for the template
> includes the BIOMT transformation matrix for both crystallographic and
> non-crystallographic operation. That is, the pdb includes as many
> identical chains to open directly the homotrimer for the
> crystallographic pose. Is that BIOMT matrix usable by Chimera for the
> homology model? Or the way ti take is another one?
> I used much technical language, well above - however - my expertise in
> these affairs. That in view of any help, for which I'll be most
> grateful.
> Thanks
> francesco pietra

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