[Chimera-users] symmetric fitting

[Elaine Meng]

Hi Sudheer,
Here is an description of the BIOMT matrix format, which you would add  
with a text editor:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt>

However, it does not explain how you would figure out what values to  
put into those lines, which is not simple.  I would probably try to  
find another GroEL PDB that already has the BIOMT matrices in it, then  
match your structure on to it, save the new coordinates for your  
structure "relative to" the coordinates of that other PDB, then edit  
in the BIOMT records copied from that other file.

However, I don't know if that is precise enough for what you had in  
mind, and an even bigger problem may be although there are many  
structures of GroEL, I don't see any with BIOMT information for  
reproducing the multimer from a single chain.  All the ones I looked  
at simply had the coordinates for all of the chains.

Neverthless, here is more information on...
superimposing structures:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#superimposing 
 >

writing coordinates, including "relative to":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Oct 5, 2008, at 8:54 PM, <skmolugu at miners.utep.edu> <skmolugu at miners.utep.edu 
 > wrote:
> HI,
> In the symmetric fitting model session that explains about the  
> symmetry generation, i did not understand the method to generate the  
> matrix. I am working on a chaperonin protein called GroEL. It has 14  
> subunits with seven fold symmetry. can you please explain me how to  
> update the pdb and the matrix values that i need to put in the pdb  
> file.
> thankyou,
> sudheer