[Chimera-users] creating a symmetric tetramer from a PDB file for a monomer?

[Elaine Meng]

Hello Gea-Ny,
The Chimera features that generate multimers (the tools Unit Cell
and Multiscale Models) all use matrix information in the PDB file.
Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records,
and Unit Cell uses MTRIX, SMTRY, and/or CRYST1.

It sounds like you don't have any of those in your PDB file.

You could either
(A) figure out what information should be in such a matrix line
and edit it into your file before using one of the Chimera tools,
or
(B) open four copies of your monomer and try to position them
by hand. If you know what the axis of rotation should be, you
can use Constrained Move (Tools... Movement... Constrained Move
in recent versions) to define and use an axis of rotation.
http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ 
constrained/constrained.html

Neither of these is very easy, but I don't know of any way to
automatically position the monomers without the matrix information.
It sounds like BIOMT (REMARK 350) records would be the most
appropriate.  Even with an appropriate example, you would still
have to change the values.

REMARK 350 is described at the PDB web site (you have to scroll
down to get to the description of REMARK 350):
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html

Here is an example from 1fav (threefold):
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -0.500000 -0.866025  0.000000       35.81900
REMARK 350   BIOMT2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3 -0.500000  0.866025  0.000000       17.90950
REMARK 350   BIOMT2   3 -0.866025 -0.500000  0.000000       31.02016
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Sep 6, 2005, at 12:53 PM, <gtseng at mail2.vcu.edu> wrote:

> Dear Chimera creators:
>     Could you please let me know whether it is possible to create a
> tetramer structure with 4-fold symmetry from a PDB file for a monomer?
> Specifically, I want to create a structure of a voltage-gated K
> channel which has 4 monomers surrounding a central pore symmetrically,
> beginning with the PDB file for a monomer. There is no 'transformation
> matrix' in the PDB file to allow me to create the tetramer easily.
>     Thank you very much for your help!
>
> Gea-Ny Tseng
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