VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Aug 12 2005 - 15:52:25 CDT

Hi Steve,

The frist matrix is the dimer. Apply the second matrix to all atoms of
the dimer and it should give you the other half of the tetramer. Save that
file out as described in the list and then combine the original files
with the newly created one using "cat".

Load in the concatenated file in vmd and you should have the tetramer.

Regards
Brian

On Thu, 11 Aug 2005, Steve Ding wrote:

> Hi all,
> I was trying to follow thread
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2621.html) that
> tried to explain how to use use the "BIOMT" function, but I couldn't
> follow. I'm new to using VMD, so please have some patience. The PDB file
> I have displays a dimer, but I would like for it to display a tetramer
> (PDB 1I1R). Below is the REMARK 350:
> REMARK 350
>
> REMARK 350 BIOMOLECULE: 1
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>
> 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 -1.000000 0.000000 0.000000 74.19668
>
> REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
>
> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.18338
>
>
> Is it that the first three lines of BIOMT are for chain A and the second
> three lines are for chain B? I tried to use the commands listed in the
> previous thread in the Tk console, but all I got was an error. Any help
> would be greatly appreciated.
>
> Steve
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
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