VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 12 2005 - 14:04:21 CDT

Hi,
  My understanding is that each of these transformation matrices
gives you another copy of the repeated parts of symmetrical structures
like viruses. There's some more discussion of this here:
  http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00010.html
  http://vivaldi.bio.bnl.gov/asda/bb/archive/pdb-l/pdb-l.200004/0150.html

Also, look at the detailed description of "REMARK 350" here:
  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 11, 2005 at 07:10:13PM -0400, 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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