VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 31 2006 - 15:52:08 CST

Hi,
  I've got a VMD script that Mashaojienuaa sent to me which
reads the BIOMT records from a PDB file, applies the appropriate
transformations to them, and writes out a new PDB file with the
complete structure. I tested it on the the 1c8e virus structure
and was able to get it to work after commenting out the line of code
he's got that assigns a new chain ID to each of the transformed
monomers (this could be fixed in a few minutes of work so that it
auto-generates its own chain list when not specified explicitly..)
If you want to assign the chains to the the transformed monomers, you'll
want to enable that code again (it's marked with an XXX comment next
to it) and you'll need to specify a chain list of the same length as
the number of transformed monomers it's going to create.

I used it like this:
  source mono2poly.tcl
  mol new 1c8e.pdb
  set sel [atomselect top all]
  set matrix [parsematrix 1c8e.pdb]
  mono2poly -o outname $sel $matrix

The script is attached to this email.

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 31, 2006 at 03:33:51PM -0500, Margaret Shun Cheung wrote:
> Dear VMD wizards,
>
> I downloaded a structure from PDB, but it only includes the monomeric
> structure from its multimeric native structure (it's from X-ray).
> Is there a script for VMD to reinstate its symmetry and give back its
> multimeric coordinates?
> Thanks!
> Sincerely,
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

-- 
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