VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 31 2006 - 16:15:14 CST

Hi,
  I've attached another version of the script which will auto-generate
chain ID codes if you don't provide a list of codes to go with each
monomer transformation matrix, this should be a bit easier to use than
the last one. (see attached script)

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 31, 2006 at 03:52:08PM -0600, John Stone wrote:
> 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
> > ------------------------------------------------------------
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078