VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 17 2006 - 03:20:39 CDT

Margaret,
  For transformations not handled automatically by scripts, you can
use the atom selection "$sel move" subcommand to apply any transformation
you want. You can create your own matrices from the MTRIXn records you're
interested in, apply them to the PDB coordinates, save out new files
and combine them all together if you like. There's more detail about
the intended use and format of the PDB MTRIXn records here:
  http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_58.html

As I didn't write the script and I'm currently swamped with other activities,
I'm not the best one to adapt it to reading these MTRIXn records, perhaps
someone else has already written a script to process those symmetry records?

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Sep 16, 2006 at 12:06:13PM -0400, Margaret Shun Cheung wrote:
>
> Hello John,
> Thank you for the script. I have another pdb entry whose syntax doesn't
> follow the format of this script (mono2poly.tcl) which I downloaded from
> the VMD website again. It started with MTRIX
> instead of REMARK as below. Somehow the script will not recognize it.
> Please help.
>
> MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1
> MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1
> MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1
>
>
> The script gave me error message as,
> >Main 78 % mono2poly -chain {} -o 2 $sel $matrix
> 0
> Unable to load structure file 2.pdb
>
> Please help.
> Sincerely,
> Margaret
>
>
> On Fri, 31 Mar 2006, 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
> >
>
> Margaret S. Cheung,
> ============================================================
> Assistant Professor
> 629C Science and Research I
> Department of Physics
> University of Houston http://thoth.phys.uh.edu/~mscheung
> Houston, TX 77204 email: mscheung_at_uh.edu
> ------------------------------------------------------------
> contact info until January 2007
> Room 2112 Tel: (301) 405-9307
> 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