From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Sat Sep 16 2006 - 11:06:13 CDT

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
============================================================