VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 13 2009 - 12:36:37 CDT

Hi,
  The mono2poly script was contributed by another VMD user, and it's
not guaranteed to be flawless. Most likely you found a PDB structure
that has an unusual set of BIOMT records, which is what that script
is using in order to reconstruct the full structure. I suspect that
with a little work you can figure out what's wrong with the script,
or what assumption it's making that isn't true for the PDB file that's
giving you trouble. If you can figure out what's different for the
structures that are giving trouble, I might be able to help you work
through updating the script to deal with whatever it is.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 13, 2009 at 05:46:44PM +0100, Fabio Trovato wrote:
> Hello
>
> my name is Fabio and I was trying to generate the complete
> biomolecule of a list of pdb files
> using the script mono2poly found at http://ftp.ks.uiuc.edu/Research/
> vmd/script_library/
> In some cases the script didn't work fine. For example if I do it for
> the molecule 2JAD:
>
> source mono2poly.tcl
> mol delete all
> mol new 2JAD.pdb
> set sel [atomselect top all]
> set matrix [parsematrix 2JAD.pdb]
> mono2poly -o 2JAD_biological $sel $matrix
>
> I obtain, after the command set matrix [parsematrix 2JAD.pdb]
> the following error:
>
> unmatched open brace in list
>
> Can you help me to fix this problem?
> Thank you 

-- 
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