VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 15 2009 - 14:22:19 CDT

Fabio,
  While I didn't write the script, I'll see if I can have a look
a the structures you mention and reproduce the parsing issue you
encountered. Could be one of several things cropping up.

Cheers,
  John

On Sat, Mar 14, 2009 at 10:56:17AM +0100, Fabio Trovato wrote:
> Thank you for your reply
>
> I tried to have a look at the mono2poly script but I didn't solved
> the problem.
> I can tell you that the problem is inside proc parsematrix
> {orig_file} and before
> set matrixlist {}.
> I tried to print the values of the variables lineelement after "set
> lineelement [lrange $line 4 7]" and matrix just after "lappend matrix
> ($mtnum) $lineelement"
> in the two following cases:
> 1) molecule 1B9C
> 2) molecule 2JAD
>
> and I got the same output
>
> vmd > 1.000000 0.000000 0.000000 0.00000
> matrix(1)
> 0.000000 1.000000 0.000000 0.00000
> matrix(1)
> 0.000000 0.000000 1.000000 0.00000
> matrix(1)
>
> except that in the second case I got the error message "unmatched
> open brace in list"
>
> I am not able to understand what's going wrong!
> The two files are similar at the REMARK 350 where BIOMT
> transformations are written
> and the BIOMT transformations are the identity in both the example.
>
> Can you please help me understand and fix the problem?
>
> Thank you
>
>
> Il giorno 13/mar/09, alle ore 18:36, John Stone ha scritto:
>
> >
> >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 

-- 
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