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From: Fabio Trovato (f.trovato_at_sns.it)
Date: Sat Mar 14 2009 - 04:56:17 CDT

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