Re: [modeller_usage] structure not read in

[J B Procter <>]

Concerning your specific query about the BEGINNING OF COMMAND error :

On Tue, 13 Jan 2004 11:54:44 +0530 (IST)
"Jaimin Shah" <> wrote:

> check_a_343_> >> BEGINNING OF COMMAND
> pdbnam__217W> Filename for PDB code not found:  1piea
>               Directories:  ./
>               Extensions :   :.atm:.pdb:.ent:.crd
> rdabrk__288W> Protein not accepted:        1
> check_a_337E> Structure not read in:        1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

The line beginning 'pddbnam__217W' actually says what the error is.
MODELLER cannot find 1piea.atm, 1piea.pdb, 1piea.ent, or 1piea.crd in
any of the directories given in ATOM_FILES_DIRECTORY.

When you have problems with MODELLER, you should examine the output very
carefully. It has given you some warnings (these lines begin with a
code like :
afuncnam__123W>
The W> indicates a warning message. E> indicates an error message (which
may have arisen because of the previous warnings).

There are several warnings given in the output, telling you that the PIR
headers in your alignment file are incorrect (these are lines like :
structure:1pdb:Start:C:End:C:.:.:.:.

In your case, you need to add some extra ':' separated fields in each
of the PIR headers in the alignment file. Look at the example above :
I have used'.' as a wildcard, to specify that there is no required value
for these fields.

Hope this helps, 
j.

______________________________________________________________________
Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics
Hamburg       http://www.zbh.uni-hamburg.de/staff.php