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[modeller_usage] Fwd: problem reading alignment file

Hi everybody,

thanks for all the suggestions how to solve my problem with reading
an alignment file (see below). The solution was to remove all spaces
from the alignment!

Clemens



Date: Tue, 30 Mar 2004 16:55:59 -0500
To: modeller_usage@salilab.org
From: Clemens Steegborn <cls2001@med.cornell.edu>
Subject: problem reading alignment file


Hi,

I'm using the WINDOWS version of MODELLER6v2

I get the following error when reading the template and alignment files:

>
>TOP_________>   121  107 CHECK_ALIGNMENT
>
>check_a_343_> >> BEGINNING OF COMMAND
>openf5__224_> Open       11  OLD  SEQUENTIAL  myt.atm
>rdabrk__290E> Number of residues in the alignment and pdb files are different: 433 392 
>              For alignment entry:        1
>recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>
the problem seems to be that MODELLER doesn't understand the gap residue '-', as it also doesn't understand '/' (using '/' gives an error stating it doesn't know this residue)! 
I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib 
file, but that didn't help.

Any suggestions would be appreciated!

Clemens