[modeller_usage] Fwd: problem reading alignment file

["Clemens Steegborn" <>]

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: 
> From: Clemens Steegborn <>
> 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