> Message: 4
> Date: Tue, 30 Mar 2004 16:55:59 -0500
> From: "Clemens Steegborn" <>
> Subject: [modeller_usage] problem reading alignment file
> To:
> Message-ID: <>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>
> 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!
>
Hi, Clemens,
Weird. It is not clear why would you have to modify
your libs.lib file, since normally it contains the setting for RESTYP_LIB?
Do you have your own customized restyp.lib at a different location?
I assume your *LIB settings in libs.lib are more or
less similar (like in the default setting). If that is the case and if
RESTYP_LIB setting would be incorrect, then other library settings would
cause problems as well.
I wonder if you can send your input files (.pdb, .ali,
libs.lib and restyp.lib).