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