[modeller_usage] problem reading alignment file

["Clemens Steegborn" <cls2001 AT med.cornell.edu>]

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