> Message: 4 > Date: Tue, 30 Mar 2004 16:55:59 -0500 > From: "Clemens Steegborn" cls2001@med.cornell.edu > Subject: [modeller_usage] problem reading alignment file > To: modeller_usage@salilab.org > Message-ID: 5.2.0.9.2.20040330164627.00b485d0@pop.med.cornell.edu > 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).

Azat

A.Ya.Badretdinov, PhD, Sr. Scientist x5728 http://intranet.accelrys.com/~azat

> Clemens > > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 3, Issue 36 > *********************************************