Hi Clemens,

the error you describe usually appears when your pdb- file has some missing aminoacids in respect to the sequence you use in the alignment-file. Modeller states that your pdb contains 392 residues, but your alignment contains 433. You can use DeepView to open your template and save its aminoacid-sequence (File-Save-Save Sequence as FASTA). Compare it to the sequence in your alignment file, they should be identical. If not, correct the align- ment. Hope this helps. Concerning the '/' and '-', I have no problems using them on the linux-version.

Best wishes,

Thorsten Schweikardt Molecular Biophysics University Mainz, Germany

> I'm using the WINDOWS version of MODELLER6v2 > > I get the following error when reading the template and > alignment files:

> >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)! >