Hi,

The error message is unlikely to be due to numbering reasons. Modeller does not keep numbering unless specifically requested, even in that case there is no reason for error message like this. It just reads in sequentially all ATOM records and renumbers them: all resulting models will start with residue 1 or assign the same numbers as in PDB.

You probably have such an alignment file that does not correspond to the ATOM records. These - the residue sequence(s) and the corresponding coordinate entries - must match.

You can test what modeller 'sees' when 'reading' you structure in:

################# read_model FILE = 'MY.pdb' sequence_to_ali atom_files = 'MY.pdb', align_codes = 'MY.pdb' write_alignment file='outputmyseq.pir' #####################

this will output a pir formatted sequence entry for your protein coordinate file. Compare it with the seq. that you currently use in your alignment.

best wishes, Andras Fiser

On Mon, 2003-12-22 at 13:38, MacFarlane, Amanda J. wrote: > Dear Modellers, > > > > I'm relatively new to Modeller, and I have a question which I hope has > an easy answer. Whenever the pdb file for a solved structure has a > gap in the residue numbers (so, for instance, it jumps from residue > 300 to 315), I get an error saying that the number of residues in the > alignment file and the pdb file are different. How can I fix this > problem? > > > > Thanks! > > > > Amanda MacFarlane > > > > Amanda MacFarlane > > Autoimmune Disease Group/Diabetes > > Ottawa Health Research Institute > > Lab N1 Box 221 > > 501 Smyth Road > > Ottawa ON K1S 5B7 > >