David Mathog wrote: > First time trying to use Modeller and the log file terminates > with: > > check_a_337E> Structure not read in.
There is usually a warning before this with more information. Usually it's because your alignment sequence doesn't match the PDB ATOM and/or HETATM records (Modeller does not read SEQRES).
> Modeller seems to have read the alignment alright, although this bit: > > (def)remove_gaps=True > > is a little worrisome, since there are a couple of gaps in the > alignment.
That doesn't remove all gaps, of course - only gaps which are present in every sequence (which would be redundant, of course). See http://salilab.org/modeller/manual/node177.html
It sounds like your PDB has missing residues, in which case these residues would need to be removed from your alignment. See http://salilab.org/modeller/wiki/Missing_residues for an example.
Ben Webb, Modeller Caretaker