[modeller_usage] Check_a_337E> Structure not read in

First time trying to use Modeller and the log file terminates with:

check_a_337E> Structure not read in.

There's nothing wrong with the PDB file as far as I can tell, several other programs will read it.

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. In fact, that's the whole point, I want to see if modeller can close the gaps so that I don't have to do it manually in a modelling program. The gaps are part of the structure that flaps around in solution so it isn't in the PDB file, but it has to be added before Gromacs will accept the structure.

Thanks,

David Mathog mathog@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech