Hi Andrew,
it's hard to say what goes wrong as your email does not contain
the error message or your input files, but I would guess the line
X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: :
causes the problem, it should read like this:
structureX:1L9H:37 : :307 : :rhodopsin:Bos Taurus: :
You should consult the modeller manual about the correct
input file formats, to make sure there is not anything else
wrong with your alignment:
http://salilab.org/modeller/manual/node64.html
I hope that helps.
Best wishes,
Thorsten Schweikardt
Molekulare Biophysik
Universität Mainz