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