barwellj@aston.ac.uk wrote: > I have just started using the programme and have already ran into some > difficulty. I am trying to do a homology model .The error message I get > suggests that my alignment file does not match my pdb file. Although, all > my files are in the same directory as modeller and both written in the > same case. > > I'm not sure why it is not working? Before running the programme I edited > the PDB file using DEEPVIEW to remove the antagonist from the structure. > Also I used GENEDOC to produce the alignment and saved it in a PIR format. > Not sure if this has something to do with my problem? > > attached is my PDB file (called a.pdb), my alignment file (a.pir) and my > script file (called script.py) and the log file.

Vadim's answer is exactly correct - your alignment file header does not contain the correct chain ID for the template. But the error message in your log file does not make that very clear. This is because you're using a very old version of Modeller (8v2); I recommend that you upgrade to the latest version (9v3) which gives a much clearer error message in this case.

Ben Webb, Modeller Caretaker