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Re: [modeller_usage] ALIGN_CODE

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage