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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 19


There seems to be a problem with your a.pir file. In particular, instead of

the file should read:

Note the difference, I am telling modeller to look for residue 29 of
chain A in the pdb. otherwise, it looks like it looks for residue 29
of chain " ". Take a look at the manual to see how the PIR format
works: http://www.salilab.org/modeller/manual/node421.html.


>  Hello modellers,
>  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.
>  Any help would really be appreciated