Hello,
There seems to be a problem with your a.pir file. In particular, instead of
structure:a.pdb:29::122:::::
the file should read:
structure:a.pdb:29:A:122:A::::
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.
Best,
Vadim
> 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