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