Michael Mazanetz wrote: > I get this error message " rdpir___648E> Alignment sequence not found > in PDB file: 1 ../atom_files\1ba4.pdb " in my log file when > I try and run a homology model. When I reduce the number of > residues in the sequence to just four the model runs OK. What is > wrong, can anyone suggest anything?? I've enclosed my files :screen > output, B04_2742_111_002.ali, Loop-005.py and Loop-005.log
See http://salilab.org/modeller/FAQ.html#19
Like it says, the sequence in your alignment does not match that in your PDB file. You should replace the '.' characters in your alignment header with the residue number and chain ID of the start and end of the sequence in the PDB file, and then Modeller will show you the two sequences and where they don't match.
Also, you need to remove the spaces from the alignment. Modeller considers ' ' as a valid residue type, so it won't match your PDB.
> And the -v command always gives an error too??
The message suggesting you add '-v' is from the Python interpreter, and does not apply to Modeller itself. You can ignore this warning; see http://salilab.org/modeller/release.html#issues
According to the python man page on my system, you can set the PYTHONVERBOSE environment variable to get the same effect as '-v'.
Ben Webb, Modeller Caretaker