Re: [modeller_usage] rdpir___648E> Alignment sequence not found in PDB file

[Modeller Caretaker <>]

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
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