Re: [modeller_usage] build_profile.py help

[Modeller Caretaker <>]

Eeson Rajendra wrote:
> I get an error:
> **************
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
>   File "build_profile.py", line 10, in ?
>     chains_list='ALL', minmax_db_seq_len=(1, 40000), clean_sequences=True)
>   File "C:\Program Files\Modeller9v1\modlib\modeller\sequence_db.py", line 
> 48, i n read
>     minmax_db_seq_len)
> IOError: openf______E> Cannot open file pdb95.fsa: No such file or directory
> *************
>
> The pdb95.fsa file is located in my Modeller9v1\examples\commands folder. 
> Should it be moved?

Since you called the filed "pdb95.fsa" in your script, it has to be in 
the current directory. Otherwise you can specify a full or relative 
path, in standard Unix or DOS fashion - consult your favorite Unix or 
DOS reference.

The .cod and .grp files are clustered PDB databases used by the obsolete 
sequence_db.search() method - you don't need them for the more 
sophisticated profile searching methods. The pdb95.bin file is just the 
binary equivalent of the pdb95.fsa file, so is faster for Modeller to 
read but is not human readable.

	Ben Webb, Modeller Caretaker
--
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