Hi
I have a sequence that I want to check against known structures and am trying to run "build_profile.py".
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?
Additionally, I have downloaded the pdb_95.cod.gz, pdb_40.cod.gz and pdball.pir.gz files. I have unzipped them but am not sure which directory to place them in (or the files that they replace). Do I need to change their file extensions? Is pdb_95.cod the pdb95.bin file referenced in the example build_profile.py script?
Any help would be appreciated.
Eeson
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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Eeson Rajendra -
Modeller Caretaker