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where is

Where can I find script to add extra pdb structures to the fragment libraries? I've searched through Rosetta3.4 bundle, Rosetta3.3_fragments and PyRosetta but couldn't find it.

Post Situation: 
Thu, 2013-01-24 13:35

I can see it at ./rosetta_tools/fragment_tools/pdb2vall/ I've attached it.

Thu, 2013-01-24 13:37


I get an error I encountered with other python scripts from the Rosetta 3.4 bundle as well. I am using CentOS 6.3 64-bit, do you have any idea what package is needed?

$ python /home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/ --help
Traceback (most recent call last):
File "/home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/", line 8, in
from amino_acids import longer_names
ImportError: No module named amino_acids

Sat, 2013-01-26 12:27

I don't have a copy of 3.4 tools handy. Using the developer-trunk version, it appears to be looking for "" in the same directory. Is that not there for you? I can make you a copy of the whole directory.

EDIT: I looked into the 3.4 release...none of this stuff is there! I guess it's newer than 3.4. I have made a copy of this whole directory off developer trunk for you and temporarily stashed it at since it's too large to attach. I'll delete it after you signal that you downloaded it.

Mon, 2013-01-28 07:37

Thanks for the archive. I tried to run but got the following error:

$ python /home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/ --no_structure_profile -d -p 4h99M getting fasta from pdb_seqres.txt ...
Traceback (most recent call last):
File "/home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/", line 75, in
tmp_results = numbering_back_to_pdbseqres( pdb )
File "/home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/", line 48, in numbering_back_to_pdbseqres
file = open( pdb_seqres_fn, "r")
IOError: [Errno 2] No such file or directory: '/home/thomas/Programs/Rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/database/rcsb_data/derived_data/pdb_seqres.txt'

Is the directory you sent me complete?

Wed, 2013-01-30 02:57

The file "rosetta_tools/fragment_tools/pdb2vall/database/rcsb_data/derived_data/pdb_seqres.txt" does not exist in developer's trunk. (The whole subdirectory derived_data does not exist). The README implies:

Databases which may need to be updated in the future:
derived_data ss_dis.txt

So apparently that file was either left out as incomplete, or you should supply an updated version somehow? I've contacted the code's authors for comment.

Wed, 2013-01-30 09:06

In the README file from the pdb2vall folder:

3. Edit pdb2vall.cfg:

you need to modify the configuration file to give correct paths for scripts/databases.

Wed, 2013-01-30 10:06

In addition to reading the README and following the installation directions which includes editing the config file:

it looks like the script that installs/updates the PDB data (which is missing and causing the error) will only install/update Tues-Thursday to save bandwidth.

As a quick fix:

edit database/rcsb_data/

by commenting out the line:

exit(0) if ($wday < 2 || $wday > 4);

line 10.

and then rerun the main pdb2vall script.
If that gives the same error, run ./database/rcsb_data/ and then rerun the main script.

Wed, 2013-01-30 10:38