Update Surface Library
23 Jul 2014Update the local PDB
We are using /Volumes/Alpha/BackpocketLint/
as the local version for space reasons.
You need to run it twice for some reason.
perl /Users/tbinkowski/Box\ Sync/xScripts/pdb-syncAndExtract.pl -sync -verbose
perl /Users/tbinkowski/Box\ Sync/xScripts/pdb-syncAndExtract.pl
Generate Surfaces using FPocket
Walk the PDB-style directory and run FPocket on each file. It uses the file as it is written so you may want to preprocess it depending on needs.
python create_pockets.py
Generate Surfaces using HetContacts
Walks the PDB directory and uses the files as input. It outputs the surfaces into a separate directory (HetSurfaces). As of now some of the atoms may not be solvent accessible. This could be fixed by only looking at atoms in FPocket output.
python create_surfaceFromHetatms.py
Generate The Surface library
This is simply a list of all the surfaces that we want to use for comparison to our query. It walks the PDB-style folder hierarchy and prints the full path to a JSON file named surface-library_prefix_date.json.
It is current hardcoded to use the ‘HetSurfaces’ library located at /Volumes/Alpha/BackpocketLint/HetSurfaces/
.
cd /Users/tbinkowski/Box\ Sync/xScripts/Proteinworks/bin
python create_library.py prefix_name