[Feature-dev] [ feature-Bugs-1262 ] Can't find PDB files when using RCSB "divided" data store on case-sensitive OSes

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Bugs item #1262, was opened at 2010-07-16 16:05
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Category: Application - featurize
Group: Environment and setup
Status: Open
Resolution: None
Priority: 1
Submitted By: Mike Wong (mikewong899)
Assigned to: Mike Wong (mikewong899)
Summary: Can't find PDB files when using RCSB "divided" data store on case-sensitive OSes

Initial Comment:
Revision: 699

Description:

featurize gives warnings that it can't find PDB files when using RCSB "divided" data stores. RCSB "divided" data stores uses a directory called "divided" and a subdirectory named for the middle two letters of the PDB ID. For example:

Given PDB_DIR=/usr/local/feature/data/pdb

1A2L would be found as

/usr/local/feature/data/pdb/divided/A2/1A2L.pdb.gz

Somehow featurize calculates the subdirectory to be "A2a2" and fails to find the file.

How to Repeat:

1. Download PDBs using the RCSB "divided" data store structure.
2. Checkout and build r699 on Linux.
3. Run featurize on a pointfile.

Repeatability: 100%

Workaround:

Don't use the RCSB "divided" data store and instead use a flat file system. Current SeqFEATURE models and Thioredoxin use about 5,000 or so PDB files. All targeted systems (Mac OS X, Desktop Linux, and Cluster Linux) can handle this many files in a directory.

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You can respond by visiting: 
https://simtk.org/tracker/?func=detail&atid=145&aid=1262&group_id=16