Db2multipdb.py

db2multipdb.py is a small python script used to decode Flexibase .db files to multipdb files (that can be read by any viewer) and do some simple checking on the .db file.

Usage: db2multipdb.py [options] file.db [more db files]

Convert .db files to multiple pdb files, check for errors

Options:
 -h, --help     show this help message and exit
 -v, --verbose  lots of debugging output
 -n, --nopdb    don't write pdb files, just do broken checking

The script is located at

~rgc/Source/bks_src/db2multipdb.py

If you don't have python2.6 in your path you'll have to put it there or run the program like this

/usr/arch/bin/python2.6 ~rgc/Source/bks_src/db2multipdb.py

Verbose output (-v flag) is not typically needed but available. Not writing pdb files (-n flag) is a useful option if you don't need the pdb files and just want to do the broken checking. Each separate .db entry generates the following output to stdout:

P00000008 being processed now 1
P00000008 1 errors of each type: 542 0 0 0 no errors: 817 total models 1359
zincid^^^ #times zincid seen^^^^ a^^ b c d ^^^^^^^^^^ #without errors  #total

where a,b,c,d type errors are defined as

a is atoms closer than 0.95 angstroms
b is oxygen atoms closer than 2.0 angstroms
c is heavy atoms closer than 1.07 angstroms
d is no other atoms within 2.2 angstroms

Exactly which atoms have these errors can be seen with the -v option. Errors of the first 3 types are expected due to the 'mix-and-match' conformations generated by separate flexible branches being recombined and overlapping. Errors of type d should not occur but have been known to previously.

Questions? contact Ryan Coleman