DARS_potential is a program for assessment of protein-RNA structure complexes. Next it clusters best 100 scored models. It is possible to define different number structures for clustering. 

INSTALATION

To use DARS_potential script you need to install a Python language interpreter (version 2.6 or later), the BioPython library (version 1.45 or later) and the Numeric library.


Program was tested on Biopython releases: 1.45, 1.49 and 1.55.

To check Biopython version please write:
$ python
>>> import Bio
>>> print Bio.__version__
1.56

If it does not work, please try:

$ python
>>> import Martel
>>> print Martel.__version__
1.45


RUNNING

To verify that Python and BioPython are usable with DARS_potential script, run the it without any arguments. It should produce the following usage synopsis.

$ python DARS_potential.py

Usage: DARS_potential.py [<options>]

Options:
  -h, --help            show this help message and exit
  -f LIST_OF_STRUCTURES
                        A file with list of PDB files. One path per line
  -s STRUCTURE          A filename with structure of protein-RNA complex
  -m NR_TO_CLUST        Number best scored structures to clustering (default
                        100)
  -c CUT_OFF            Threeshold in angstrems for clustering best scored
                        decoys. Default value = 5


Now run it with the one of example pdb files provided with script:

$ python QUASI_potential_3.py -s 3bso-rna_4592.pdb

file   E       Edis    Eang    Esite   Epen
3bso-rna_4592.pdb       -4893493.92     -1675270.54     -3349798.25     -628425.13      760000.00

It should give the energy of given structurei (E) and values of all terms of energy function: distance term (Edis), angular term (Eang), site of nucleotide term (Esite) and penalty term (Epen) (see above).

IMPORTANT!!!
The clustering function was provided for clustering GRAMM decoys,which have the same geometry of chain A. So, during the clustering RMAD is calculated only for chains B.

