[Owl-devel] Pisa connection

[Henning Stehr]

Hi Jose,

the stuff in owl.connections.pisa looks amazing. Just some quick
questions. What I'm interested in is getting the residues which are
involved in protein-protein interfaces in the most likely assembly.

1. Are the interfaces returned by getInterfacesDescription()
automatically taken from the "best" assembly or all assemblies or some
other default one?
2. I assume that PisaInterface.firstMolecule and
PisaInterface.secondMolecule are the two molecules which are in
contact via the interface. If the assembly is e.g. a homo-dimer, would
firstMolecule and secondMolecule then be the same?
3. Say I list the residues by PisaInterface.getFirst().getResidues().
Are these only the ones in contact in this interface (and this
assembly) or all residues in the chain/molecule?
4. Currently you are downloading pre-calculated data for existing PDB
codes, right? How different/difficult would it be to get data for
custom uploaded structures?
5. Maybe a question for the other Pisa experts on the list: Would it
even make sense to run such delicate calculations as Pisa does on
predicted structures?

BTW, did you know there is also a standalone version of PISA in CCP4?
(see http://smb.slac.stanford.edu/facilities/software/ccp4/html/pisa.html)

Cheers,
Henning