Unsolved

I am working with calculating the rotamer-rotamer pairwise energies over the rotamer library for a fixed backbone. To do this I've essentially reimplemented the body of pack_rotamers_setup(), which ultimately calls RoatmersSet.calculate_energy(). I have a few questions on the topic, some of these are code-based others are to clear up my lack of biology background:

* What is the field RotamerSets.nmoltenres? This appears to be the number of rotamer positions, but is strictly less than the number of residues on the backbone. Shouldn't there be rotamers at every residue?

Hi all,

I am successfully using InterfaceAnalyzer to get a binding score between a protein and a peptide.
InterfaceAnalyzer is great in that it breaks down the score into different parameters.
However, I am looking to break down the score contribution into the contribution by each residue.

For instance, I'd like to know the hydrogen bond contribution of residue 6 (this is made up, but illustrates the point).
Or perhaps I'd like to know the vdw for residue 10. Etc.

Hi
I am currentlt working with implementing saxs into the docking protocol. The only reference I have found is “Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual couplings” by Nikolaos G. Sgourakis et. Al.
Basically I have added the lines:

-score:saxs:ref_spectrum saxsdatafile.dat
-score:weights docking.wts

where I have copied the docking.wts file to my own directory and added the line
fastsaxs 2.5

Hi,

I want to know what are the criteria used by pyrosetta in detecting a hydrogen bond. If anybody can guide me to a ref., it will be more useful.