Scoring

Hi,

I am trying to import SAXS energy function in PyRosetta, However, I failed to call it in python. The code I tried is: 

>>> from rosetta import *
>>> rosetta.init()

>>> from toolbox import cleanATOM

>>> cleanATOM("1YY8.pdb")

Dear All,

I use IteratedConvergence in my Rosetta Script. Is there a convenient way to monitor the number of cycles that that passed before the convergence? Would it be possible to have this value for the individual models in the score file, together with total_score etc.?

This brings a more general question - how to monitor/debug Rosetta scripts, e.g. track energy values, behavior of filters etc.

Thank you for suggestions & best wishes,

Staszek

Hi everyone,

I'm writing a pilot app in Rosetta and I want to cluster results (all pdbs) of global dock. After calculating the scores, they are completly different with the original scores I got from docking_protocol. I'm using following codes:

        core::scoring::ScoreFunctionOP scorefxn( core::scoring::get_score_function() );
        ( *scorefxn )( init_pose );

I found that the input pdbs do not have sidechains, however using following command just made the scores better but the difference is still remained:

Hello Everyone,

Does anyone know if it is possible to use InterfaceAnalyzer only on a subset of atoms instead of the whole proteins?

Specifically, I've recently completed 4x 2 us simulations in GROMACS and would like to understand how different positions/polar/hydrogen bonding networks of an interface loop affect interaction energy between the two proteins.

If this cannot be done, I suppose an alternative approach would be to strip all non-relevant residues with awk and then run only the subsets through InterfaceAnalyzer