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Scoring

reporting IteratedConvergence status

Category: 
Scoring

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

 

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error--rosetta fragment‐based refinement protocol for refinement against EM density

Category: 
Scoring

I am trying to fit my pdb structure into EM density and the following information happened:

tupdens=======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MinMover - cenmin=======================

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scoring input pdbs as the same as docking score

Category: 
Scoring

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:

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InterfaceAnalyzer atom subset

Category: 
Scoring

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

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No RMS and IRMS values in protein/nucleic acid docking

Category: 
Docking
Scoring
Nucleic Acids

Hello,

I am docking a small protein / nucleic acid structure to generate dockings. The scoring contains only -nan for rms and 0.000 for Irms. Why doesn't the docking result in valid rms/irms values? Fnat and I_sc as well as total_score seem ok. What do I have to change in order to receive rms and irms values?

XML Rosetta Script (prot2.xml):

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Question on eval_atom_derivative function.

Category: 
Scoring

Hello again,

So I am working on incorporating pseudocontact shifts into the Relax protocol and I need to implement the derivatives for minimization. As I understand it, to do this I need to implement the eval_atom_derivative function. However, I do not understand the vector parameters F1 and F2. Could you explain them to me? Are they just the vector along the gradient for the atom?

Thank you in advance.

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rama vs p_aa_pp vs ref score terms

Category: 
Scoring

Do these three terms in Score12.wts_patch and after have significant overlap?

How would one go ahead to explain a delta_delta_G upon a mutation that has contributon coming from these terms? In one protein case, three mutations T61N, H135Y and H257P, showed significant gain in half-life. The score terms show contribution from Rama, p_aa_pp and ref. 

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RASREC - finding lowest energy structure

Category: 
Scoring

Hi Rosetta community,

After finally getting the RASREC run to successfully generate full 6 stages, now I'm at the point where I want to score the pdbs to find the lowest energy structures which suppose to be the closest to the native structure. But in this website: https://www.rosettacommons.org/demos/latest/protocol_capture/rasrec_evolutionary_restraints/README

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