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Scoring

dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.

Category: 
Docking
Scoring

Hello,

I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.

A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.

Post Situation: 

How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

Post Situation: 

DomainAssembly Mover with constraints (using RosettaScripts)

Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

Post Situation: 

RMSD calculation

Category: 
Scoring

Dear all,

Hi,

I need help with Ca-RMSD calculation. I've used docking protocol to generate some models and now I want to calculate Ca-RMSD between these models and the native. Each model has 5 chains: e.g. model_AB_CDE. I want to calculate Ca-RMSD in a way that the model_AB chains would be aligned on native_AB and the RMSD between model_CDE and Native CDE will be computed. How can I do that? I've used score protocol but it computes the total RMSD between all the chains.

Thanks in advance,

Best,

Post Situation: 

BridgeChainsMover

Category: 
Design
Scoring
Loop Modeling

Hi,

I am using the 2016.28 build and have the some problems with "BridgeChainsMover" from Brian's recent method paper: DOI:10.1007/978-1-4939-3569-7_20

I get this error "ERROR: 'scorefxn' is not a valid option for BridgeChainsMover".  Here is the part of script that returns an error:

<BridgeChainsMover name="connect" chain1="1" chain2="2" motif="3LX-3LA-3LX" overlap="3" scorefxn="centroid_scorefunction" />

Post Situation: 

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

 

Post Situation: 

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=======================

Post Situation: 

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:

Post Situation: 

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