You are here

Scoring

Error with SapScoreMetric (SimpleMetric sap_score not found in basic::datacache::DataMap)

Category: 
Scoring

Hello, I encountered an error while attempting to use the 'SapScoreMetric' in RosettaScript.

I encountered the following error, but when I exclude the 'SapScoreMetric' parts, it works well.

---------------------------------------------------------------

[ ERROR ]: An issue with your Rosetta run was detected

Please correct the following issue and retry:

 

SimpleMetric sap_score not found in basic::datacache::DataMap.

---------------------------------------------------------------

Post Situation: 

JD3 w/ Silent file output crashing - Option filename not found

Category: 
Scoring
<Job nstruct="5">
     <Input>
          <PDB filename="pdb_basename.pdb" />
     </Input>
     <Output>
          <SilentFile path="pdb_basename" filename="pdb_basename_relaxed.silent"  />
     </Output>
     <SecondaryOutput>
          <ScoreFile path="pdb_basename" filename="score_pdb_basename.sc" />
     </SecondaryOutput>
     <Options>
          <parser__protocol value="path/to/RELAX_MONOMER_RS" />
     </Options>
</Job>

Post Situation: 

different relaxed energy scores for one same protein structure

Category: 
Scoring

Hello everyone,

 

By chance, I tried several times relax module for one same protein structure.

I got all different relaxed energy socres.

Which score is representive for this protein structure?

 

And of two similar structures mutated by 1 or 2 different positions, which structure can have the better structure?

By what criteria did you think that?

Post Situation: 

Calculating SAP score using RosettaScripts

Category: 
Scoring

Hello,

I am trying to calculate the per residue SAP scores of a protein structure using Rosetta scripts. The .xml script I am using is shown below.

<ROSETTASCRIPTS>

    <SCOREFXNS>

    </SCOREFXNS>

    <RESIDUE_SELECTORS>

    </RESIDUE_SELECTORS>

    <FILTERS>

    </FILTERS>

    <SIMPLE_METRICS>

        <PerResidueSapScoreMetric name="sapscore"/>

    </SIMPLE_METRICS>

Post Situation: 

ERROR: beta_nov16(.wts) requested, but -corrections::beta_nov16 not set to true. This leads to a garbage scorefunction.

Category: 
Scoring

Hello everyone, while running a scoring file, I entered the following command line:

Post Situation: 

Score function in protein-protein docking with constrains

Category: 
Scoring

Hi, everyone!

I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:

a. Whether the ref2015  or ref2015_cst function considers the ligand (with params file)?

b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?

Post Situation: 

Pages

Subscribe to RSS - Scoring