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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: 

No values for total score while running Rosetta score file.

Category: 
Scoring

I am running the Rosetta version - rosetta.source.release-334.tar.bz2 for designing two proteins but no values are generated for the total score. All the important files regarding this are attached. Please look at it and help me with this. 

Post Situation: 

Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi

Category: 
Scoring

Hi,

using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context

...................................

 

the flags and log file were attached.

Please help, thanks

Post Situation: 

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

Category: 
Scoring

Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?

So far I thought the soft score function is supposed to feature lower repulsive terms.

ref2015_soft.wts:

Post Situation: 

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