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Scoring

"caught exception" for PDB with membrane "DUM" residues

Category: 
Scoring
Membrane
Non-Canonical Peptides

If I run this command:

residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true

on the attached pdb, I get this error:

caught exception 

 

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Total Rama Score

Category: 
Scoring

Can anyone point to how the rama score is evaluated for ALL residues in a given run by a Rosetta application?

I have been looking through the src/core/scoring/Ramachandran* and src/core/scoring/methods/Ramachandran* code pieces and see in most places only the individual residue measurements ( eval_rama_score_residue() ). There is a void function in Ramachandran.cc that goes through all residues (eval_rama_score_all() ), but this function is not called in any of the protocols or applications in Rosetta.

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Problem with Scoring function and PlaceStub mover

Category: 
Design
Scoring

Hi everyone,

I am using PlaceStub application (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PlaceStubMover) for placing two sets of different stubs on the scaffold.

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eval_ci_2b() with hydrogen bonds

Category: 
Scoring

I am trying to compute the residue-residue pairwise energy for several residues inside a protein structure. I found the method scorefxn.eval_ci_2b() can compute the pairwise energy between residues for a given scorefxn. This works for the LJ, Solvation and electrostatic potentials. Also as epxected, it ignores intra-residue interactions and backbone parameters when computing with eval_ci_2b(). However, I was wondering why the Hydrogen bonded potential is also not included? Is there an easy way to include the hydrogen bond energy in the pairwise energy?

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Clustering issue

Category: 
Scoring

Dear all,

 

I am using Calibur to create my clusters. I dont understand the output.

It shows there are two large clusters and lists the centroid. Then it goes on showing the content on the largest cluster, but the not the second cluster. Then it lists another 2 clusters. However, why is the second cluster missing?

Also, the total of decoys doesnt add up. It should be 1000 but its much less.

I am a bit confused as to how many clusters do I have in total and where there are listed.

 

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ΔΔG Calculation of a Mutation with PyRosetta

Category: 
Scoring

Hi everyone,

We are trying to replicate the experiment by Alford et al. (2017) in our lab to calculate the ΔΔG of T193V mutation for the RT-RH-derived peptide bound to HIV-1 protease (PDB entry 1kjg). However, we have been getting values that are different from the reported ΔΔG of –4.95 kcal/mol and it’s likely due to errors in our code.

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Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI

Category: 
Scoring

Hello,

I'm running the enzyme_design application using MPI and in the scorefile that is produced, the 'description' field isn't unique across the processors, so if I run on 10 processors, I get 10 PDB files named mypdb___DE_10.pdb. Firstly, is there a way to ensure that the PDB files have unique names?

As I can't correlate the scores in the scorefile to the individual PDB file, I've renamed all my PDB files to give them unique names and am then trying to use the score_jd2 to generate a scorefile. I'm using the following flags:

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