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Scoring

Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

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SPLINE EPR_DISTANCE Constraint Error

Category: 
Scoring

Hello,

I'm getting an unusal error when using SPLINE EPR_DISTANCE constraints with the score.linuxgccrelease function. I generated some structures ab initio using SPLINE EPR_DISTANCE constraints with rosetta_scripts.linuxgccrelease and I wanted to rescore the binary output file with some different constraint weights using score.linuxgccrelease. However, if my input constraint file (cst_fa_file) to the score.linuxgccrelease release function contains any SPLINE EPR_DISTANCE constraints, I get:

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rosettaScore.py has a typo, I think. Can I fix it in my own copy?

Category: 
Scoring

I'm using a protein_tools script that calls up the rosettaScore.py script.  In line 85 of rosettaScore.py, it says:

print "theres some problem with this score line, possible corruption, skipping line"

But I think it should be:

print ("theres some problem with this score line, possible corruption, skipping line")

It won't let me write over the script file, even though I think I have ownership of the software.  What can I do?

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"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.

 

Post Situation: 

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