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InterfaceAnalyzer packstat score = 0.000

Submitted by vmc99 on Fri, 2018-11-16 11:30
Category: 
Scoring

Hello

I am using the InterfaceAnalyzer to obtain packing scores of antibody-antigen strucutres from the PDB database but the packstat score always ends up being 0 for some reason. I am specifying for the activation of packstat calculation as can be seen in my flags.txt file below

-in:file:s 1A14_atomlines.pdb
-interface HL_N
-compute_packstat = 1
-out:file:score_only 1a14_interface.out

The output file is attached below. 

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Rosetta 3 - General

Rosetta lack of necessary application

Submitted by ylwang on Wed, 2018-11-07 01:13
Category: 
Scoring

Hi

    when i learn denovo_model_building from demos/public/electron_density_structure_refinement.In step 1 and step2 ,they ask for place_fragment_into_density.linuxgccrelease,  cal_overlap_score.static.linuxgccrelease,cal_nonoverlap_score.static.linuxgccrelease.In my rosetta 3.0 i can not find these application.I dont know why,thanks for help

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Rosetta 3 - General

SPLINE EPR_DISTANCE Constraint Error

Submitted by mmw88 on Tue, 2018-09-18 14:39
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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Rosetta 3 - Applications

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

Submitted by mdeklotz on Thu, 2018-08-02 15:15
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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Rosetta 3 - General

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

Submitted by nitroamos on Wed, 2018-05-30 08:35
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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Rosetta 3 - General

Total Rama Score

Submitted by jcminerlanl on Thu, 2018-05-10 07:19
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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Rosetta 3 - General

Problem with Scoring function and PlaceStub mover

Submitted by a-eatemadi@razi... on Sat, 2018-04-07 09:22
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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Rosetta 3 - Applications

eval_ci_2b() with hydrogen bonds

Submitted by TensorDuck on Fri, 2018-03-30 14:05
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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PyRosetta - General

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