You are here

Home

Scoring

Memory leak when PDB preparation

Submitted by Jacky010 on Mon, 2019-05-06 01:28
Category: 
Scoring

Hi everyone,

   I am preparing the pdbs from pdb.org for scaffold. About more than 6000 pdbs were downloaded and have been preparing. However, the memory leak was encountered. I have try to use -linmem_ig 10 and -jd2:delete_old_poses to resolve the problem. But the memory leak is still there. 

Could you help me to solve this problem?

   Thanks a lot.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Error with etable_atom_pair_energies()

Submitted by yijietseng on Mon, 2019-01-28 14:00
Category: 
Scoring

I am new to Pyrosetta and programing and I am learning how to use Pyrosetta. So when I was practicing scoring with Workshop #3 bullet point 5, I came across a error, and I have no idea what's wrong with.

Here is what I did. 

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom("N")

a2 = r1.atom("O")

etable_atom_pair_energies(a1, a2, scorefxn)

Post Situation: 
Solved
Forums: 
PyRosetta - General

ddG calculations to study point mutations

Submitted by N.Chopra on Fri, 2018-12-07 12:36
Category: 
Scoring

Hi,

I am using Rosetta protocol to determine ddG changes on point mutations in a peptide bound to a protein complex. I first used FastRelax to remove any steric clashes in the protein structure and then ran the ddG protocol to generate ~1000 structures till there is no change in ddG values. I now want to build a correlation plot between the Rosetta ddG values and experimental calculations.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

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. 

Post Situation: 
Solved
Forums: 
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

Post Situation: 
Unsolved
Forums: 
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:

Post Situation: 
Solved
Forums: 
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?

Post Situation: 
Unsolved
Forums: 
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 

 

Post Situation: 
Unsolved
Forums: 
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.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Scoring