You are here

Scoring

Packstat application output

Category: 
Scoring

Hello!

I am trying to use the packstat application for measuring the quality of my model. But, I'm not sure what the terms in output mean? (there is no info in user guide/documentation). I came up with the flags I've used from the RosettaHoles2 paper. As per the paper, it should output some pdb and also output explicit representation of voids. But, I donot see any output files. I only get the commandline output with three score columns.

Could someone clarify?

Post Situation: 

Total score for individual residue

Category: 
Scoring

Dear PyRosetta People,

 

I am trying to find the total score of an individual residue. This is my script so far:

 

scorefxn = get_fa_scorefxn()
scorefxn(pose)
AA_Score = pose.energies().residue_total_energies(5)
print(AA_Score)

 

It seems i get a massive print out, and when repeated for different residues gives the exact same values, so i am sure my script is wrong.

 

What is the correct way to get the total score for just 1 amino acid?

Post Situation: 

Energy scores of D-amino acids

Category: 
Scoring

I used PyMOL and Maestro to invert the chirality of single L-amino acids into D-amino acids, as well as all L-residue polypeptide to all D-residue polypeptides. Even though they are mutually mirror images, but D-amino acids and D-polypeptides all have remarkably higher energy scores than their counterparts by using PyRosetta scoring protocol. May I ask what are some possible reasons for this difference? I am wondering whether it is caused by computational error or more delicate design, such as strong and weak nuclear forces, in Rosetta tool.

Post Situation: 

optimisation of a protein-protein interface

Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

Post Situation: 

Docking Prepack protocol working or not ?

Category: 
Docking
Scoring

Hi Rosetta community, 

I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning : 

[ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

and my score_sc file contains 0.000 for the total score for every generated structure.

Here the command I used to run prepack:

Post Situation: 

score_jd2 errors out with: ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'

Category: 
Scoring

I am trying to calculate rmsd using a template pdb structure using score_jd2. When I try to run the following command,

$ROSETTA3/bin/score_jd2.macosclangrelease -in:file:silent decoys_alp_tcn.out -evaluation:rmsd 2alp.pdb `cat pdb_list` FULL -out:file:silent rescored_decoys.out

it errors out saying ERROR: Unrecognized residue: SO4. Then I rerun the same with -ignore_unrecognized_res

Then I get the following error:

ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'

Post Situation: 

[dev] not seeing energy in pose row for new energy term in design

Category: 
Scoring

Hi all,

I made an EnergyMethod to add a few new energy terms and am trying to use them in fixbb. However, for two of these terms, the 'pose' row shows only 0, even though the individual position rows show non-zero values that sum to non-zero. This is how I set my terms in the emap:

Post Situation: 

Pages

Subscribe to RSS - Scoring