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Scoring

Interesting scoring performance in flexpepdock against random peptides

Category: 
Scoring

Dear all,

recently I have tried to dock some different peptides to binding pocket of protein kinase and see their performance in flexpepdock. In the meanwhile I also dock some random peptides, such as poly G (GGGGGSGG) and poly E peptide(EEEEESEE). Interestingly, the energy score of good peptides and random peptides didn't show much differences(from -650 to -690), sometimes the random peptides even showed the better energy score. In order to keep them in the pocket I have made some constraint. The orientation of peptides are similar. 

Post Situation: 

residue_pair_energies

Category: 
Scoring

Hello!

I am trying to find the residues interacting with a particular residue of interest so as I can determine which residue-residue interaction is making the most contribution to a specific scoring term. However, I have not been able to find the residue_pair_energy function. 

Do I need to write the function class to obtain this or is there a function that already available (e.g. to get atom-atom pairwise energies). If the latter case where is the function  located. 

I have tried core.scoring.Energies but it does not exist there

Post Situation: 

score_jd2.macosclangrelease No such file or directory

Category: 
Scoring

I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:

#!/bin/bash

$ROSETTA3/home/labusr/rosetta/main/source/bin/score_jd2.macosclangrelease \
 -database $ROSETTA3/database/ \
 -database ~/Rosetta/database/ \
 -in::file::s /home/labusr/Documents/1issA.pdb \
 -ignore_unrecognized_res \
 -edensity::mapfile /home/labusr/Documents/1issA_6A.mrc \
 -edensity::mapreso 5.0 \
 -edensity::grid_spacing 2.0 \
 -edensity::fastdens_wt 35.0 \
 -beta \
 -edensity::cryoem_scatterers \
 -crystal_refine

 

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[dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?

Category: 
Scoring

Hey,

Can anyone point me to good examples of implmentations for setup_for_packing and prepare_rotamers_for_packing (and I guess update_residue_for_packing while I'm at it)? I'm not entirely sure I understand what the arguments are for these methods and the use case for when I would want to implement these methods.

Thanks in advance!

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[dev] determine which score_type's enabled in create_energy_method?

Category: 
Scoring

Hey,

I have created an energy method and it works. However, I want to do a check at the time it is created for whether a particular score_type is enabled. Is there any way to know which score_types are enabled from within my create_energy_method function?

Thanks!

- Igor

Post Situation: 

Ineffective Constraints

Category: 
Scoring

Hi all,

I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:

AtomPair CA 1 CA 41 HARMONIC 55.0 .1

My flags are:

Post Situation: 

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: 

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