You are here

Home

Scoring

Clustering issue

Submitted by Loki01 on Thu, 2018-03-29 10:16
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: 
Unsolved
Forums: 
Rosetta 3 - Applications

ΔΔG Calculation of a Mutation with PyRosetta

Submitted by akaashvenkat on Fri, 2018-03-09 01:44
Category: 
Scoring

Hi everyone,

We are trying to replicate the experiment by Alford et al. (2017) in our lab to calculate the ΔΔG of T193V mutation for the RT-RH-derived peptide bound to HIV-1 protease (PDB entry 1kjg). However, we have been getting values that are different from the reported ΔΔG of –4.95 kcal/mol and it’s likely due to errors in our code.

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI

Submitted by linucks on Tue, 2018-02-13 03:41
Category: 
Scoring

Hello,

I'm running the enzyme_design application using MPI and in the scorefile that is produced, the 'description' field isn't unique across the processors, so if I run on 10 processors, I get 10 PDB files named mypdb___DE_10.pdb. Firstly, is there a way to ensure that the PDB files have unique names?

As I can't correlate the scores in the scorefile to the individual PDB file, I've renamed all my PDB files to give them unique names and am then trying to use the score_jd2 to generate a scorefile. I'm using the following flags:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Interesting scoring performance in flexpepdock against random peptides

Submitted by ziqi1234 on Fri, 2017-12-08 07:52
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: 
Unsolved
Forums: 
Rosetta 3 - Applications

residue_pair_energies

Submitted by kamau on Fri, 2017-12-01 09:21
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: 
Unsolved
Forums: 
PyRosetta - Applications

score_jd2.macosclangrelease No such file or directory

Submitted by ahmadkhalifa on Mon, 2017-11-27 09:26
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

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Scoring