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Scoring

Relaxation vs minimisation

Submitted by mm on Fri, 2020-03-13 04:49
Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

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PyRosetta - Applications

dump_scored_pdb

Submitted by allan.ferrari on Wed, 2020-02-19 07:21
Category: 
Scoring

I am new to Pyrosetta and trying to dump the modified pose along with its total energy.

I have used pose.dump_score_pdb('model.pdb', scorefxn) to have the total score printed out with the PDB file.

However, this method prints out way more information. What would be the equivalent way of having the total score printed out (as the fileters work in the xml file at rosetta scripts)?

 

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PyRosetta - Scripts

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Submitted by TLP on Tue, 2020-01-21 11:18
Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

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PyRosetta - Applications

Working through tutorials: expected output scorces differ from calculated results

Submitted by j.schmue on Sat, 2020-01-18 13:16
Category: 
Scoring

Hi,

I'm new to Rosetta and currently working through the tutorials.

I often recognized that  the the score values produced by the recent version "Rosetta 2019.47" on my computer differ from the ones cited in the tutorials and given expected_output.

e.g.:

in the Scoring Tutorial  (subchapter "Changing the Score Function") the command 

ROSETTA3/bin/score_jd2.linuxgccrelease @flag_docking

with flags

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Rosetta 3 - General

Compaing interface socre of different ligands with the same protein structure

Submitted by Caulobacter on Tue, 2019-12-10 12:53
Category: 
Scoring

I am trying to dock molecules with the same parent core but different substitution groups into the same PDB structure using ROISE. 

I tried to read through some published papers on ResettaLigand but still was not able to find out the answer for:

Since we are only allowed to include on ligand in each run, can we submit a few different runs and compare the interface score directly?

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ROSIE - General

Ddg calculation for a metalloprotein using APBS

Submitted by dfcoelho on Tue, 2019-11-19 10:06
Category: 
Scoring

Hi all,

I am trying to calculate Ddg for a protein complex, which is made of 3 chains: A, B and C.

The chains B and C have a zinc-finger each, which are a zinc ion complexed by four CYS side-chains.

To calculate the Ddg I am using the SetupPoissonBoltzmannPotential mover followed by the Ddg filter, in order to separate chain B from chain A+C and calculate the binding energy.

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Rosetta 3 - General

running in MPI mode and multiple scores per output PDB file?

Submitted by dantimatter on Wed, 2019-10-30 09:42
Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

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Rosetta 3 - Applications

An error with score app

Submitted by Genta on Tue, 2019-10-29 18:46
Category: 
Scoring

Hello, I am trying the score app in the tutorials and meet an fatal error.

I work on CentOS 7 and my rosetta version is rosetta_src_2019.40.60963_bundle.

At first, I just used the command given by the instruction, it is:

score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters

however, it stoped after a few seconds and the last lines of log is:

 

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Rosetta 3 - Applications

Alanine Scanning for 1 Protein (no interface)

Submitted by mags33 on Fri, 2019-10-25 10:08
Category: 
Design
Scoring
Enzyme Design

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

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Rosetta 3 - Applications

InterfaceAnalyzer：“too many tries in fill_missing_atoms!”

Submitted by mxp on Tue, 2019-08-06 00:41
Category: 
Scoring

Hey Guys,

We are trying to use  "InterfaceAnalyzer"  to  analyze a  PDB,  then we get this:

......

.....

core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue pdb_HSD 152
core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue pdb_HSD 152
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'complex_0_0001'
Error: [ ERROR ] 

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Rosetta 3 - Applications

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