Scoring

Building loop extensions in a membrane protein with Remodel

Category:
Design
Scoring
Loop Modeling
Membrane

Hi All,

I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.

Here are the flags that I'm using:

Post Situation:

mp_transform optimize with franklin2019 scoring

Category:
Design
Scoring
Enzyme Design
Membrane

Hi All,

I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:

Post Situation:

Setting output values using a database (with relax app)

Category:
Scoring

Hello all,

I noticed rosetta creates 23 tables in MySQL when using it as output backend in the RELAX application.

For my specific research I only need to hold the per-residue energies and the total energies... I don't need the atoms, topology or PDB data to be saved after each cycle, as it consumes a lot of memory.

Post Situation:

Output "per-residue" energy score to database

Category:
Scoring

Hello all.

I noticed that when I output a relax cycle to a PDB, the residue scores are in the bottom of the PDB.

When I output the results to a database (MySQL), the table structure_scores holds the energy scores of the whole PDB, but I can't find the per-residue values anywhere.

Post Situation:

BUG REPORT: MySql column protocol.protocol_id must have the AUTO_INCREMENT flag set

Category:
Scoring

I tried running relax compiled with MPI and MYSQL.

MySQL was configured properly. A test run without MPI successfully created tables and wrote data to MySQL.
The protocol file @relax.flags was created with the following options:

-list pdblist.txt
-relax:script relax.script
-relax:bb_move false
-score:output_residue_energies
-score:weights res2015

Post Situation:

Relaxation vs minimisation

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.

Post Situation:

dump_scored_pdb

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)?

Post Situation:

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

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.

Post Situation:

Working through tutorials: expected output scorces differ from calculated results

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

Post Situation:

Compaing interface socre of different ligands with the same protein structure

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?

Post Situation: