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Scoring

Scoring after HBNet

Category: 
Scoring

Hi all,

I've recently been asked to try to use RosettaScripts for some enzyme design. In this particular case I am trying to use the HBNet mover to predict hydrogen bond network mutations. I have created scripts with just the HBNet mover and also calling the Multiple Pose mover afterwards. However, I am having the same issue. I don't know how to score the resulting binary silent file.

I am trying to select the top 5 results and extract their PDBs.

Some common errors include:

Post Situation: 

str::out_of_range with mpiexec and relax

Category: 
Scoring

I'm doing a very simple relax to optimize and score 100.000 pdb files.

Rosetta was compiled with MPI+MYSQL support. 

If I call the relax application on a single PDB file, it works.

Since I have a 64 core machine + 196 GB RAM (with MPI installed), I would like to relax 63 structures in parallel.
This is the command i'm executing with MPI:

mpiexec -np 63 /rosetta2020/main/source/bin/relax.mpimysql.linuxgccrelease @relax.flags.database

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Interface Analyzer with Glycans

Category: 
Scoring

Hello all, 

            Is it possible to run InterfaceAnalyzer with a structure with Glycans? Everytime I apply the InterfaceAnalyzerMover on my structure I get a segmentation fault. If I just delete the carbohydrates it works just fine. The pose has been processed with all of the usual flags(below). Is there some trick to using glycans and InterfaceAnalyzerMover or can someone point me in the right direction? Thanks so much.

                                                                                                        Drew

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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:

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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:

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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.

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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. 

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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)?

 

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