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Controlling Input in the Tutorial

Category: 
Scoring

Hi All,

I am trying tor learn Rosetta basics using the tutorial https://www.rosettacommons.org/demos/latest/tutorials/input_and_output/input_and_output 

However, when I try like it is instructed in the tutorial following error happens:

Infinity4s-iMac-2:main smbatgevorgyan$ cd demos/tutorials/input_and_output/

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Quick mysql output question

Category: 
Scoring

Hello everyone,

I have compiled rosetta with OpenMPI and MySQL. It works.

I'm using relax to pack+score a few thousand poses but the output will create lots of tables with A LOT of info. I just need to output the pose name and the total score of the pose.

I was wondering which flags should I use (@relax.flags) to output only the SCORE table to MySQL, not the atom coordinates and the rest of the info.

By this I mean the same info as the default.sc file, but sent to a single table in mysql.

Thanks in advance.

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Segfault when loading scorefxn() and load_from_pdb()

Category: 
Scoring
PyRosetta

Hi,

I am trying to load a structure from PDB and then calculate pairwise residue energies between residues in the structure. For this, I want to first load the scorefxn and then the structure (or viceversa), but whenever I try, either of them gives me a segfault, i.e. if I do scorefxn = get_fa_scorefxn(); pose_from_pdb() the latter crashes and if I do the opposite, get_fa_scorefxn() crashes. 

 

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"Rosetta predictions of density, heat of vaporization (∆Hvap) and heat capacity (Cp(l))"

Category: 
Scoring

In the supplementary material of the all-informative 2015 JChem paper The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design  there is one detail that I do not understand and was curious about. Namely, "Rosetta predictions of density, heat of vaporization (∆Hvap) and heat capacity (Cp(l))".

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Warning: Fold tree is not set properly for density scoring

Category: 
Scoring

I am trying to build glycans into a cryoEM density following the Meiler Lab tutorial here: http://www.meilerlab.org/jobs/downloadfile/name/Apr2019_glycan_modeling_talk.pdf

 

Using the provided XML file, I am able to run the job, but I see the following warning throughout the output file:

0mcore.scoring.electron_density.FastDensEnergy: ^[[0m^[[1m[ WARNING ]^[[0m Fold tree is not set properly for density scoring!

 

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Problem with mpirun/mpiexec

Category: 
Scoring

I am attempting to relax a glycosylated protein into a cryoEM map and get the following error: 

"mpirun noticed that process rank 2 with PID 8288 on node imsb0632 exited on signal 9 (Killed)."

I get this error with both mpirun and mpiexec.

Can anyone explain more about what is causing this issue?

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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:

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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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