# Solved

The problem has been solved

## r_frag_quality

Category:
Fragment Generation

Hi everyone,

I would like to assess my designs using the fragment quality metric and biased forward folding. In both cases Rosetta documentation suggests to use the r_frag_quality application. However I cannot find it in my locally compiled versions of rosetta (for example in rosetta_src_2020.08.61146_bundle). Can anybody help?

Thanks

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## arm64 processor is not supported for new M1 chip

Category:
Compilation

Hello,

I'm fairly new to dealing with these kinds of software installation and compilation. I want to download the latest release of rosetta on my M1 Macbook air laptop and I've run into the following problem when I try to compile the rosetta bundle in the Rosetta/main/source directory:

source % ./scons.py -j6 mode=release bin

Traceback (most recent call last):

File "/Users/martinfe/Rosetta/main/source/SConstruct", line 183, in main

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## RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()

Category:
Docking

Dear Rosetta Users,

I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:

[FILE]: src/core/conformation/util.cc

[LINE]: 654

[START_MESSAGE]

[ ERROR ] UtilityExitException

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## clean_pdb.py

Category:
Structure prediction

Hi guys,

I just installed Rosetta in my Mac and trying to do the ResettaCM following the tutorials (https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial). when i do the first step: Rosetta/demos/tutorials/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A

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## MPI optimization on TACC stampede2 HPC

Category:
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.

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## Individual Residue Energy

Category:
Scoring

Hi everyone,

I'm trying to get the energies of individual residues in a pose and am encountering an error that I can't seem to find much information on. Here is a sample of my script:

from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.scoring import *

pyrosetta.init('-ignore_zero_occupancy false')

pose = pose_from_pdb(pdb_file)

sfxn = create_score_function('ref2015.wts')

score = pose.energies().residue_total_energy(1)

And here is the error I encounter:

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## [Solved] Resetting a pose with RigidBodyTransMover

Category:
Docking

I'm trying to seperate a protein-protein complex, apply residue labels based on core/surface/boundary layer definitions, and then reset the protein-protein complex for design. My first thought was to use the RigidBodyTransMover, however, I cannot perform the reverse rigid body translation to recombine the protein-protein complex; the ouput file has the proteins out of contact. I'm unfamiliar with the coordinates, but am noticing that the end coordinate differs after back transformation:

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## Docking high and low resolution

Category:
Docking

Hello,

I need to know about the method that is used for both high and low resolution docking. I know it is markov chain monte carlo, but I need to know in more details. Could you please provide me with a paper or any other resources about the method used for docking (in details)?

Thank you very much

Post Situation:

Category:
Docking

Hi,

Post Situation: