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arm64 processor is not supported for new M1 chip

Submitted by mart_ger on Mon, 2021-03-29 11:36
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

scons: Reading SConscript files ...

Traceback (most recent call last):

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

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Rosetta 3 - Build/Install

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

Submitted by sam_dc on Thu, 2021-03-25 09:32
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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Rosetta 3 - Applications

clean_pdb.py

Submitted by duz on Wed, 2021-03-24 13:36
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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Rosetta 3 - General

MPI optimization on TACC stampede2 HPC

Submitted by rlwoltz on Tue, 2021-03-16 18:07
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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Rosetta 3 - General

Individual Residue Energy

Submitted by Peik on Fri, 2021-02-19 10:13
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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PyRosetta - General

[Solved] Resetting a pose with RigidBodyTransMover

Submitted by bjharris on Wed, 2021-01-13 14:01
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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Rosetta 3 - Applications

Docking high and low resolution

Submitted by nasim.soltani58 on Thu, 2020-12-17 10:26
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

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PyRosetta - Applications

Assesing the docking

Submitted by nasim.soltani58 on Sat, 2020-12-05 21:19
Category: 
Docking

Hello,

I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:

Name of Chain_1: predicted.pdb
Name of Chain_2: true.pdb
Length of Chain_1:  289 residues
Length of Chain_2:  579 residues

 

TM-score= 1.00000 (if normalized by length of Chain_1)
TM-score= 0.49914 (if normalized by length of Chain_2)

 

 

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PyRosetta - General

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