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Cannot run binaries after successful compilation

Submitted by ac.research on Mon, 2017-08-14 02:56
Category: 
Compilation

Dear all,

I have been trying to compile rosetta 3.8 for a while now without success (meathod worked will with 3.7). I have a 17.04 Ubuntu Gnome Operating System.

Compile Commands:

sudo apt install zlib1g-dev scons build-essential -y
tar -xvzf rosetta_src_3.8_bundle.tgz
cd {ROSETTA}/main/source
./scons.py mode=release bin

 

Result:

Successfully compiles everything, no errors printed.

 

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Rosetta 3 - General

Getting error with Rosetta "antibody.linuxgccrelease" command

Submitted by Sunyp_IM on Mon, 2017-08-07 19:40
Category: 
Structure prediction

Dear all, 

I installed ROSETTA3 (rosetta_src_2017.08.59291_bundle) on my centos 7 system. The install process seemed ok without error.

when I use the antibody.linuxgccrelease to prediction antibody structure according to the tutorial in the Nature Protocol 2017, 12(2),401 paper with the follow commad:

antibody.linuxgccrelease -fasta antibody.fasta -exclude_homologs -exclude_homologs_cdr_cutoff 95 -exclude_homologs_fr_cutoff 90 -antibody::grafting_database $ROSETTA/tools/antibody | tee grafting.log
 

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Rosetta 3 - Applications

How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS?

Submitted by Sunyp_IM on Thu, 2017-07-27 01:07
Category: 
Compilation

Dear all,

The "How To Read These Tutorials" section (https://www.rosettacommons.org/demos/latest/tutorials/How_To_Read_These_Tutorials/Tutorial_Setup) of the tutorial of Rosetta  requires the following environment variables are set: 

 

env $ROSETTA3=the path to your Rosetta/source directory

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Rosetta 3 - General

Did RosettaScripts recently switch to fully parallel MPI?

Submitted by beowulfey on Thu, 2017-07-13 09:02
Category: 
Structure prediction
Design

Hi, trying to figure out if something isn't working properly or if it's working as intended and I missed it. I was using the Topology Broker via Rosetta Scripts from the 2016/Week 46 build of Rosetta and when I ran my script via MPI, it would create one nstruct per core, not including the controlling core. I was able to see this in the log; different commands were marked with (0), (1), (2) etc, for presumably which core the message came from. So if my command was: 

mpiexec -np 4 rosetta_scripts @flags -nstruct 10

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Rosetta 3 - Build/Install

Fragment Quality

Submitted by ac.research on Mon, 2017-07-10 10:23
Category: 
PyRosetta

Dear All,

 

I am trying to measure the quality of the 9-mer fragment file in order to debug the Abinitio fold of a structure I have designed. I am trying to do it in PyRosetta.

 

This is my script so far: 

#Choose Fragment
fragset = ConstantLengthFragSet(9)
fragset.read_fragment_file('9-mer')

#Setup Calculator
calc = FragQualCalculator(fragset , 1.0 , 30.0)

Am I in the right track?

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PyRosetta - General

How To Read PyRosetta Documentation - GenericMonteCarloMover as example

Submitted by ac.research on Wed, 2017-07-05 09:08
Category: 
PyRosetta

Dear All,

Is it possible to explain how to read these PyRosetta documents? it seems they show what each function takes, but it is not clear what are these arguments specifically and where to get them from.
URL: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.simple_moves.html#GenericMonteCarloMover-apply

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PyRosetta - General

PyRosetta FastDesign

Submitted by ac.research on Tue, 2017-07-04 10:23
Category: 
Design

Dear Community,

 

I have been trying to implement FastDesign in PyRosetta. This is my code so far, I could not find documentation or examples to help me get the code running:

 

x = FastDesign()
x.apply(pose)

 

I get the folloing error:

Segmentation fault (core dumped)

 

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PyRosetta - General

RosettaHoles for PyRosetta - Void Detection/Scoring

Submitted by ac.research on Sat, 2017-07-01 11:28
Category: 
Design

Dear All,

 

Is there a mover in PyRosetta for scoring/detecting/desining a protein's core especially getting rid of voids?

 

I understand there was a RosettaHoles, which i cannot find in Rosetta 3.8 (where did it go)? Nor any info about it and how to use it, or its .cc file so i can try and write something similar in python.

 

I tried RosettaVIP in C++, but i could not get it to work properly (get rid of voids), nor could i find something similar in PyRosetta.

 

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PyRosetta - General

SASA of pose

Submitted by ac.research on Mon, 2017-06-26 03:55
Category: 
PyRosetta

Dear All,

 

Is there a way to isolate or select the different structure layers from the pose according to their SASA (surface accessable surface area) in PyRosetta?

 

I have a python script that can do this from a .pdb file, but is there a way to do it from a PyRosetta pose?

 

I read that there are movers called LayerSelector and SelectBySASA both in Rosetta for Rosetta Script, is there their equivilent in PyRosetta?

 

Thank you

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PyRosetta - General

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