The problem has been solved
Dear All,
I am trying to use the BluePrintBDR() for De Novo Design. I am trying to use with it a constraints file to guide the desin towards a certain topology. This is my code so far:
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
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
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?
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
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)
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.
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
Dear all,
I am new to rosetta. I am studying the Rosetta tutorials and I am there is a problem with output path control. I followed the tutorial 4 (controlling input and output) and type the following command in the section "Setting output paths" of this tutorial into my CentOS 7 linux shell:
$> $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb -out:pdb -out:path output_files
generate_nonstandard_residue_set is giving me an error I don't understand. Can anyone tell what I'm doing wrong here?
In [2]: %paste
from rosetta import *
from pyrosetta import *
init()
params_paths = utility.vector1_string()
params_paths.extend(["GUA.params"])
In [3]: nonstandard_residue_set = generate_nonstandard_residue_set( params_paths )
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