The problem has been solved
I use FastRelax to do refinement for my pose. However, the structure becomes completely different and of bad quality after refinement. why did this happen? I added the original and refined pdb file.
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
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
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
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
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.
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:
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:
Hello,
What is exactly "lbfgs_armijo" (when it passed to MinMover()). Is it gradient descent?
Thank you
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