The problem has been solved
Hello everyone,
I am trying to read a silent file with the function poses_from_silent(), but I get an error about an unrecognized residue:
Hello everyone,
I have checked the D070_Refinement.py* script provided by the Graylab, and I would like to make my own little refinement script based on it and the other guides and tutorials available.
I have, however, run into problems as the ‘MinMover’ method is not available under pyrosetta.rosetta.protocols.simple_moves which prevents me from using the approach outlined in D070_refinement.py to minimize the pose score.
Hello,
I'm having trouble relaxing multiple PDB files via MPI and a pdblist on the TACC Stampede2 cluster. Apparently, only the first file in the pdblist is relaxed, regardless of which PBD file is first in the list. My pdblist has Unix EOL breaks, so that should be good. Do I need to add some flag to relax multiple files in batch using MPI? What am I missing?
Here's the SLURM file I'm using:
-----------------------------------------------------
#!/bin/bash
Hello people,
I my attempt to get a working RosettaDesign protocol, I have come across the RemodelMover() class.
From the Rosetta C++ documentation, the RemodelMover should take a blueprint file in order to specify which residues to remodel. but the RemodelMover() class in PyRosetta has no method to input a blueprint file nor a resfile.
on its own the RemodelMover works without any errors, but would remodel the entire structure.
Hello People,
I have setup a generic montecarlo mover with backrub, but I do not get any accepted nor rejected moves, the following is my code:
backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()
backrub.pivot_residues(pose)
GMC = pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover()
GMC.set_mover(backrub)
GMC.set_scorefxn(scorefxn)
GMC.set_maxtrials(500)
GMC.set_temperature(1.0)
GMC.set_preapply(False)
GMC.set_recover_low(True)
GMC.apply(pose)
Dear Everyone,
I think I heard somewhere that it is possible to capture a video of an abinitio fold from pyrosetta on PyMOL? can someone point me to where I can learn how to do that? I would like to show a folding video of my protein in a presentation.
Thanks
Hello Everyone,
I am trying to preform RosettaDesign using thr FastRelax() mover. As I understand this is the correct mover? or should i be using FastDesign()?
Anyway, What is the difference between the GenericMonteCarloMover() and the GenericSimulatedAnnealer() movers? and which one should I be using with FastRelax() to preform correct RosettaDesign?
I tried both, but both fail to change the structure's sequence. Here is my code:
Hello community,
I have found that I am using Rosetta (C++) only to run Abinitio folding simulations.
Is it possible to isolate just the Abinitio executable from the Rosetta bundle and compile it on its own, rather than keep moving and compiling the entire Rosetta (C++) software?
Hello,
I am trying to dock two proteins but I keep getting this error. I am not sure why its there as there are two chains in the pdb.
Can anyone help?
Thank you
