The problem hasn't been solved
I'm trying to run the below script, I'm getting a lot of lines liek the following. I would appreciate your help with that. Thanks.
Dear Developers,
PyMOL has just been updated to use Python 3 by default, thus the PyMOL-RosettaServer.py script to view the structure changes in PyMOL no longer works.
The print statements needs to be changed as well as the 'from cStringIO import StringIO' along with other changes to update the script from python 2 to python 3.
I hope this helps.
I want to code the below scripts using PyRosetta. I'm totally new to Pyrosetta, only starting to read the tutorials today. However, I know Python very well. Anyway, all the scripts seem to be calling the denovo_density.linuxgccrelease binary so I'm guessing, if there's a Pyrosetta class or module built on that, it shouldn't be but a few lines of code.
My qustions are, can it be done? How?
Dear All,
I have designed some protein binders based on pre-structured models.
I have a question regarding parallelizing some of the bash scripts from the refinement and denovo prediction tutorials. They usually rely on GNU parallel to run across many cores, substituting some variable in the script with a number from the GNU parallel run command . I wonder how I can run the same scripts on a server running slurm workload manager, or any other possible multiprocessing strategy using Python.
Hi everyone,
I am using PlaceStub application (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PlaceStubMover) for placing two sets of different stubs on the scaffold.
Also - is Ubuntu 16 LTS the best choice for running rosetta in the cloud ?
Hello,
I am docking a pep to a receptor with two chain, using FlexPepDock ab initio. Both the chains are number starting with 1
In the flag file, I set -flexPepDocking:receptor_chain A,B
However, it ouput the errors such as
protocols.TrialMover: Acceptance rate: 0.02
core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-1, 556-2, 556-3, 557-1!
core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-2, 556-3, 557-1, 557-2!