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I am trying to get pymol mover to work in jupyter notebooks along with pyrosetta. I am working on windows 10 using a linux subsystem.
PyRosetta works great. I have installed pymol via anaconda3 and I have files that are a part of pymol that I can see in my terminal. When I run the following
from pyrosetta import PyMOLMover
pymol = PyMOLMover()
I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis.
I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.
Hello Rosetta community
I am trying to install Pyrosetta3.7 in Linux-windows. The installation appears to go without a hitch. But then when I run the self-test.py script, all tests fail. Error messages look like the one below
I've been trying to create a pose with trans-ACPC, but when I use the X[TAC] in the sequence, it doesn't seem to know what residue it is. I know there's a params file for it... I tried loading a pdb structure with ACPC in it as my pose to see what'd happen and it says that:
"ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta)."
I am using PyRosetta to minimize several complexes and obtain the rosetta calculated energy values. In order to obtain all the rosetta scoring terms, I am using the get_fa_scorefxn function. Whereas I want to retain all the scoring terms, the only option that seems available to see all of them is with the following lines:
scorefxn = get_fa_scorefxn()
pose = pose_from_pdb(<minimized_complex_pdb>)