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I just started working with PyRosetta, and i stumbled upon a lot of questions.
I would like to introduce rotamers, and calculate their pairwise energies, and the total energy of the system with given rotamers.
To test, i created a very simple PDB that consist only 2 amino acid.
I have the following code:
I'm currently working on a loop modeling script in PyRosetta, for inclusion as a protocol in InteractiveRosetta. Essentially, the script takes a collection of protein fragments, attempts to insert them into a scaffold using AnchoredGraftMover, and scores each pose. The script works fine, but some time after it finishes running I'll get a message saying that libmini.so has stopped working. Does anyone have any idea why this could be happening? I've included the script below. I'm using PyRosetta 3.
I've recently changed to a more recent version of pyrosetta (upgraded from rosetta_src_2016.18.58680_bundle to rosetta_src_2016.46.59086_bundle). One of my scripts no longer works,as it seems I can no longer find the function "dump_pdb_residue". This function still looks like it exists in the C++ code:
In : from rosetta.core.io.pdb import dump_pdb
I'm keep studying PyRosetta using tutorials from http://www.pyrosetta.org/tutorials
I've got several errors when going through Scoring workshop.
Using Ubuntu 16.04.1 LTS 64-bit, python 2.7.12, IPython 2.4.1, PyRosetta-4
(1) Setting up a custom score function rises an error:
I was not sure if this is 'build/install' question, but it seems that 'general' forum is for more advanced issues..
I'm a beginner in PyRosetta and not really a "tech" person, more wet biologist so sorry if the question is stupid..
Currently using tutorial from http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRosetta_Intro.pdf to try basics of PyRosetta.
I need to measure the Rosetta "energy" of a set of conformations taken from the PDB. Before computing the energy I would like to relax the structures while keeping them as close as possible to the experimental structure. I guess I want something like this. Is that protocal available using PyRosseta? Or I should try to "implement it" my self.
I guess I could do something like:
I'm trying to implement FeatureReporters in PyRosetta (compiled from release 3.5). I'm implementing the following methods:
Both of these methods get utility::sql_database::sessionOP as input. When I try to run the code I get the following error message:
I am using the antibody.py script that comes with PyRosetta (rosetta_src_2016.13.58602_bundle, v3.6) and associated software to generate structural models for VH/VL sequences. For most of the sequences that I am using as input, the script terminates at the antibody_graft step with an error (pasted below):
I have a design protocol implemented in PyRosetta that has a very large memory footprint ~ 4Gb. I ran a python memory profiler on the design script and discovered that the sharp memory consumption increase occurs upon the initialization of PackRotamerMover (I presume this is where the rotamer library is instantiated). I have taken the following measures to reduce the memory consumption with no success: