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PyRosetta

hbond_sr_bb, hbond_lr_bb, fa_intra_rep energies from ScoreFunction()

Category: 
PyRosetta

I would like to compute the whole energy of a pose object by accumulating the individual energy terms. 

I have a POSE object, and a scoring fucnction called SCOREFXN. What i do is the following: 

Post Situation: 

Creating rotamers, computing pairwise and total energies

Category: 
PyRosetta

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:

Post Situation: 

Libmini crashes after protocol run

Category: 
PyRosetta

Hi, 

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. 

Thanks,

Will

Post Situation: 

Writing out individual residues to a pdbfile

Category: 
PyRosetta

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 [1]: from rosetta.core.io.pdb import dump_pdb

Post Situation: 

basic scoring issues

Category: 
PyRosetta

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:

Post Situation: 

can't find toolbox module

Category: 
PyRosetta

 

Hi!

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.

Post Situation: 

Relaxing experimental structure

Category: 
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:

Post Situation: 

Creating FeatureReporters in PyRosetta

Category: 
PyRosetta

Hi,

I'm trying to implement FeatureReporters in PyRosetta (compiled from release 3.5). I'm implementing the following methods:

  • write_schema_to_db
  • report_features

Both of these methods get utility::sql_database::sessionOP as input. When I try to run the code I get the following error message:

Post Situation: 

antibody.py

Category: 
Loop Modeling
PyRosetta

Dear all,

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):

Post Situation: 

PyRosetta memory footprint

Category: 
PyRosetta

Hi All,

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:

Post Situation: 

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