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Cutout part of a protein

Category: 
PyRosetta

Hello People,

 

I am trying to find a way to cut out part of a protein and save to a new .pdb file.

 

So i have a protein and i want to cut out a section (from amino acid 315 to 330 for example), and save that cut out (and maintain the original 3D structure) into a new .pdb file.

 

I tried searching if there is a built-in PyRosetta function/method that does this, or if there is a script that does this, but i could not find.

 

Anyone can help me or guide me?

 

Post Situation: 

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: 

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