Confusion between PyRosetta and Rosetta and how to operate PyRosetta
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4.2 years ago
skim ▴ 50

I am trying to use modelling and docking with rosetta. However, I am comparably fluent in Python, so I would like to use PyRosetta if there are no differences in experience except for the language. However, I am confused with some setup processes. First, how do I link the rosetta binaries with the wrapper pyrosetta? Also, are there any intuitive docs for Pyrosetta to easily see what class/methods I have to use in order to automate mutations (using supercharge to lower pI) and model, dock molecules to see if the protein reacts correctly, and iterate until the pI is maximal acidic while the protein does its function?
On PyRosetta 4:

import pyrosetta; pyrosetta.init()
Found rosetta database at: /media/user/hdd/skim/python/lib/python2.7/site-packages/pyrosetta-4.0-py2.7-linux-x86_64.egg/pyrosetta/database; using it....
PyRosetta-4 2016 [Rosetta 2016 unknown:b1dc16ff17da7a38b52c000abb74f85e4f0333c8 2017-10-25 13:12:29 -0700] retrieved from:
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: Rosetta version from
core.init: command: PyRosetta -ex1 -ex2aro -database /media/user/hdd/skim/python/lib/python2.7/site-packages/pyrosetta-4.0-py2.7-linux-x86_64.egg/pyrosetta/database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1174408211 seed_offset=0 real_seed=-1174408211
core.init.random: RandomGenerator:init: Normal mode, seed=-1174408211 RG_type=mt19937

I got the following messages after I installed pyrosetta without touching anything to Anaconda, but I do not know where to link my rosetta binaries or what this means.

Found rosetta database at: /media/user/hdd/skim/python/lib/python2.7/site-packages/pyrosetta-4.0-py2.7-linux-x86_64.egg/pyrosetta/database; using it....

(/media/user/hdd/skim/python/ is my anaconda python directory)
Thank you very much in advance.

rosetta pyrosetta homology protein Assembly • 1.7k views

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