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Approximating CHARMM energy by the rosetta scoring function

Submitted by ajasja on Fri, 2014-06-20 02:16
Category: 
Scoring
PyRosetta

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič

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PyRosetta - General

What build to download?

Submitted by ajasja on Wed, 2014-06-18 09:10
Category: 
PyRosetta

In the list of full releases there are a number of newer files than what is listed on the pyrosseta.org/dow.

Are these also stable releases?  What does the monolith mode mean? (as in mode=release.branch=release.monolith.html)  And what is the namespace mode?

Thank you for satisying my curiosity,
Ajasja Ljubetič

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PyRosetta - Build/Install

Error runining PyRosetta "undefined symbol: __sinh_finite"

Submitted by ajasja on Wed, 2014-06-18 08:09
Category: 
PyRosetta

Hi all!
*OS*: Mint Linux 17,
64bit Linux (3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
*Python*: Python 2.7.7 |Continuum Analytics, Inc.| (default, Jun 2 2014, 12:34:02) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
*PyRosseta*: PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795

While trying to import PyRosseta I get the following error:
"ImportError: rosetta/libmini.so: undefined symbol: __sinh_finite"

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PyRosetta - Build/Install

Enabling N-Linked Glycans

Submitted by jzabilansky on Thu, 2014-06-05 11:51
Category: 
PyRosetta

Hello,

I am currently trying to analyze a crystal structure that has various N-linked Glycans attached and would like to be able to work with these glycans in PyRosetta. However, if I try to work with the structure without cleaning it I receive the error message:

>>>pose = pose_from_pdb("my_molecule.pdb")
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types

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PyRosetta - Applications

Architecture Problem

Submitted by jzabilansky on Wed, 2014-06-04 13:30
Category: 
PyRosetta

Hello,

I am currently trying to work with PyRosetta on my system:

Mac OS X 10.9.1 64 Bit

with Python 2.7.6 64 Bit

I've downloaded PyRosetta.MacOSX.Lion-r55641.64Bit and after decompressing the file, setting the PyRosetta Environment and opening Python, I run import rosetta and get the following error.

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PyRosetta - Build/Install

Problem with PyRosetta install

Submitted by fcazals on Wed, 2014-05-21 09:11
Category: 
PyRosetta

Dear Rosetta gurus,

I thought I was pretty fluent in python, yet, I stumble on serious problems while trying to use D020_Pose_scoring.py -- essentially a rosetta package is missing.
thus, I had two questions:

1. do I miss a key install recommendation?
2. since I am interested in scoring, is there a tutorial on the C++ functionalities offered for scoring?

thanks a lot and best regards, Frederic Cazals.

-- we installed rosetta and set the following env. variables:

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PyRosetta - Applications

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