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Failure in local docking

Submitted by Fei on Thu, 2014-06-26 12:24
Category: 
Docking

Hi all,

I have a set of low resonant protein complex models generated from global docking. I did local docking on each model. Some of them have given the "energy funnel" with its lowest energy structures located around a point, but some don't as the low energy structures are dispersed over the plot, which I guess is a sign of failure in docking. Would this suggest that my starting structures are not good, I mean, not energetically favorable? All these starting models are predicted from XL-mass spec results and a global docking program.

Thanks,
Fei

Post Situation: 
Unsolved
Forums: 
ROSIE - General

Capturing the output of scorefxn.show(pose)

Submitted by ajasja on Fri, 2014-06-20 05:30
Category: 
PyRosetta

I'm using PyRosetta-r21 on Ubuntu togather with IPython 2.0.0 notebooks. This works extremly well, with one small problem:
Some output is redirected to the console in which "ipython notebook" command was started instead of the notebook cell. 
So the question is: is it possible to capture the output of scorefxn.show(pose)?

I have tried to use the example in "test/T007_TracerIO.py"

 

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Unsolved
Forums: 
PyRosetta - General

Possible minor mistakes in SetPyRosettaEnvironment.sh (in r21 for Ubuntu)

Submitted by ajasja on Fri, 2014-06-20 05:10
Category: 
PyRosetta

Dear all,
There may be some minor mistakes in the SetPyRosettaEnvironment.sh in the r21 release of PyRosetta:

On line 34 "export LD_LIBRARY_PATH=$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
$PYROSETTA is not added to the LD_LIBRARY_PATH and "libboost_python.so.1.55.0.so" is consequently not found.
Corrected: "export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
(Or just move the offending so to rosseta subdir)

 

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Unsolved
Forums: 
PyRosetta - Build/Install

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