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pymover = PyMOL_Mover() hangs IPython?

Submitted by cossio on Fri, 2015-04-10 07:38
Category: 
PyRosetta

I followed the instructions here (http://www.pyrosetta.org/pymol_mover-tutorial) to setup the PyMol Mover. But when I try to execute

pymover = PyMOL_Mover()

my IPython session hangs. This statement never finishes execution.

I am using Ubuntu 14.04.1, 64bits, and PyRosetta r48.

Any idea on what's the problem here? I can provide more specs about my system if needed.

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PyRosetta - General

Windows Dunbrack10.lib.bin "out dated"

Submitted by protos_heis on Thu, 2015-02-26 13:35
Category: 
PyRosetta

I seem to be having an issue with getting the binary version of the Dunbrack library to load properly in PyRosetta on Windows and I was wondering if anyone knows if there is a fix for it. Obviously it takes about 30 seconds or so to load the Dunbrack libraries from text so it can turn into a rate-limiting step if you have to read these files a lot.

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London

Submitted by MarkW on Sun, 2015-02-08 14:14
Category: 
PyRosetta

I was wondering of there are any PyRosetta people based in London? Does the forum know of any research people or groups in London? I have a little project in mind....

Thanks

Mark

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pose_from_pdb gives RuntimeError: unidentifiable C++ exception?

Submitted by cossio on Thu, 2014-11-27 14:43
Category: 
PyRosetta

I am following this tutorial:

http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRos...

When I get to the line:

pose = pose_from_pdb("1YY8.clean.pdb")

it results in an error:

RuntimeError Traceback (most recent call last)
<ipython-input-9-755d9c16f3f1> in <module>()
----> 1 pose = pose_from_pdb("1YY8.clean.pdb")

RuntimeError: unidentifiable C++ exception

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Coordinates in pose do not match those in PDB

Submitted by ajasja on Tue, 2014-10-28 12:29
Category: 
PyRosetta

When I load a PDB file the coordinates for residue 18 (R1A) reported by pyrosetta do not match those found in the PDB. An example notebook is attached.

What is the reason for this mismatch and how could I fix it? Is it connected to the internal coordinates of R1A.params?

The CB atoms of the other residues (ALA)  are correct.

Thank you for your help and best regards,

Ajasja

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