- This topic has 3 replies, 3 voices, and was last updated 13 years, 10 months ago by Anonymous.
November 24, 2009 at 12:44 am #405Anonymous
Is there a way to dump a pdb to an object instead of a file?
This would allow a script running inside PyMol to update the displayed structure.
If I’m missing something obvious a pointer in the right direction would be appreciated…
December 14, 2009 at 7:20 pm #4275Anonymous
What object are you referring to? PyRosetta uses the Pose object exclusively and PDB file format for input/output. It wouldn’t be too hard to write a Python object that takes in a Pose object however and can interface with PyMol.
We’re still working on integrating PyRosetta with Pymol. There is a script called “PyRosetta-Pymol.py” in the pyrosetta directory which starts to address the issue. If you want to tackle the problem, try starting with that.
January 25, 2010 at 9:01 pm #4316Anonymous
__ I’ve been trying to incorporate PyRosetta into PyMOL. The process is:__
1. in the shell script which launches PyMOL, include:
if [ -f “/u/srballard/PyRosetta/SetPyRosettaEnvironment.sh” ]
2. After PyMOL loads:
–this runs fine
Traceback (most recent call last):
File “/u/srballard/Desktop/PyMOLX11Hybrid.app/pymol/modules/pymol/parser.py”, line 338, in parse
File “/u/srballard/Desktop/PyMOLX11Hybrid.app/pymol/modules/pymol/parsing.py”, line 455, in run_file
File “PyRosetta/PyRosetta-PyMol.py”, line 56, in
from rosetta import *
File “/u/srballard/PyRosetta/rosetta/__init__.py”, line 14, in
import utility, core
File “/u/srballard/PyRosetta/rosetta/utility/__init__.py”, line 1, in
from _rosetta_utility import *
ImportError: dlopen(/u/srballard/PyRosetta/rosetta/utility/_rosetta_utility.so, 2): Library not loaded: libboost_python-xgcc40-mt-1_38.dylib
Referenced from: /u/srballard/PyRosetta/rosetta/utility/_rosetta_utility.so
Reason: image not found
__If anyone can work out why this occurs, or better yet how to fix it, that would be great to know.__
February 7, 2010 at 2:16 am #4338Anonymous
My initial (simple minded) idea was that one might dump a pose to a pdb as a string and then use the PyMol’s read_pdbstr as a easy way to ‘refresh’ the structure displayed in PyMol after its been altered with PyRosetta.
I’ll try to test the PyRosetta-PyMol script after I compile a PyMol with Python 2.5.
> Is there a way to dump a pdb to an object instead of a file?
> This would allow a script running inside PyMol to update the displayed structure.
> If I’m missing something obvious a pointer in the right direction would be appreciated…
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