PyRosetta + PyMol

[Anonymous]

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…

Thanks!

-da

[Anonymous]

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.

Good luck!

[Anonymous]

__ 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” ]
then
source /u/srballard/PyRosetta/SetPyRosettaEnvironment.sh
PyRosetta=1
fi
2. After PyMOL loads:

PyMOL>run SetLibPaths.py

–this runs fine

PyMOL>run PyRosetta/PyRosetta-PyMol.py

Traceback (most recent call last):
File “/u/srballard/Desktop/PyMOLX11Hybrid.app/pymol/modules/pymol/parser.py”, line 338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File “/u/srballard/Desktop/PyMOLX11Hybrid.app/pymol/modules/pymol/parsing.py”, line 455, in run_file
execfile(file,global_ns,local_ns)
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.__

[Anonymous]

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…
>
> Thanks!
>
> -da

[Author]

Posts