Hi all,
So there is no way to run and control PyMol from within another python program?
The reason for asking is that we are working on a python platform to
run and evaluate protein-protein docking calculations. It would be a
nice feature to be able to call up interaction surfaces and
protein-protein clusters for display in PyMol and then interact with
them from within our program.
As things are now I'm forced to treat PyMol as I would treat any
molecular graphics program, that is write macros macros for it. This
is of course much less convenient and less flexible compared to
running PyMol from within our python code.
Has anyone been able to run and quit PyMol from within python without
killing the interpreter? Is it possible? How?
Cheers, Johan
> I'm having problems running PyMol from within another Python program.
This is not the recommended way to run PyMOL and may lead to
problems. You can run Python programs within PyMOL as follows:
from the command-line:
pymol example.py # synchronous, in PyMOL module
pymol -r example.py # synchronous in __main__ module
pymol -l example.py # asychronous in a new module
You can also launch python programs from within PyMOL with the commands:
run example.py # synchronous in pymol module
run example.py,main # synchronous in __main__ module
spawn example.py # asychronous in a new module
spawn example.py,global # asychronous in the PyMOL module
spawn example.py,main # asychronous in the __main__ module
see:
help launching
help run
help spawn
> Following the examples in /pymol/examples/devel I have been able to
> launch and controll PyMOL. The problem occur when I try to quit PyMol
> (version. 0.82) however I do it I end up with a fault terminating my
> Python interpreter.
>
> Under Redhat 7.1/Python 2.1 i get a segmentation fault and under
> MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same
> result both when quitting from the gui or within python with the
> command cmd.quit()
>
> How can I quit PyMol properly?
I know for a fact that the Mac take-down process is currently
flawed, and frequently gives a bus error. Because it only happens
after you quit the program, its a low priority issue...
Not sure about Redhat.
Warren
