pymol-users

[PyMOL] Release of ScriptBox 0.2 for PyMOL

[Kristian R. <kri...@be...>]

Hello PyMOL users,

I have written a small program that lets you select your favorite PyMOL 
script from a comfortable box floating beside your PyMOL window.

ScriptBox 0.2 can be found at:
http://www.rubor.de/bioinf/scriptBox.html

Its my first release, so the program might still have bugs.

BTW, is there any collection of scripts on the internet to browse through?


Kristian Rother

Re: [PyMOL] Release of ScriptBox 0.2 for PyMOL

[Warren L. D. <wa...@su...>]

> I have written a small program that lets you select your favorite PyMOL 
> script from a comfortable box floating beside your PyMOL window.

Kristian, thanks for sharing! 

> ScriptBox 0.2 can be found at:
> http://www.rubor.de/bioinf/scriptBox.html
> 
> Its my first release, so the program might still have bugs.

Specifically, this script may be incompatible with the standard external
GUI since Tcl/Tk/Tkinter does not multi-thread, and currently ScriptBox
fires up its own thread.  However, if you turn off the external GUI, then
the program works fine.

pymol -x ScriptBox.py

If you want to have both GUIs running simulaneously, then try using the
startup directory in modules/pmg_tk (you'll need to modify ScriptBox.py
to have an __init__ method which creates the window, but simply
returns instead of forking a thread or calling mainloop)

[However, if you are currently using the accelerated test version on a
mac, then you can ignore my comments about the external GUI, since it
doesn't yet exist on that platform.]

> BTW, is there any collection of scripts on the internet to browse through?

Clearly there is a consensus that this needs to be done.  I can't do 
it myself, but what I can do is place high visibility links on the
PyMOL web page.  So here goes...

You'll now see a "Scripts" item on the top of http://pymol.sf.net.  This
will take you to a page of submitted links, of which we have exactly one.

Please post your scripts somewhere on the internet and then send in the
URLs!  

By the way, while I personally disfavor GPL, I respect everyone's freedom
to choose their own license for their own code.  Please understand though
that I can't add a GPL component like ScriptBox to PyMOL without 
compromising on the overall PyMOL vision.  PyMOL exists to serve ALL
scientists, institutions, and companies -- including closed-source
software companies.

However, I do encourage use of PyMOL with GPL packages such as OELib and
GROMACS, and I have no objection to people distributing PyMOL derivatives
as GPL or even closed-source, particularly if they want to prevent their
code from being swallowed by the blue vortex ; ).  As for PyMOL, well,
that contingency has been part of the experiment from day one...

Cheers,
Warren

Re: [PyMOL] Update to ScriptBox 0.3 for PyMOL

[Kristian R. <kri...@be...>]

Hello PyMOL users,

As suggested by Warren, i have made some improvements to the ScriptBox, 
which should integrate better into PyMOL now,

>>I have written a small program that lets you select your favorite PyMOL 
>>script from a comfortable box floating beside your PyMOL window.

The URL is still the same:

>>http://www.rubor.de/bioinf/scriptBox.html
On my page, there is also a 'quick and dirty' hack for PyMOL.
FilePipe.py allows to execute PyMOL commands from a shell. It starts its 
own thread and reads lines from a text file. This doesn't work well, but 
it works.
Does anyone have a better idea to do this?


> If you want to have both GUIs running simulaneously, then try using the
> startup directory in modules/pmg_tk (you'll need to modify ScriptBox.py
> to have an __init__ method which creates the window, but simply
> returns instead of forking a thread or calling mainloop)

Thanks, this works in fact really well.


     Kristian