Bob,
We emailed Warren about this as well, hoping to discover from him something
similar to Jmol's State function.
If there is going to be an effort to translate between Jmol and Pymol, then
ideally PyMOL should be able to export a "state script" as well. We don't
think it is sufficient to translate script files. Everyone's script file,
Jmol or Pymol, will look different, but a "state" output will be some sort
of standardized output.
Here's what Warren had to say:
Great! Jmol <-> PyMOL interoperability would be a very desirable and
worthwhile thing. Unfortunately, it will be quite difficult to accomplish.
PyMOL's session file is nothing more than a binary Python pickle. The good
news is that you can extract its contents with Python. The bad news is that
you need Python to extract its contents. Hopefully Jython will be able to
read PyMOL PSE files from Java into Jython data structures. If so, then the
bulk of the effort will be conversion of PyMOL data over to Jmol and back.
Before launching down that track, can you describe what Jmol's state files
are like? It might be easier to read/write them with PyMOL...
Cheers,
Warren
We sent him an example state script from Jmol.
Bob, we agree that the common capabilities should be the first aspect on
which to focus. In particular we are most interested in translating view,
colors, and representations (and of course to do that, translating atom
expressions is necessary).
If anyone else is interested in helping, we would certainly welcome it.
Best,
Eran and Jaime
On Sun, Apr 13, 2008 at 9:41 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Eran, Both Warren and I are very interested in this; if you are game for
> it, by all means go for it. I think what you will find is that certain
> aspects will be easier than others. Warren and I sat down some time ago
> and compared notes, and we were both quite amazed how differently two
> people can conceptualize the same thing. So be ready for some
> frustrations.
>
> The first task Warren and I thought important would be to investigate
> what are the common capabilities -- not to worry about aspects that only
> Jmol or only PyMol do -- and then determine how differently they might
> be implemented. Start simple; be ready to refactor extensively as
> necessary. Then consider some of the fancier aspects of each program.
>
> If you do this, you need to think about whether you want it for the
> applet or just the standalone application.
>
> Looking forward to hearing more about this,
>
> Bob
>
>
> Eran Hodis wrote:
>
> > Has anyone started to create a pymol to jmol translator? In other
> > words, a display in pymol could be ported into jmol.
> >
> > Jaime Prilusky and I are ready to start on such an initiative and want
> > to see if anyone has already started or if anyone wants to help.
> >
> > Warren Delano: if you're reading this, is it possible to have some
> > "state" script output from PyMOL? I'm sure you're saving something
> > like this when you save a session file in PyMOL, but that is in
> > binary. What I'd like to be able to do is to ask PyMOL what is the
> > current state and get a response that tells me the current view, the
> > coloring, and the representations. Barring that, we'll have to just
> > translate PyMOL scripts to Jmol ones...
> >
> > Best,
> > Eran
> >
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>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
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