Eran Hodis wrote: > Bob, > > We emailed Warren about this as well, hoping to discover from him > something similar to Jmol's State function. > PyMol uses binary serialization to dump the entire structure of all the classes.
> 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. right -- exactly. Go for that. But it may be a compromise -- for example, not just loading all the atoms and their properties, but loading the PDB file. > > 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] > <mailto:[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 > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > >Don't miss this year's exciting event. There's still time to save > $100. > >Use priority code J8TL2D2. > > >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-users mailing list > >[email protected] > <mailto:[email protected]> > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > 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 > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save > $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > [email protected] > <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
