Riccardo, like me, I think you forgot to "reply all." (I gather that from your  addressing two of us and not just me.)

Yes, Jmol does that. It's not perfect, but it's a respectable amount of PyMOL functionality. This is actually something that Warren and I talked about not too long before his untimely death, and it took a trip last January for me to the Weizmann Institute to get my head around.  See http://ispcsrv.weizmann.ac.il/a2jmolb/browse  It's actually pretty fun to see PyMOL sessions appear in pure JavaScript!

There will always be aspects of biomolecular visualization that only PyMOL can reproduce, and that I have no hope of implementing in Jmol, still it's a good challenge to try, and we feel it fills a need in the area of interactive web content, at least until Schrodinger comes out with their own web viewer, which I'm guessing is not far off... (Sorry, that was a looong sentence!)

I haven't explored JyMOL, but I guess it has the potential to do that, and like Jmol could probably be converted to JavaScript. I don't know. But I'm guessing it uses WebGL which isn't an adequate solution in my opinion. Thomas...?

Bob Hanson

On Mon, Feb 10, 2014 at 6:49 PM, Riccardo <mitma07@gmail.com> wrote:
@Jared: Hello! Thanks for you reply! I supposed it... So, must be implemented yet; is that the only interested file for that exporting function? Thanks a lot.

@Bob: Hello! Nice to hear you here! Thanks.
Yes. So JmolData.jar can read a .pse file as is (with lights, transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good.

Thanks a lot to you.

Riccardo Volpe

 ChemBioScripting | X3D PyMOL Molecule Viewer | Gioacchino Riccardo Volpe

2014-02-10 23:25 GMT+01:00 Robert Hanson <hansonr@stolaf.edu>:

So in the mean time, Riccardo, I guess what you are already using:

xxx.pse -- JmolData.jar --> idtf

is your best bet.

Q: What sort of size of PDF file are you seeing in the end?
Q: Do you see this a practical and useful in some way?  If so, in what way?

Bob Hanson

Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN

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