I'm sorry for the news.. I did not know about DeLano's death ... in November of 2009, I read: I did not know about the "Open Source PyMOL Fellowship projects" of which Jared has spoken, so I made a web search, finding this web page, and so the news, with the date ... I'm Sorry.

Yes, Bob, I never used that button to "replay to all", sorry! I'm glad to meet you, Bob, and I'm happy to hear that there was cooperation between you and DeLano. I accidentally discovered PyMOL. Nobody has never mentioned both this opensource programs, PyMOL and Jmol, to the students at my Faculty, before to discover them from me, as well as nobody has never talked about everything on which I'm applying by myself as total self-taught but, surfing the web is a good school, and I saw that, at international level, there are development groups as you, which work on it, and there are publications in this area on PubMed, too. In Pisa I discovered now the Scientific Visualization Unit at CNR (SciVis), and this is a very good news for me, because it gives me a justification to my efforts in this context. I have learned by myself scripting and what is necessary to bring the 3D chemistry on the web ..., and this only thanks to the web resources and the opensource, to whom I am grateful.

I didn't know existed fellowships for this, so the news is totally new for me: thanks Jared! I'd like to see enhanced this area, because I found it rather useful for descriptions, although I would not totally deviate from the research on pharmaceutics ... I like all this areas, Computational Chemistry, pharmaceutical synthesis and Molecular Biology (this latter is my address, chosen for my degree in Pharmaceutical Chemistry and Technology at Faculty of Pharmacy of Pisa University), and would be great merge them together with a PhD. I would like to know of any possibility!

I will send the email again, Bob: no, it hasn't an attached 1crn; I have attached 2 files, one of which is the pdf exported from my script (to show you the size of the file and the output, which needs no-polar hydrogens to be removed yet), and the other attached file is a zip file with a .tex source, which makes use of media9 LaTeX package instead of movie15, because I proposed you (in that email) to replace movie15 with media9, in the source code of Jmol idtf exporter, being movie15 obsolete, as the LaTeX log file says, compiling 3 times the tex file (media9 requires that the source is compiled two times instead).

@ Jared: Yeah, I wanted to know what were all the files affected by that function, to see if I could figure out how to implement the PyMOL idtf exporter, thanks.

A big salute and thank you for the information,

Riccardo


 ChemBioScripting | X3D PyMOL Molecule Viewer | Gioacchino Riccardo Volpe


2014-02-11 2:54 GMT+01:00 Sampson, Jared <Jared.Sampson@nyumc.org>:
Hi Riccardo -

I guess you are asking if "layer1/Ray.c" is the only place you'd have to write code to implement IDTF export of spheres, cylinders, etc.?  Then I believe the answer is "yes."  I'm working on a COLLADA implementation as one of my PyMOL Open Source Fellowship projects this year, and have been modeling my code's layout after the function RayRenderVRML2() in that same file.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 10, 2014, at 7:51 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.

Regards,
Riccardo Volpe


 ChemBioScripting | X3D PyMOL Molecule Viewer | Gioacchino Riccardo Volpe


2014-02-10 23:15 GMT+01:00 Sampson, Jared <Jared.Sampson@nyumc.org>:
Hi Riccardo -

Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter.  Currently only triangle mesh representations (cartoon, surface) are supported.

Hope that answers your question,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 9, 2014, at 12:26 PM, Riccardo <mitma07@gmail.com> wrote:

Hello to the PyMOL mailing list,
this is my first post.

I need to ask if there is some reason for which PyMOL fails to export a good idtf file from a small molecule visualized as sticks. In this case, neither IDTFConverter nor MeshLab (under Linux and Windows) can convert the file in an u3d file, because these two programs reject the PyMOL idtf output, reporting an error.

Different if I export the idtf from Jmol: in this case, the file is dozens of times bigger in size than PyMOL's output, and the u3d is generated without errors with sticks representation.

I noticed that, only when the style is set to cartoon (for proteins, not small molecules), the idtf file is good, but always without any other graphic representation different from the cartoon. Is this a limit for PyMOL idtf exporter, for which an implementation is required?

Thanks a lot,

Riccardo Volpe



 ChemBioScripting | X3D PyMOL Molecule Viewer | Gioacchino Riccardo Volpe
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