Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

[Riccardo <mi...@gm...>]

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 <http://www.pymol.org/fellowship> 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 boththis 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 <http://www.scivis.it/>), 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
<http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe*


2014-02-11 2:54 GMT+01:00 Sampson, Jared <Jar...@ny...>:

>  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 <mi...@gm...>
>  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
> <http://chembioscripting.hol.es/> *|* Gioacchino Riccardo Volpe*
>
>
> 2014-02-10 23:15 GMT+01:00 Sampson, Jared <Jar...@ny...>:
>
>> 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 <mi...@gm...> 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
>> <http://chembioscripting.hol.es/> *|* Gioacchino Riccardo Volpe*
>>
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