Very interesting features!

I have never tried and was trying to do it, following the tutorial in pymolwiki but at :

save pymol.idtf,
 *
PyMOL will print a line that looks like:
 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45
I did not have any line like this, not in the window panel neither in the idtf file. Where should I take this line?

I used Hybrid PyMOL 1.5.0.3 on an iMAC.

Thanks,

Gianluigi




Da: Troels Emtekær Linnet <tlinnet@gmail.com>
A: Mike Marchywka <marchywka@hotmail.com>
Cc: pymol-users@lists.sourceforge.net
Inviato: Mercoledì 13 Marzo 2013 13:01
Oggetto: Re: [PyMOL] PyMOL to 3D PDF

Hi Mike.

Try the example pdfs at:
http://pymolwiki.org/index.php/3d_pdf



Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil:
+45 60210234


2013/3/13 Mike Marchywka <marchywka@hotmail.com>



----------------------------------------
> From: Blaine-Mooers@ouhsc.edu
> To: tlinnet@gmail.com
> Date: Wed, 13 Mar 2013 04:45:59 -0500
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] PyMOL to 3D PDF
>
> PyMOL will also save surfaces in addition to cartoons to vwrl and idtf.
> Any representation composed of triangular surfaces should work.
>
> Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of
> JMOL over PyMOL at present.


When you make 3D PDF how well do they display and manipulate? I thought this would be a nice
feature for even 3D plots and IIRC tried it with an example from CRAN's R a while back , I can't remember how it 
came out in detail but seem to recall the pages took a while to load etc and at the time it
was easier to load the data in an app rather than try to publish it that way.  for many actual
pubs, they provide links in supplementary information section and it may be just as easy to publish
a viewer script along with static images for illustration. A plugin would be nice, I always liked CHIME
and that worked well on Internet Explorer about 10 years ago.  


>
>
>
> Blaine Mooers
> Assistant Professor
> Director Macromolecular Crystallography Lab
> Member Stephenson Cancer Center
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
>
> Letter address:
> P.O. Box 26901, BRC 466
> Oklahoma City, OK 73190
>
> Shipping address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
>
> e-mail: blaine-mooers@ouhsc.edu
>
> Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
> X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
> SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0
>
> ________________________________________
> From: Troels Emtekær Linnet [tlinnet@gmail.com]
> Sent: Wednesday, March 13, 2013 4:19 AM
> To: Mooers, Blaine H.M. (HSC)
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] PyMOL to 3D PDF
>
> Yeah.
>
> That is a cool feature, and is kind of the "future" of publishing. :-)
> Or at least, a very powerful tool for teaching.
>
> But it is sad that it only have cartoon export.
> I wish that it could include other representations.
>
> For now I use Jmol, which can export the whole representation in the window.
> I can import small molecules through. Files->Get MOL-> And then CAS number or smiles.
> For proteins I scoop into rcsb.org<https://urldefense.proofpoint.com/v1/url?u=http://rcsb.org&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091>, and find the protein in the Jmol online viewer. (Just changing to white back ground).
>
> Right click in Jmol window->Export file->Export IDTF 3D model.
>
> That saves a .idtf file, and a .tex file ready for LaTeX.
> Rename the .idtf file, so it only ends on .idtf and not: filename.xyz.idtf
>
> Simpy converting the .idtf to .u3d as instructed in, http://www.pymolwiki.org/index.php/3d_pdf<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd>)
> and you are ready to go from the given .tex file. (Removing the last looong comment section.)
>
> With a little practice, it only takes 3 min, to have 3d implementation of your molecule
> in teaching material / beamer presentation.
>
> I wish that could be implemented in PyMOL, and I have been looking for a wish list,
> but I don't know where that exists?
>
> Best
>
> Troels Emtekær Linnet
> Ved kløvermarken 9, 1.th<https://urldefense.proofpoint.com/v1/url?u=http://1.th&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63>
> 2300 København S
> Mobil: +45 60210234
>
>
> 2013/3/12 Mooers, Blaine H.M. (HSC) <Blaine-Mooers@ouhsc.edu<mailto:Blaine-Mooers@ouhsc.edu>>
> I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdf<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd>.
> It has the address to the source code for u3d-1.4.3. I could not compile earlier
> versions of this program on a Mac running Snow Leopard, but I had
> success with this version. I followed Jason's directions for compiling on
> Linux through chmod g+wx. I had installed cmake earlier.
>
> The program compiles fine on Ubuntu 12.04 too.
>
> I used pdflatex from fink with beamer and the movies15 package.
>
>
> Blaine Mooers
> Assistant Professor
> Director Macromolecular Crystallography Lab
> Member Stephenson Cancer Center
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
>
> Letter address:
> P.O. Box 26901, BRC 466
> Oklahoma City, OK 73190
>
> Shipping address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
>
> e-mail: blaine-mooers@ouhsc.edu<mailto:blaine-mooers@ouhsc.edu>
>
> Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
> X-ray<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-%2520X-ray&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=7effd9a5dfc7406f62b612b40552c3ff1db33051b259ac785358f3b82708b6bb> lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=974ecd1dbde88223553e3af3fa345386f53ff187ea5ed34118851de8b8412aa2>
> SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0<https://urldefense.proofpoint.com/v1/url?u=http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn%3D0&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=5d4e1e063b313cb193ae4e8a88770724f44a2c438c85e69e833c3d7f2afa9729>
>
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> Everyone hates slow websites. So do we.
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.net&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=3361c0409e75f1296ae346ff46b307f7fcc1bc6a3274c663c132d87b299bf7a6>
>
>
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