Hi Mike.
Try the example pdfs at:
http://pymolwiki.org/index.php/3d_pdf
1zqa PDF <http://www.fys.ku.dk/~tlinnet/1zqa.pdf>
beamer 1zqa PDF <http://www.fys.ku.dk/~tlinnet/beamer_1zqa.pdf>
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
2013/3/13 Mike Marchywka <marchy...@hotmail.com>
>
>
>
> ----------------------------------------
> > From: blaine-moo...@ouhsc.edu
> > To: tlin...@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-moo...@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 [tlin...@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-moo...@ouhsc.edu<mailto:
> blaine-moo...@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-moo...@ouhsc.edu<mailto:blaine-moo...@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
> >
> >
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_mar<
> https://urldefense.proofpoint.com/v1/url?u=http://p.sf.net/sfu/appdyn_d2d_mar&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=e69f9a186785d4669c6f642dfd0cf9e233a0733becb22fce98f1b2216549c40c
> >
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:
> PyMOL-users@lists.sourceforge.net>)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users<
> https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-users&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0A&s=27578b0acd8417ee5ad041b8fb3405e11533086c77123f6c89d8eb5ab3687a96
> >
> > 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
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_mar
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
