Very interesting features!
I have never tried and was trying to do it, following the tutorial in pymolwiki
but at :
* Save your molecule to an IDTF file in PyMOL:
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 <tlin...@gmail.com>
A: Mike Marchywka <marchy...@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
1zqa PDF
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.
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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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