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. 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: [email protected] 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 [[email protected]] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: [email protected] 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) <[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]> 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 ([email protected]<mailto:[email protected]>) 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/[email protected]<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. 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