Hi Gianluigi. The line goes into LaTeX. I guess it tells something about the center of the molecule, or some light settings.
Have you tried: save pymol.idtf, all (or some other selection) The line should come out in the command window, like the get_view command. Jmol automatically write this line in the .tex file it exports. Best Troels 2013/3/13, Gianluigi Caltabiano <chimic...@yahoo.it>: > > > 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. >>> 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 -- Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 ------------------------------------------------------------------------------ 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
