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, 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) 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 2300 København S Mobil: +45 60210234 2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edu I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdf. 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 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 -- 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
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. 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.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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.thhttps://urldefense.proofpoint.com/v1/url?u=http://1.thk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63 2300 København S Mobil: +45 60210234 2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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.edumailto:blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
Re: [PyMOL] PyMOL to 3D PDF
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.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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.thhttps://urldefense.proofpoint.com/v1/url?u=http://1.thk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63 2300 København S Mobil: +45 60210234 2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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
Re: [PyMOL] PyMOL to 3D PDF
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.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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.thk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63 2300 København S Mobil: +45 60210234 2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edumailto: blaine-moo...@ouhsc.edu I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdf
Re: [PyMOL] PyMOL to 3D PDF
I hit this link, the image was blank in evince but did come up in Adobe Reader 9 if I click on it ( also prompted for security issues) http://www.fys.ku.dk/~tlinnet/1zqa.pdf It was a bit sluggish but did zoom and rotate acceptably. I guess in this case the more useful thing would be all the information needed to manipulate in the dedicated app, in this case pymol, but it seems the pdf would be helpful for those without it. My concern is that in the past it had not been functional and only served to obscure data that the author intended to be useful to others. It is getting better however :) I may try this again if I have 3D data from pymol or R Thanks. From: tlin...@gmail.com Date: Wed, 13 Mar 2013 13:01:17 +0100 Subject: Re: [PyMOL] PyMOL to 3D PDF To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Mike. Try the example pdfs at: http://pymolwiki.org/index.php/3d_pdf 1zqa PDFhttp://www.fys.ku.dk/~tlinnet/1zqa.pdf beamer 1zqa PDFhttp://www.fys.ku.dk/~tlinnet/beamer_1zqa.pdf Troels Emtekær Linnet Ved kløvermarken 9, 1.thhttp://1.th 2300 København S Mobil: +45 60210234 2013/3/13 Mike Marchywka marchy...@hotmail.commailto:marchy...@hotmail.com From: blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu To: tlin...@gmail.commailto:tlin...@gmail.com Date: Wed, 13 Mar 2013 04:45:59 -0500 CC: pymol-users@lists.sourceforge.netmailto: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.edumailto: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.commailto:tlin...@gmail.com] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.netmailto: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.orghttp://rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091https://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0am=9qhiQpTD7yw1v1CYn82swYWLHkc/kmViU2tMT7DUu9c%3D%0as=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091, and find the protein in the Jmol online viewer. (Just changing to white back ground). Right
Re: [PyMOL] PyMOL to 3D PDF
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.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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
Re: [PyMOL] PyMOL to 3D PDF
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.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=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,
