Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)
Hi Bob, On 10 Feb 2014, at 20:43, Robert Hanson hans...@stolaf.edu wrote: I haven't explored JyMOL, but I guess it has the potential to do that, and like Jmol could probably be converted to JavaScript. I don't know. But I'm guessing it uses WebGL which isn't an adequate solution in my opinion. Thomas...? JyMOL actually runs native PyMOL graphics (without the Python) using Java and JOGL. It can't just be converted to JavaScript, but provides a JavaScript API similar to our Python API. WebGL is a different, but very interesting story. Why do you think it's not adequate? Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ 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] Corrupted IDTF file from small molecule (sticks representation)
My only real objection is that WebGL is not supported on iOS in browsers. Beyond that, I probably just don't know enough about it to do it right. On Wed, Feb 12, 2014 at 1:50 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Bob, On 10 Feb 2014, at 20:43, Robert Hanson hans...@stolaf.edu wrote: I haven't explored JyMOL, but I guess it has the potential to do that, and like Jmol could probably be converted to JavaScript. I don't know. But I'm guessing it uses WebGL which isn't an adequate solution in my opinion. Thomas...? JyMOL actually runs native PyMOL graphics (without the Python) using Java and JOGL. It can't just be converted to JavaScript, but provides a JavaScript API similar to our Python API. WebGL is a different, but very interesting story. Why do you think it's not adequate? Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Corrupted IDTF file from small molecule (sticks representation)
Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are supported. Hope that answers your question, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 9, 2014, at 12:26 PM, Riccardo mitm...@gmail.commailto:mitm...@gmail.com wrote: Hello to the PyMOL mailing list, this is my first post. I need to ask if there is some reason for which PyMOL fails to export a good idtf file from a small molecule visualized as sticks. In this case, neither IDTFConverter nor MeshLab (under Linux and Windows) can convert the file in an u3d file, because these two programs reject the PyMOL idtf output, reporting an error. Different if I export the idtf from Jmol: in this case, the file is dozens of times bigger in size than PyMOL's output, and the u3d is generated without errors with sticks representation. I noticed that, only when the style is set to cartoon (for proteins, not small molecules), the idtf file is good, but always without any other graphic representation different from the cartoon. Is this a limit for PyMOL idtf exporter, for which an implementation is required? Thanks a lot, Riccardo Volpe [http://lh3.googleusercontent.com/-l_W2_-XQUNc/AAI/AAA/aYl9hZ3l-PU/s30-c/photo.jpg] ChemBioScripting | X3D PyMOL Molecule Viewerhttp://chembioscripting.hol.es/ | Gioacchino Riccardo Volpe -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Corrupted IDTF file from small molecule (sticks representation)
So in the mean time, Riccardo, I guess what you are already using: xxx.pse -- JmolData.jar -- idtf is your best bet. Q: What sort of size of PDF file are you seeing in the end? Q: Do you see this a practical and useful in some way? If so, in what way? Bob Hanson -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Corrupted IDTF file from small molecule (sticks representation)
Riccardo, like me, I think you forgot to reply all. (I gather that from your addressing two of us and not just me.) Yes, Jmol does that. It's not perfect, but it's a respectable amount of PyMOL functionality. This is actually something that Warren and I talked about not too long before his untimely death, and it took a trip last January for me to the Weizmann Institute to get my head around. See http://ispcsrv.weizmann.ac.il/a2jmolb/browse It's actually pretty fun to see PyMOL sessions appear in pure JavaScript! There will always be aspects of biomolecular visualization that only PyMOL can reproduce, and that I have no hope of implementing in Jmol, still it's a good challenge to try, and we feel it fills a need in the area of interactive web content, at least until Schrodinger comes out with their own web viewer, which I'm guessing is not far off... (Sorry, that was a looong sentence!) I haven't explored JyMOL, but I guess it has the potential to do that, and like Jmol could probably be converted to JavaScript. I don't know. But I'm guessing it uses WebGL which isn't an adequate solution in my opinion. Thomas...? Bob Hanson On Mon, Feb 10, 2014 at 6:49 PM, Riccardo mitm...@gmail.com wrote: @Jared: Hello! Thanks for you reply! I supposed it... So, must be implemented yet; is that the only interested file for that exporting function? Thanks a lot. @Bob: Hello! Nice to hear you here! Thanks. Yes. So JmolData.jar can read a .pse file as is (with lights, transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good. Thanks a lot to you. Regards, Riccardo Volpe *ChemBioScripting | X3D PyMOL Molecule Viewer http://chembioscripting.hol.es *|* Gioacchino Riccardo Volpe* 2014-02-10 23:25 GMT+01:00 Robert Hanson hans...@stolaf.edu: So in the mean time, Riccardo, I guess what you are already using: xxx.pse -- JmolData.jar -- idtf is your best bet. Q: What sort of size of PDF file are you seeing in the end? Q: Do you see this a practical and useful in some way? If so, in what way? Bob Hanson -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Corrupted IDTF file from small molecule (sticks representation)
Hi Riccardo - I guess you are asking if layer1/Ray.c is the only place you'd have to write code to implement IDTF export of spheres, cylinders, etc.? Then I believe the answer is yes. I'm working on a COLLADA implementation as one of my PyMOL Open Source Fellowship projects this year, and have been modeling my code's layout after the function RayRenderVRML2() in that same file. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 10, 2014, at 7:51 PM, Riccardo mitm...@gmail.commailto:mitm...@gmail.com wrote: @Jared: Hello! Thanks for you reply! I supposed it... So, must be implemented yet; is that the only interested file for that exporting function? Thanks a lot. @Bob: Hello! Nice to hear you here! Thanks. Yes. So JmolData.jar can read a .pse file as is (with lights, transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good. Thanks a lot to you. Regards, Riccardo Volpe [http://lh3.googleusercontent.com/-l_W2_-XQUNc/AAI/AAA/aYl9hZ3l-PU/s30-c/photo.jpg] ChemBioScripting | X3D PyMOL Molecule Viewerhttp://chembioscripting.hol.es/ | Gioacchino Riccardo Volpe 2014-02-10 23:15 GMT+01:00 Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org: Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are supported. Hope that answers your question, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 9, 2014, at 12:26 PM, Riccardo mitm...@gmail.commailto:mitm...@gmail.com wrote: Hello to the PyMOL mailing list, this is my first post. I need to ask if there is some reason for which PyMOL fails to export a good idtf file from a small molecule visualized as sticks. In this case, neither IDTFConverter nor MeshLab (under Linux and Windows) can convert the file in an u3d file, because these two programs reject the PyMOL idtf output, reporting an error. Different if I export the idtf from Jmol: in this case, the file is dozens of times bigger in size than PyMOL's output, and the u3d is generated without errors with sticks representation. I noticed that, only when the style is set to cartoon (for proteins, not small molecules), the idtf file is good, but always without any other graphic representation different from the cartoon. Is this a limit for PyMOL idtf exporter, for which an implementation is required? Thanks a lot, Riccardo Volpe [X] ChemBioScripting | X3D PyMOL Molecule Viewerhttp://chembioscripting.hol.es/ | Gioacchino Riccardo Volpe -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Android apps run on
Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)
I'm sorry for the news.. I did not know about DeLano's death ... in November of 2009, I read: I did not know about the Open Source PyMOL Fellowship projects of which Jared has spoken, so I made a web search, finding this http://www.pymol.org/fellowship web page, and so the news, with the date ... I'm Sorry. Yes, Bob, I never used that button to replay to all, sorry! I'm glad to meet you, Bob, and I'm happy to hear that there was cooperation between you and DeLano. I accidentally discovered PyMOL. Nobody has never mentioned boththis opensource programs, PyMOL and Jmol, to the students at my Faculty, before to discover them from me, as well as nobody has never talked about everything on which I'm applying by myself as total self-taught but, surfing the web is a good school, and I saw that, at international level, there are development groups as you, which work on it, and there are publications in this area on PubMed, too. In Pisa I discovered now the Scientific Visualization Unit at CNR (SciVis http://www.scivis.it/), and this is a very good news for me, because it gives me a justification to my efforts in this context. I have learned by myself scripting and what is necessary to bring the 3D chemistry on the web ..., and this only thanks to the web resources and the opensource, to whom I am grateful. I didn't know existed fellowships for this, so the news is totally new for me: thanks Jared! I'd like to see enhanced this area, because I found it rather useful for descriptions, although I would not totally deviate from the research on pharmaceutics ... I like all this areas, Computational Chemistry, pharmaceutical synthesis and Molecular Biology (this latter is my address, chosen for my degree in Pharmaceutical Chemistry and Technology at Faculty of Pharmacy of Pisa University), and would be great merge them together with a PhD. I would like to know of any possibility! I will send the email again, Bob: no, it hasn't an attached 1crn; I have attached 2 files, one of which is the pdf exported from my script (to show you the size of the file and the output, which needs *no-polar hydrogens*to be removed yet), and the other attached file is a zip file with a .tex source, which makes use of media9 LaTeX package instead of movie15, because I proposed you (in that email) to replace movie15 with media9, in the source code of Jmol idtf exporter, being movie15 obsolete, as the LaTeX log file says, compiling 3 times the tex file (media9 requires that the source is compiled two times instead). @ Jared: Yeah, I wanted to know what were all the files affected by that function, to see if I could figure out how to implement the PyMOL idtf exporter, thanks. A big salute and thank you for the information, Riccardo *ChemBioScripting | X3D PyMOL Molecule Viewer http://chembioscripting.hol.es *|* Gioacchino Riccardo Volpe* 2014-02-11 2:54 GMT+01:00 Sampson, Jared jared.samp...@nyumc.org: Hi Riccardo - I guess you are asking if layer1/Ray.c is the only place you'd have to write code to implement IDTF export of spheres, cylinders, etc.? Then I believe the answer is yes. I'm working on a COLLADA implementation as one of my PyMOL Open Source Fellowship projects this year, and have been modeling my code's layout after the function RayRenderVRML2() in that same file. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 10, 2014, at 7:51 PM, Riccardo mitm...@gmail.com wrote: @Jared: Hello! Thanks for you reply! I supposed it... So, must be implemented yet; is that the only interested file for that exporting function? Thanks a lot. @Bob: Hello! Nice to hear you here! Thanks. Yes. So JmolData.jar can read a .pse file as is (with lights, transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good. Thanks a lot to you. Regards, Riccardo Volpe *ChemBioScripting | X3D PyMOL Molecule Viewer http://chembioscripting.hol.es/ *|* Gioacchino Riccardo Volpe* 2014-02-10 23:15 GMT+01:00 Sampson, Jared jared.samp...@nyumc.org: Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are supported. Hope that answers your question, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 9, 2014, at 12:26 PM, Riccardo mitm...@gmail.com wrote: Hello to the PyMOL mailing list, this is my first post. I need to ask if there is some reason for which PyMOL fails to export a good idtf file from a small molecule visualized as sticks. In this case, neither IDTFConverter nor MeshLab (under Linux and Windows) can convert the
[PyMOL] Corrupted IDTF file from small molecule (sticks representation)
Hello to the PyMOL mailing list, this is my first post. I need to ask if there is some reason for which PyMOL fails to export a good idtf file from a small molecule visualized as sticks. In this case, neither IDTFConverter nor MeshLab (under Linux and Windows) can convert the file in an u3d file, because these two programs reject the PyMOL idtf output, reporting an error. Different if I export the idtf from Jmol: in this case, the file is dozens of times bigger in size than PyMOL's output, and the u3d is generated without errors with sticks representation. I noticed that, only when the style is set to cartoon (for proteins, not small molecules), the idtf file is good, but always without any other graphic representation different from the cartoon. Is this a limit for PyMOL idtf exporter, for which an implementation is required? Thanks a lot, Riccardo Volpe *ChemBioScripting | X3D PyMOL Molecule Viewer http://chembioscripting.hol.es *|* Gioacchino Riccardo Volpe* -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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
