From angel.herraez at uah.es Wed Dec 9 12:12:05 2015 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Wed, 9 Dec 2015 14:12:05 -0300 Subject: [Proteopedia] using pre-prepared PNGJ file in Proteopedia Message-ID: <566860E5.24880.2D1C6A91@angel.herraez.uah.es> Dear Proteopedians, I am interested on the possibility of uploading and using in Proteopedia a file prepared in Jmol application and saved to the PNGJ format. These files have a PNG extension. I tried uploading to Proteopedia, it is seen as an image (ok), then I create a scene and choose that "image" as the source of molecule. JSmol loads it and finds the internal pdb or mol file, however the customized style, color, orientation, contained in the PNGJ file is lost since SAT applies its own default rendering. So my question: is there a way to preserve the custom style (state script saved as part of the PNGJ file) and avoid the default Proteopedia/SAT styling? Thans for any hints, Angel From jaime.prilusky at weizmann.ac.il Thu Dec 10 14:30:33 2015 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Thu, 10 Dec 2015 19:30:33 +0000 Subject: [Proteopedia] using pre-prepared PNGJ file in Proteopedia In-Reply-To: <566860E5.24880.2D1C6A91@angel.herraez.uah.es> References: <566860E5.24880.2D1C6A91@angel.herraez.uah.es> Message-ID: Dear Angel, Drag and drop a PNGJ file on the JSmol applet of SAT. Let me know how it goes, since here might be a conflict when saving the internal structure file, at the time of saving the new scene. Eventually, we can try to implement the missing pieces. Jaim __ Dr Jaime Prilusky R&D Bioinformatics and Data Management mail: Jaime.Prilusky at weizmann.ac.il OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) > On 9 Dec 2015, at 7:12 PM, Angel Herr?ez wrote: > > Dear Proteopedians, > > I am interested on the possibility of uploading and using in Proteopedia a file > prepared in Jmol application and saved to the PNGJ format. > > These files have a PNG extension. I tried uploading to Proteopedia, it is seen > as an image (ok), then I create a scene and choose that "image" as the > source of molecule. > JSmol loads it and finds the internal pdb or mol file, however the customized > style, color, orientation, contained in the PNGJ file is lost since SAT applies > its own default rendering. > > So my question: is there a way to preserve the custom style (state script > saved as part of the PNGJ file) and avoid the default Proteopedia/SAT > styling? > > Thans for any hints, > > Angel > > > _______________________________________________ > Proteopedialist-for-users mailing list > Proteopedialist-for-users at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users From angel.herraez at uah.es Thu Dec 10 18:51:43 2015 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Thu, 10 Dec 2015 20:51:43 -0300 Subject: [Proteopedia] using pre-prepared PNGJ file in Proteopedia In-Reply-To: References: <566860E5.24880.2D1C6A91@angel.herraez.uah.es>, Message-ID: <566A100F.23059.55CE480@angel.herraez.uah.es> Thanks, Jaime It works in the SAT, but the saved scene later renders in the page with a mixture, a deviation of the original rendering and orientation. I will investigate and report details next week. I have no more available time now. On 10 Dec 2015 at 19:30, Jaime Prilusky wrote: > Drag and drop a PNGJ file on the JSmol applet of SAT. From jaime.prilusky at weizmann.ac.il Thu Dec 24 08:16:23 2015 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Thu, 24 Dec 2015 13:16:23 +0000 Subject: [Proteopedia] Proteopedia Read-Only mode on December 26th Message-ID: Dear Proteopedians, On Sunday, December 26, Proteopedia will remain on Read-Only for most of the day, to allow us to switch the current hardware. If everything goes Ok (why it shouldn't?) , Proteopedia will resume the editing capabilities on a server with more disk space. In the meantime, Merry Christmas and a Happy New Year! Jaim __ Dr Jaime Prilusky R&D Bioinformatics and Data Management Skype: jaime.prilusky.wis mail: Jaime.Prilusky at weizmann.ac.il OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -------------- next part -------------- An HTML attachment was scrubbed... URL: