From angel.herraez at uah.es Wed Jul 9 12:39:43 2014 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Wed, 9 Jul 2014 18:39:43 +0200 Subject: [Proteopedia] problem with uploaded gzipped file Message-ID: <53BD704F.16070.C3C633C@angel.herraez.uah.es> Dear Proteopedians, Has any of you successfully used an uploaded gzipped model file? Today I noticed that this page http://proteopedia.org/wiki/index.php/Gramicidin_Channel_in_Lipid_Bila yer does not load the model, showing errors in file format. I think that JSmol should load the gzipped file, for reasons I have commented in http://proteopedia.org/wiki/index.php/Talk:Gramicidin_Channel_in_Lipid _Bilayer The Java modality loads the file without problem, so it must be something related to loading binary files in JSmol. On the other hand, the model does display in the SAT when you are creating a new scene, like in http://proteopedia.org/wiki/index.php/User:Angel_Herraez/Sandbox_5 but then it does not load in the page itself. Any hints? From jaime.prilusky at weizmann.ac.il Wed Jul 9 14:34:12 2014 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Wed, 9 Jul 2014 18:34:12 +0000 Subject: [Proteopedia] problem with uploaded gzipped file In-Reply-To: <53BD704F.16070.C3C633C@angel.herraez.uah.es> References: <53BD704F.16070.C3C633C@angel.herraez.uah.es> Message-ID: <316D872C-C447-45AE-9E1F-C6EE1BDEC595@weizmann.ac.il> Dear ?ngel, Thank you for the report. I'll take a look to that problem. Jaim On Jul 9, 2014, at 7:39 PM, Angel Herr?ez wrote: > Dear Proteopedians, > > Has any of you successfully used an uploaded gzipped model file? > > Today I noticed that this page > http://proteopedia.org/wiki/index.php/Gramicidin_Channel_in_Lipid_Bila > yer > does not load the model, showing errors in file format. > > I think that JSmol should load the gzipped file, for reasons I have > commented in > http://proteopedia.org/wiki/index.php/Talk:Gramicidin_Channel_in_Lipid > _Bilayer > > The Java modality loads the file without problem, so it must be > something related to loading binary files in JSmol. > > On the other hand, the model does display in the SAT when you are > creating a new scene, like in > http://proteopedia.org/wiki/index.php/User:Angel_Herraez/Sandbox_5 > but then it does not load in the page itself. > > Any hints? > > _______________________________________________ > Proteopedialist-for-users mailing list > Proteopedialist-for-users at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users From jaime.prilusky at weizmann.ac.il Thu Jul 10 04:34:13 2014 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Thu, 10 Jul 2014 08:34:13 +0000 Subject: [Proteopedia] problem with uploaded gzipped file In-Reply-To: <53BD704F.16070.C3C633C@angel.herraez.uah.es> References: <53BD704F.16070.C3C633C@angel.herraez.uah.es> Message-ID: <7FA3E590-3B59-434F-9E06-ED30959E7F89@weizmann.ac.il> Dear ?ngel, Thank you again for bringing this up. The page http://proteopedia.org/w/Gramicidin_Channel_in_Lipid_Bilayer now renders Ok. It took some time to find the source of the problem: the loaded structure had a double gzip compression. This is, uncompressing the .gz file produced another file in gzip status. Only a second gunzip produced a plain text structure content. I?m now checking and dealing with this in Proteopedia, at the time of sending the file to JSmol. Jaim On Jul 9, 2014, at 7:39 PM, Angel Herr?ez wrote: > Dear Proteopedians, > > Has any of you successfully used an uploaded gzipped model file? > > Today I noticed that this page > http://proteopedia.org/wiki/index.php/Gramicidin_Channel_in_Lipid_Bila > yer > does not load the model, showing errors in file format. > > I think that JSmol should load the gzipped file, for reasons I have > commented in > http://proteopedia.org/wiki/index.php/Talk:Gramicidin_Channel_in_Lipid > _Bilayer > > The Java modality loads the file without problem, so it must be > something related to loading binary files in JSmol. > > On the other hand, the model does display in the SAT when you are > creating a new scene, like in > http://proteopedia.org/wiki/index.php/User:Angel_Herraez/Sandbox_5 > but then it does not load in the page itself. > > Any hints? > > _______________________________________________ > 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 Jul 10 04:46:57 2014 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Thu, 10 Jul 2014 10:46:57 +0200 Subject: [Proteopedia] problem with uploaded gzipped file In-Reply-To: <7FA3E590-3B59-434F-9E06-ED30959E7F89@weizmann.ac.il> References: <53BD704F.16070.C3C633C@angel.herraez.uah.es>, <7FA3E590-3B59-434F-9E06-ED30959E7F89@weizmann.ac.il> Message-ID: <53BE5301.8939.FB1E963@angel.herraez.uah.es> Excellent! Thank you. I'm glad to know it was the particular file and not a general problem. Eric, the scenes are not working well; the lipids and water do not display. From emartz at microbio.umass.edu Sun Jul 13 16:57:15 2014 From: emartz at microbio.umass.edu (Eric Martz) Date: Sun, 13 Jul 2014 16:57:15 -0400 Subject: [Proteopedia] problem with uploaded gzipped file In-Reply-To: <7FA3E590-3B59-434F-9E06-ED30959E7F89@weizmann.ac.il> References: <53BD704F.16070.C3C633C@angel.herraez.uah.es> <7FA3E590-3B59-434F-9E06-ED30959E7F89@weizmann.ac.il> Message-ID: <201407132057.s6DKvYN5008466@marlin.bio.umass.edu> Dear Jaim and Angel, Thank you for solving the gzip problem! I was mystified as was Angel. I had downloaded the file from Proteopedia and it loaded just fine into the Jmol application. Eventually I will find time to investigate the scenes in various articles I wrote years ago that still work in Jmol (Java) but don't work in JSmol. I cannot promise when, however. Meanwhile, anyone else is welcome to jump in and fix some of those scenes! Best regards, Eric At 7/10/14, you wrote: >Dear ?ngel, > >Thank you again for bringing this up. The page >http://proteopedia.org/w/Gramicidin_Channel_in_Lipid_Bilayer now renders Ok. > >It took some time to find the source of the >problem: the loaded structure had a double gzip >compression. This is, uncompressing the .gz file >produced another file in gzip status. Only a >second gunzip produced a plain text structure content. > >I?m now checking and dealing with this in >Proteopedia, at the time of sending the file to JSmol. > >Jaim > >On Jul 9, 2014, at 7:39 PM, Angel Herr?ez wrote: > > > Dear Proteopedians, > > > > Has any of you successfully used an uploaded gzipped model file? > > > > Today I noticed that this page > > http://proteopedia.org/wiki/index.php/Gramicidin_Channel_in_Lipid_Bila > > yer > > does not load the model, showing errors in file format. > > > > I think that JSmol should load the gzipped file, for reasons I have > > commented in > > http://proteopedia.org/wiki/index.php/Talk:Gramicidin_Channel_in_Lipid > > _Bilayer > > > > The Java modality loads the file without problem, so it must be > > something related to loading binary files in JSmol. > > > > On the other hand, the model does display in the SAT when you are > > creating a new scene, like in > > http://proteopedia.org/wiki/index.php/User:Angel_Herraez/Sandbox_5 > > but then it does not load in the page itself. > > > > Any hints? > > > > _______________________________________________ > > Proteopedialist-for-users mailing list > > Proteopedialist-for-users at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users > >_______________________________________________ >Proteopedialist-for-users mailing list >Proteopedialist-for-users at bioinformatics.org >http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance: 3D Views in Nature - http://firstglance.jmol.org 3D Protein Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ From angel.herraez at uah.es Tue Sep 23 11:50:43 2014 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Tue, 23 Sep 2014 17:50:43 +0200 Subject: [Proteopedia] announcement: course on Proteopedia with JSmol Message-ID: <542196D3.1291.11801B3@angel.herraez.uah.es> Dear Proteopedia aficionados, For those to happen to be in Spain (or able to come, you will be most welcome), I'd like to share the information about a 2-day course that we will held in Alcal? thanks to a visit of Jaime Prilusky. Dates are October 2nd and 3rd (Thu-Fri), in my University (Alcal? de Henares, in Madrid province) The course will focus on Proteopedia and its uses to study, display and teach macromolecules. It will be run in English and/or Spanish, according to the audience. All information is available at http://bit.ly/P14UAH Hope to see some of you! ? Dr. Angel Herr?ez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcal? E-28871 Alcal? de Henares (Madrid), Spain