Re: [ccp4bb] Java based structural database websites
I can second the recommendation of the Mol* project. Some of the data which is used for Olderado and Vivaldi is now part of the wwPDB validation report. This data is available from the PDBe API http://www.ebi.ac.uk/pdbe/api/doc/validation.html Additional data NMR validation data is planned to be added to the wwPDB validation report later this year. This data will be displayed in Mol* on PDBe webpages when Mol* is incorporated into our web pages. John From: CCP4 bulletin board On Behalf Of Jose Duarte Sent: 19 March 2019 18:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Java based structural database websites Indeed java in the browser was killed a long time ago. But the good news is that plenty of alternatives exist, written in native (to the browser) javascript. Wikipedia has a nice compilation of the different viewers, under the "Web-based systems" section: https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems I would particularly recommend the Mol* project: https://molstar.org/ Jose On Tue, 19 Mar 2019 at 10:37, Robbie Joosten mailto:robbie_joos...@hotmail.com> > wrote: Hi Nick, A bit of a hack I suppose, but you could use a (single use) VM with some old windows version that still works. E-mailing the developers directly is the way to go to figure out whether you can expect an update. We had a similar problem with our own webserver (the Crystallographic Construct Designer ccd.rhpc.nki.nl <http://ccd.rhpc.nki.nl> ) which was completely a java applet. The only real solution was a full rewrite. But that requires funding which we luckily got from the West-Life project. Keeping websites online is is not easy with changing technology and getting funding is hard because it is not new science. Cheers, Robbie On 19 Mar 2019 17:43, Nicholas Keep mailto:n.k...@mail.cryst.bbk.ac.uk> > wrote: This is slightly off topic but I suspect people from PDBe etc read this bulletin board. Quite a number of very useful structural biology web sites (Olderado, Vivaldi, EMDB to name but a few) require java based viewers and hence no longer have full (or in the case of vivaldi any) functionality on up to date browsers. On a new computer it may prove hard or even impossible to find a browser that will work Are there plans to update these websites and is there any suggeted time scale? Any work rounds? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk <mailto:n.k...@mail.cryst.bbk.ac.uk> Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> =1 _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> =1 _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> =1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Java based structural database websites
Indeed java in the browser was killed a long time ago. But the good news is that plenty of alternatives exist, written in native (to the browser) javascript. Wikipedia has a nice compilation of the different viewers, under the "Web-based systems" section: https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems I would particularly recommend the Mol* project: https://molstar.org/ Jose On Tue, 19 Mar 2019 at 10:37, Robbie Joosten wrote: > Hi Nick, > > A bit of a hack I suppose, but you could use a (single use) VM with some > old windows version that still works. > E-mailing the developers directly is the way to go to figure out whether > you can expect an update. > > We had a similar problem with our own webserver (the Crystallographic > Construct Designer ccd.rhpc.nki.nl) which was completely a java applet. > The only real solution was a full rewrite. But that requires funding which > we luckily got from the West-Life project. > Keeping websites online is is not easy with changing technology and > getting funding is hard because it is not new science. > > Cheers, > Robbie > > > > On 19 Mar 2019 17:43, Nicholas Keep wrote: > > This is slightly off topic but I suspect people from PDBe etc read this > bulletin board. > > Quite a number of very useful structural biology web sites (Olderado, > Vivaldi, EMDB to name but a few) require java based viewers and hence no > longer have full (or in the case of vivaldi any) functionality on up to > date browsers. > > On a new computer it may prove hard or even impossible to find a browser > that will work > > Are there plans to update these websites and is there any suggeted time > scale? > > Any work rounds? > > Best wishes > > Nick > > -- > Prof Nicholas H. Keep > Executive Dean of School of Science > Professor of Biomolecular Science > Crystallography, Institute for Structural and Molecular Biology, > Department of Biological Sciences > Birkbeck, University of London, > Malet Street, > Bloomsbury > LONDON > WC1E 7HX > > email n.k...@mail.cryst.bbk.ac.uk > Telephone 020-7631-6852 (Room G54a Office) >020-7631-6800 (Department Office) > Fax 020-7631-6803 > If you want to access me in person you have to come to the crystallography > entrance > and ring me or the department office from the internal phone by the door > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Java based structural database websites
Hi Nick, A bit of a hack I suppose, but you could use a (single use) VM with some old windows version that still works. E-mailing the developers directly is the way to go to figure out whether you can expect an update. We had a similar problem with our own webserver (the Crystallographic Construct Designer ccd.rhpc.nki.nl) which was completely a java applet. The only real solution was a full rewrite. But that requires funding which we luckily got from the West-Life project. Keeping websites online is is not easy with changing technology and getting funding is hard because it is not new science. Cheers, Robbie On 19 Mar 2019 17:43, Nicholas Keep wrote: This is slightly off topic but I suspect people from PDBe etc read this bulletin board. Quite a number of very useful structural biology web sites (Olderado, Vivaldi, EMDB to name but a few) require java based viewers and hence no longer have full (or in the case of vivaldi any) functionality on up to date browsers. On a new computer it may prove hard or even impossible to find a browser that will work Are there plans to update these websites and is there any suggeted time scale? Any work rounds? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Java based structural database websites
This is slightly off topic but I suspect people from PDBe etc read this bulletin board. Quite a number of very useful structural biology web sites (Olderado, Vivaldi, EMDB to name but a few) require java based viewers and hence no longer have full (or in the case of vivaldi any) functionality on up to date browsers. On a new computer it may prove hard or even impossible to find a browser that will work Are there plans to update these websites and is there any suggeted time scale? Any work rounds? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
