Re: [PyMOL] Start PyMOL session in web browser
Hi Martin, On Sun, Dec 19, 2010 at 7:37 AM, Martin Hediger wrote: > Dear all > Is it possible to start a PyMOL viewer through a web browser? What I > mean by this is, is it possible to view a protein over the internet > where the viewing features are provided by some "limited" PyMOL server? > The only thing able to do that right now is Jmol, but i think its very > inconvenient to use when viewing large structures such as proteins. Luckily, your peers have given you quite a few options so you can weigh the pros/cons against your necessities and proposed platform (eg. Java vs JavaScript+AJAX vs ActiveX vs HTML5). As a developer I'd also consider the following. First, do you need something that can launch a viewer from the browser or a plugin that embeds the content inside the browser window? If the former, Carsten noted the "p1m" format, which you can associate with PyMOL. If the latter, then I'd next consider platforms (stability, speed, future): HTML5/WebGL: * looks promising as the technology develops, but may be too new for your users to quickly adopt and performance might not be what you want (yet). Java: * been around for ages, but Apple just deprecated their JVM (http://developer.apple.com/library/mac/#releasenotes/Java/JavaSnowLeopardUpdate3LeopardUpdate8RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40010380-CH4-SW1) * Jmol and JyMOL both work well for their intended uses: -- Jmol is good software with a small footprint, fewer dependencies than JyMOL, a large user base, and is open source in case you need to modify the Jmol source -- JyMOL has PyMOL graphics, speed, and is free-to-academics, but needs JOGL or LWJGL and is proprietary--which means you cannot modify JyMOL itself ActiveX: * Consistent cross platform deployment would be my largest concern Use whatever's best for your project. Hope this helps and good luck! Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
Hi Martin, not directly applicable to your question, but may be it directs your thinking into a different direction. If I remember correctly Warren pointed out a couple of year ago the p1m file format was supposed to support downloading of structural information from the web with some limited scripting options. Hope this helps. Cheers, Carsten > -Original Message- > From: Martin Hediger [mailto:ma@bluewin.ch] > Sent: Sunday, December 19, 2010 7:38 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Start PyMOL session in web browser > > Dear all > Is it possible to start a PyMOL viewer through a web browser? What I > mean by this is, is it possible to view a protein over the internet > where the viewing features are provided by some "limited" PyMOL server? > The only thing able to do that right now is Jmol, but i think its very > inconvenient to use when viewing large structures such as proteins. > > Thanks for your answers > Martin > > --- > --- > Lotusphere 2011 > Register now for Lotusphere 2011 and learn how > to connect the dots, take your collaborative environment > to the next level, and enter the era of Social Business. > http://p.sf.net/sfu/lotusphere-d2d > ___ > 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 B_spectrum.p1m Description: B_spectrum.p1m -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d___ 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] Start PyMOL session in web browser
I was thinking of something like a browser plug-in, just as it is available for PowerPoint. We'll see, where it goes. Am 19.12.10 17:06, schrieb Rich: > On 19-12-2010 10:27, Martin Hediger wrote: >> Of course, Jmol is very poweful and I am using it as well for many things. >> Inconvenient probably is the wrong word, I just find the PyMOL handling >> of large molecules a bit more intuitive. > Understood. > >As far as I can see, there are >> more view options in PyMOL (Ribbons, Surfaces, etc), this would be >> particularyl helpful. > As long as you are basing your evaluation on the latest versions of Jmol > because it has changed a lot over the last couple of years. Current > versions do handle ribbons and surfaces. > >> Anyway, the questions remains, how one could run a PyMOL session through >> a web browser. I will be looking at the input from the previous postings. > As far as I know it isn't possible which is why Jmol is a choice. > Although one of the other options may fit better with your needs even > though they aren't PyMol either. > > There was some talk quite a while ago about a different version of PyMol > that could do this but I don't think it ever got off the ground. > > Rich > > -- > Lotusphere 2011 > Register now for Lotusphere 2011 and learn how > to connect the dots, take your collaborative environment > to the next level, and enter the era of Social Business. > http://p.sf.net/sfu/lotusphere-d2d > ___ > 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 > -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
On 19-12-2010 10:27, Martin Hediger wrote: > Of course, Jmol is very poweful and I am using it as well for many things. > Inconvenient probably is the wrong word, I just find the PyMOL handling > of large molecules a bit more intuitive. Understood. As far as I can see, there are > more view options in PyMOL (Ribbons, Surfaces, etc), this would be > particularyl helpful. As long as you are basing your evaluation on the latest versions of Jmol because it has changed a lot over the last couple of years. Current versions do handle ribbons and surfaces. > Anyway, the questions remains, how one could run a PyMOL session through > a web browser. I will be looking at the input from the previous postings. As far as I know it isn't possible which is why Jmol is a choice. Although one of the other options may fit better with your needs even though they aren't PyMol either. There was some talk quite a while ago about a different version of PyMol that could do this but I don't think it ever got off the ground. Rich -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
Of course, Jmol is very poweful and I am using it as well for many things. Inconvenient probably is the wrong word, I just find the PyMOL handling of large molecules a bit more intuitive. As far as I can see, there are more view options in PyMOL (Ribbons, Surfaces, etc), this would be particularyl helpful. Anyway, the questions remains, how one could run a PyMOL session through a web browser. I will be looking at the input from the previous postings. Am 19.12.10 14:11, schrieb Rich: > On 19-12-2010 7:37, Martin Hediger wrote: >> Dear all >> Is it possible to start a PyMOL viewer through a web browser? What I >> mean by this is, is it possible to view a protein over the internet >> where the viewing features are provided by some "limited" PyMOL server? >> The only thing able to do that right now is Jmol, but i think its very >> inconvenient to use when viewing large structures such as proteins. > Have you tried asking about what you find inconvenient about Jmol on the > Jmol list? Perhaps the behaviour that you don't like could be addressed? > I know a of of people seem satisfied to use Jmol for browser-based > rendering. > > Rich > > -- > Lotusphere 2011 > Register now for Lotusphere 2011 and learn how > to connect the dots, take your collaborative environment > to the next level, and enter the era of Social Business. > http://p.sf.net/sfu/lotusphere-d2d > ___ > 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 > -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
Martin Hediger [ma@bluewin.ch] wrote: > Is it possible to start a PyMOL viewer through a web browser? What I > mean by this is, is it possible to view a protein over the internet > where the viewing features are provided by some "limited" PyMOL server? > The only thing able to do that right now is Jmol, but i think its very > inconvenient to use when viewing large structures such as proteins. Normally you do this client side by using a "mailcap" entry. It's far more powerful then a jmol applet. Old fashioned rasmol used to be popular. It would be interesting to see pymol in this usage case. I'm afraid it hasn't been done yet. Cheers, -- Michał Kurowski -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
Jmol certainly is not the only thing able to do that. In the applet world, you have at least OpenAstexViewer http://openastexviewer.net/web/ , but I also imagine it is possible to build a (jogl-accellerated) applet using jymol http://www.pymol.org/jymol , but I'm fairly certain it is not open source. In the html5 world, you have jolecules http://jolecule.appspot.com/ , canvasmol http://alteredqualia.com/canvasmol/ , and chemdoodle web components http://web.chemdoodle.com/ -David On Dec 19, 2010, at 7:37 AM, Martin Hediger wrote: > Dear all > Is it possible to start a PyMOL viewer through a web browser? What I > mean by this is, is it possible to view a protein over the internet > where the viewing features are provided by some "limited" PyMOL server? > The only thing able to do that right now is Jmol, but i think its very > inconvenient to use when viewing large structures such as proteins. > > Thanks for your answers > Martin > > -- > Lotusphere 2011 > Register now for Lotusphere 2011 and learn how > to connect the dots, take your collaborative environment > to the next level, and enter the era of Social Business. > http://p.sf.net/sfu/lotusphere-d2d > ___ > 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 -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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] Start PyMOL session in web browser
On 19-12-2010 7:37, Martin Hediger wrote: > Dear all > Is it possible to start a PyMOL viewer through a web browser? What I > mean by this is, is it possible to view a protein over the internet > where the viewing features are provided by some "limited" PyMOL server? > The only thing able to do that right now is Jmol, but i think its very > inconvenient to use when viewing large structures such as proteins. Have you tried asking about what you find inconvenient about Jmol on the Jmol list? Perhaps the behaviour that you don't like could be addressed? I know a of of people seem satisfied to use Jmol for browser-based rendering. Rich -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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
[PyMOL] Start PyMOL session in web browser
Dear all Is it possible to start a PyMOL viewer through a web browser? What I mean by this is, is it possible to view a protein over the internet where the viewing features are provided by some "limited" PyMOL server? The only thing able to do that right now is Jmol, but i think its very inconvenient to use when viewing large structures such as proteins. Thanks for your answers Martin -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ 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
