Re: [PyMOL] use PyMOL code in outer tkinter application
Hi Mike, It's possible, but at this point would be more trouble than it's worth. The newer pymol2 methods are not yet stable enough for mainstream use. The older pymol1 methods will leave you struggling with synchronization and other problems. Cheers, -- Jason On Fri, Dec 17, 2010 at 11:56 PM, Mike Turchenkov wrote: > Hello, dear All. > > Is it possible to use PyMOL as a whole in other python apps? I use > tkinter for some comfort automation and I wolud like to integrate > interactive visualiser windows into my app. Is it possible, or it just > doesn't work that way? > > Thanks. > > -- > 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 > -- 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, 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] pymol and interactive matplotlib plotting?
Hi Bjoern, I think you answered your own question. I think you need to use plot over draw. How about: import pymol pymol.finish_launching() import matplotlib import pylab pylab.ion() pylab.figure() pylab.ioff() pylab.plot([1,2],[1,2]) pylab.show() The above gives me a fully interactive PyMOL session and matplotlib window. Cheers, -- Jason On Fri, Dec 17, 2010 at 7:46 PM, Bjoern Nadrowski wrote: > Hello, > What I would like to do is write a python script that simultaneously > drives lammps (my molecular simulation program), puts lammps output to > pymol, and plot some pylab plots. > > When I try this: > > import pymol > pymol.finish_launching() > > import matplotlib > import pylab > > pylab.ion() > pylab.figure() > pylab.ioff() > pylab.draw([1,2],[1,2]) > raw_input() > > I do get my interactive pymol gui, but the pylab window is dead. It pops > up, but no line is drawn. I suspect that has something to do with the > gui handlers, so I would have to attach the pylab gui to the pymol one, > I suspect. I just don't know how to do that. > > Nota bene: > replacing the pylab lines with > pylab.figure() > pylab.plot([1,2],[1,2]) > pylab.show() > > works, but then the handler is with the pylab window, and no code after > that can be executed any more. > So you cannot update this window during execution time. > > Thanks for any help! > > > > -- > 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 > -- 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
