Re: [PyMOL] Dynoplot : Interactive plot
Hi, I reworked the broken DynoPlot script. Changes and improvements include: * much faster calculation of Phi/Psi angles * can open multiple plot windows * center on residue with right-mouse-click * different plot symbols for GLY and PRO http://pymolwiki.org/index.php/DynoPlot Cheers, Thomas Thomas Holder wrote, On 08/16/11 15:51: On 08/16/2011 03:16 PM, Joseph André wrote: Hi everybody, I want to build an interactive plot I tried to use and tweak dynoplot but DynoPlot doesn't work properly : I can display the Tk window but points aren't plotted. However the dihedrals angles are computed correctly. There isn't any traceback or error reported on the console. Do you have experienced similar problems ? I can confirm that DynoPlot does not work. This needs to be fixed. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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] Dynoplot : Interactive plot
Hi Thomas, I've read a bit about matplotlib and it seems possible to have interactive plot. However I don't know if it can interact with pymol. I'll have a look at it. Thanks 2011/8/16 Thomas Holder spel...@users.sourceforge.net Hi Joseph, thanks for your quick reply. I'm a newbie at Tk programming but from what I understand, gui code for Dynoplot had been written from scratch. Do you know if they are libraries that would facilitate the plotting and the interaction with pymol? There are many libraries for plotting, for example matplotlib which is also shipped with recent PyMOL versions. Dynoplot however also could update the structure by dragging dots on the plot, I'm not aware of a plotting library that provides this functionality (which does not mean that none such exists :) ). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- Joseph ANDRE 11 Rue de Valence 75005 Paris - FRANCE 33(0)6 75 04 64 00 -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2___ 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] Dynoplot : Interactive plot
Hi everybody, I want to build an interactive plot I tried to use and tweak dynoplot but DynoPlot doesn't work properly : I can display the Tk window but points aren't plotted. However the dihedrals angles are computed correctly. There isn't any traceback or error reported on the console. Do you have experienced similar problems ? My final goal is to obtain an interactive plot to show b-factor (or value stored in b-factor column using data2bfactor) in 2D and in 3D. Thanks. -- Joseph ANDRE -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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] Dynoplot : Interactive plot
On 08/16/2011 03:16 PM, Joseph André wrote: Hi everybody, I want to build an interactive plot I tried to use and tweak dynoplot but DynoPlot doesn't work properly : I can display the Tk window but points aren't plotted. However the dihedrals angles are computed correctly. There isn't any traceback or error reported on the console. Do you have experienced similar problems ? I can confirm that DynoPlot does not work. This needs to be fixed. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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] Dynoplot : Interactive plot
Hi Thomas, thanks for your quick reply. I'm a newbie at Tk programming but from what I understand, gui code for Dynoplot had been written from scratch. Do you know if they are libraries that would facilitate the plotting and the interaction with pymol? Best regards Joseph 2011/8/16 Thomas Holder spel...@users.sourceforge.net On 08/16/2011 03:16 PM, Joseph André wrote: Hi everybody, I want to build an interactive plot I tried to use and tweak dynoplot but DynoPlot doesn't work properly : I can display the Tk window but points aren't plotted. However the dihedrals angles are computed correctly. There isn't any traceback or error reported on the console. Do you have experienced similar problems ? I can confirm that DynoPlot does not work. This needs to be fixed. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- Joseph ANDRE -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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] Dynoplot : Interactive plot
Hi Joseph, thanks for your quick reply. I'm a newbie at Tk programming but from what I understand, gui code for Dynoplot had been written from scratch. Do you know if they are libraries that would facilitate the plotting and the interaction with pymol? There are many libraries for plotting, for example matplotlib which is also shipped with recent PyMOL versions. Dynoplot however also could update the structure by dragging dots on the plot, I'm not aware of a plotting library that provides this functionality (which does not mean that none such exists :) ). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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
