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
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] ball and stick representation of water molecule
Dear Leila, stick_ball setting can only be applied to whole object and not atoms for all I know. So, to do ball (oxygen) and sticks (hydrogen) representations is : show sticks, solvent show spheres, solvent and e. O set sphered_scale, 0.3, solvent and e. O You can adjust the size of the sphere with the last setting. Hope it will help you. Joseph On Sun, Jul 17, 2011 at 1:49 PM, leila karami karami.lei...@gmail.comwrote: Dear pymol users how to show water molecules as ball and stick representation (O atom: ball and H atoms: stick)? any help will highly appreciated. -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ 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 -- Joseph ANDRE 11 Rue de Valence 75005 Paris - FRANCE 33(0)6 75 04 64 00 -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev___ 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] Set_toggle ; new script to easily toggle settings
Hi PyMOLers, I was tired of always typing the same commands to change *grid_mode* or * seq_view*... I know it is possible to use set_key to define action but I want a key to enable/disable some settings. I wrote a small script that binds a key to a setting accepting 0/1 or on/off value. http://pymolwiki.org/index.php/Set_toggle It works as is but I'll add other features such as help, check that key is not already bound, check whether setting is known. Comments and suggestions are welcome. Thanks -- Joseph ANDRE -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev___ 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] Set_toggle ; new script to easily toggle settings
Thank you Thomas I've updated the scripts following your recommendation. I wasn't aware of the auto-completion methods. It's great. Cheers 2011/7/14 Thomas Holder spel...@users.sourceforge.net nice :) The toggle() function can be much simplified: def toggle(setting): setting_value = cmd.get(setting) if cmd.toggle_dict.get(setting_**value, 0): cmd.unset(setting) else: cmd.set(setting) And you can add auto-completion for the setting name: cmd.auto_arg[1].update({ 'set_toggle' : cmd.auto_arg[0]['set'], }) Cheers, Thomas On 07/14/2011 02:10 PM, Joseph André wrote: Hi PyMOLers, I was tired of always typing the same commands to change *grid_mode* or *seq_view*... I know it is possible to use set_key to define action but I want a key to enable/disable some settings. I wrote a small script that binds a key to a setting accepting 0/1 or on/off value. http://pymolwiki.org/index.**php/Set_togglehttp://pymolwiki.org/index.php/Set_toggle It works as is but I'll add other features such as help, check that key is not already bound, check whether setting is known. Comments and suggestions are welcome. Thanks -- Joseph ANDRE -- Thomas Holder MPI for Developmental Biology -- Joseph ANDRE 11 Rue de Valence 75005 Paris - FRANCE 33(0)6 75 04 64 00 -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev___ 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