[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
[PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Dear all, I have a small helical pseudopeptide with mixed alpha and beta amino-acids. How can I make a cartoon representation of this helix with Pymol? For the moment, I have selected the peptide backbone atoms and tried the alter command to force pymol to recognize the helix but it do not work. Thanks. Best regards, Baptiste -- 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] loading gro files
Maybe this can help you http://sourceforge.net/mailarchive/message.php?msg_id=19472192 Cheers, Marius On Tue, Aug 16, 2011 at 2:19 AM, Michael Daily mdaily.w...@gmail.com wrote: Hi all, Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I know it's simple to convert them to pdb using editconf, but I want to load gro files directly (as you can in vmd) because they permit higher max. atom and residue numbers (100K vs. 10K for pdb) and permit longer residue names (4 chars vs. 3 for vmd). Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- 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 -- 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] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Thanks Joseph and Thomas for your replies. When I use the as cartoon commands, all my molecule disappear. My *pdb file could be the problem as it is a *cif crystal structure file (converted with mercury) from the cambridge crystal data. Cheers, Baptiste 2011/8/16 Thomas Holder spel...@users.sourceforge.net Hi Baptiste, I have a small helical pseudopeptide with mixed alpha and beta amino-acids. How can I make a cartoon representation of this helix with Pymol? For the moment, I have selected the peptide backbone atoms and tried the alter command to force pymol to recognize the helix but it do not work. are you sure? What happens if you try this: alter all, ss='H' as cartoon rebuild Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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
