[PyMOL] ball and stick representation of water molecule
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
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
Re: [PyMOL] SURFACE MODEL
Dear Spyros, Do you know about the PyMOL wiki (http://pymolwiki.org/)? Take a look here: http://pymolwiki.org/index.php/Color for an explanation about colors. In the default representation Green: Carbon Blue: Nitrogen Red: Oxygen Yellow: sulfur For coloring eg. color gray will color everything gray. This is done on the command-line. You can also use the gui (top right there is a multicolored square with the letter C, for color) and select many different colors. This can be done for all or individually for each object/pdb you load. Hope this helps! Best regards, Folmer Fredslund 2011/7/17 Spyros Charonis s.charo...@gmail.com: Hello PyMOLers, A quick question on the surface model, is there anywhere where I can learn how molecules are color-coded. The default scheme has green, red, and bits of yellow (I know the accessible to solvents surface is what is shown, but I'm not sure what red, green, and yellow bits mean)? Also, is there a way I can turn the whole thing gray (monochrome) so that I can color in parts I want to examine with my own coloring method? Spyros -- 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 -- 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
