Wulf, The easiest thing would be to convert your small molecule to an SDF, MOL, or MOL2 format before loading it into PyMOL.
Short of that, you'd have to select each bond independently (ctrl-right-click while in editing mode) and use Ctrl-W to set the valences. Cheers, Warren -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net on behalf of Wulf Blankenfeldt Sent: Mon 3/6/2006 6:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Displaying/defining double bonds in a ligand molecule Hello pymolers, I'd like to display double bonds in a small molecule ligand bound to the active centre of a protein. Of course, the ligand is non-standard, i.e. pymol doesn't know about its chemical nature. Googling a bit, I found that I can set valence, 0.1 but this only display double bonds in the protein, which I don't want. How do I teach pymol to display double bonds in my ligand? Thanks for your help, Wulf ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
