Wulf, Unfortunately, the lighting model has changed...I am assuming that you are having problems with existing session files or scripts?
It may be necessary to reoptimize the lighting settings. The new defaults are: set ambient, 0.14 set gamma, 1.0 set direct, 0.45 set reflect, 0.45 set specular_intensity, 0.5 set light_count, 2 set light, [ -0.40000, -0.40000, -1.00000 ] set spec_reflect, -1 set spec_power, -1 set shininess, 55 Perhaps you can simply paste those commands into your scripts? If you want pre-0.99-like lighting model (it has an extra dot product that shouldn't be there). use set ray_legacy_lighting, 1 with the above settings Cheers, Warren -----Original Message----- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Mon 3/6/2006 7:23 AM To: Warren DeLano Subject: Re: [PyMOL] Displaying/defining double bonds in a ligand molecule Ah, bingo! Thanks for that, Warren. BTW: we have a little difficulty with the 0.99 version under windows: colours have become very glary in raytracing, like an overexposed photograph. Is this a feature, a non-optimised colour scheme or simply my mistake? Best, Wulf Warren DeLano schrieb: > > 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. >
