Re: [PyMOL] Displaying/defining double bonds in a ligand molecule; lighting problem

2006-03-07 Thread Wulf Blankenfeldt
Warren, Mark; thanks for these suggestions concerning "overexposed" images. We have dumped Warren's settings into our pymolrc file and are now getting much better results... Best, Wulf Mark A Saper schrieb: Wulf et al, I've had similar results to what you report even with a session fil

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

2006-03-06 Thread Mark A Saper
Wulf et al, I've had similar results to what you report even with a session file created with the latest version of PyMol. You should first try what Warren suggests. Then, if the specular highlights still look too contrasty, you can try reducing the specular_intensity to about 0.2 and a

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

2006-03-06 Thread Warren DeLano
;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 mol

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

2006-03-06 Thread Warren DeLano
ginal 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 smal

[PyMOL] Displaying/defining double bonds in a ligand molecule

2006-03-06 Thread Wulf Blankenfeldt
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 bon