Re: [PyMOL] Transparent surfaces and presets

2009-08-20 Thread Warren DeLano
Jose, Yes, you need to override the object-specific transparency specification from the preset: unset transparency, object-name Cheers, Warren From: Duca, Jose [mailto:jose.d...@spcorp.com] Sent: Wed 8/19/2009 10:33 AM To:

[PyMOL] Light Command Details needed

2009-08-20 Thread Sean Moore
Hello, I could not find a way to search the archived sourceforge messages, so I apologize if this has been asked and answered. I am having trouble moving the light source before a ray command (I want to shine it into the crevice of a structure from behind and above my current view). I

[PyMOL] Stick Radius different for selected residues, possible?

2009-08-20 Thread Sean Moore
Hello, I am trying to change the stick_radius for a few selected residues so they stand out relative to the surrounding mess of sticks. If I command, set stick_radius, 0.75, object name, the report states that the stick radius was changes for the correct number of atoms in the file, but

Re: [PyMOL] Light Command Details needed

2009-08-20 Thread Pete Meyer
Hi Sean, I ended up using light, [1,5,-100]. I know these are X,Y,Z coordinates, but relative to what origin and in what units? After wasting way too much time, I concluded that the values might be Angstroms relative to the eyes of the current view. In examples I found online, the

Re: [PyMOL] Light Command Details needed

2009-08-20 Thread Warren DeLano
The light and lightN settings are direction vectors, not coordinates. Intensity (reflect setting) is averaged across all such directional sources. It has recently been suggested that we need better control over lighting. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent

Re: [PyMOL] Stick Radius different for selected residues, possible?

2009-08-20 Thread Warren DeLano
Sean, Use set_bond instead of set for per-bond properties. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from a mobile device. Please forgive brevity and/or typos!) On Aug 20, 2009, at 4:18 PM, Sean Moore semo...@mail.ucf.edu wrote: Hello, I am trying to change the