[PyMOL] Surface coloring with ChemPy bricks?

2004-02-03 Thread Michael George Lerner
Does surface coloring work with ChemPy bricks? I took the script in examples/devel/brick01.py and changed it to make a ChemPy brick that goes from [0,0,0]--[5,5,5] like so ... examples/devel/brick01.py ... brik.setup_from_min_max( [0.0,0.0,0.0], [5.0,5.0,5.0], [0.5,0.5,0.5]) ...

[PyMOL] different stick_radius for different residues

2004-02-03 Thread Dr. S. Frank Yan
Hi, I was wondering if Pymol is capable of setting different stick thickness for different residues of a molecule. I tried set stick_radius=0.25 show sticks, resi 1-2 set stick_radius=0.1 show sticks, resi 12-15 It appears that the stick_radius variable is global, and it changes the thickness

Re: [PyMOL] different stick_radius for different residues

2004-02-03 Thread Morri Feldman
Dear Frank, try: create forSticks1, resi 1-2 show sticks, forSticks1 set stick_radius, .25, forSticks1 create forSticks2, resi 12-15 show sticks, forSticks2 set stick_radius, .1, forSticks2 By using create, you create a new named object with its own settings database. The new object's

[PyMOL] Outline cartoon representation

2004-02-03 Thread Todd Geders
Hello all, We'd like to render some cartoon representations of protein structures in a manner similar to the style of Jane Richardson. Basically white, opaque surfaces (no reflections) with black outlines at each of the edges. Here's a link to give you an idea what we're looking for (Figure

RE: [PyMOL] PyMOL on Powerbook G4

2004-02-03 Thread Warren DeLano
Keana, This is a problem with at least one mac web browser...for some reason the .gz gets removed from the file upon download, but the file is still compressed. If you replace the .gz, then the file will uncompress and open properly when you double-click on it. Cheers,

RE: [PyMOL] Outline cartoon representation

2004-02-03 Thread Warren DeLano
Todd, Unfortunately that is not a problem PyMOL was designed to solve, and off the top of my head I can't think of any way to bend it around to do this -- you're talking about a different rendering scheme. I think it amounts to the following: trace every sharp edge, and outline every round