Re: [PyMOL] Visualizing Molecular Orbitals in PyMol

2007-02-19 Thread Michael Lerner
Hi, I don't remember the details, but I do remember that I had some troubles using bricks when I was writing the APBS plugin. The DX file format is really simple, though, especially for this sort of thing. http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format If I recall correctl

[PyMOL] Anisotropic b-value thermal ellipsoids

2007-02-19 Thread David Shin
Hi - I'd like to make some anisotropic b-value thermal ellipsoids using PyMol. I found one script at google, but can't get it to recognize the 5 programs I had to download to try to get it to run. Does anyone have an easy way to do this. I want to use the ANISOU terms genereated by shelxl. I'm u

[PyMOL] Visualizing Molecular Orbitals in PyMol

2007-02-19 Thread BuzB
Hi All, Thanks to everyone and for the responses to and encouragement about my query on visualizing molecular orbitals in pymol. I'm using PyMol 0.99rc6. I feel like I'm quite close to a solution. I've developed a routine to compute a 3 dimensional matrix containing the probability amplitudes o

Re: [PyMOL] mesure line width

2007-02-19 Thread Mike Summers
This works great! Is there any way I can draw two different types of dashed lines, one set with a given color and dash parameters another set with a different color, linewidth, etc.? Mike On Fri, Feb 02, 2007 at 11:56:49AM -0500, Robert Campbell wrote: > Hi Andrea, > > * andrea carotti [2007

Re: [PyMOL] simple cgo question

2007-02-19 Thread Richard Gillilan
Thanks Rob, that worked! Load it into PyMOL with: PyMOL> run arrows.py

Re: [PyMOL] simple cgo question

2007-02-19 Thread Robert Campbell
Hi Richard, * Richard Gillilan [2007-02-19 10:22] wrote: > > I'm probably making a simpler mistake here, or perhaps there is > something wrong with my installation or paths. > I'm trying to load and display the simple cgo example in the manual. > I created a file named "arrows" containing th

[PyMOL] simple cgo question

2007-02-19 Thread Richard Gillilan
I'm probably making a simpler mistake here, or perhaps there is something wrong with my installation or paths. I'm trying to load and display the simple cgo example in the manual. I created a file named "arrows" containing this definition: from pymol.cgo import *# get constants from pym