This is cool. I've been wanting to do this for a while, but never got around to it.
I added a photo generated from the defaults and an example script for the users.
Thanks for the feedback. It actually took a very long time to get it to all work properly. I had to play around with different ways to draw the arrows and figuring out the geometry for the cone was quite challenging. Eventually, it all came together and then I added all of the bells and whistles. The original motivation was for a publication image but I thought other people would be interested. My next goal would be to draw a curved line rather than a straight vector/cylinder that could pass through multiple states which would likely require cubic spline interpolation. Although, it's not currently high on the priority list (graduating is...).
I think people will use this for publication images if tuned & advertised. IIRC, in NMA/MD these are called porcupine plots. If you could provide a few examples that people could copy/paste & see results I think that'd help quite a bit, too. Again, great stuff.
Tree 16:30, 2 April 2009 (CDT)
As per your request, I beefed up the examples. Somewhat tedious but feel free to rearrange to improve the clarity. Thanks.
Sean 01:23, 3 April 2009 (CDT)
I updated the way that the cones were being drawn since version 1.1 has cone primitive. The code will check the version of PyMOL being used before defaulting to the old method of drawing the cones. However, the cone primitive significantly decreases the time and resources needed for ray tracing so users should upgrade to version 1.1 if possible or otherwise use the "pymol -qc" option.
Sean 09:11, 10 April 2009 (CDT)
Great work! Tree 16:24, 10 April 2009 (CDT)