[Molvis-list] Interactive visualization of phi/psi?

Eric Martz emartz at microbio.umass.edu
Wed Jun 7 11:05:19 EDT 2006


[Apologies if you already received this via pdb-l]

I have been looking for interactive visualizations of phi/psi to help 
convey the steric basis for the Ramachandran plot. Ideally, I would like:

1. Model freely rotatable with the mouse, to view from any perspective,
2. Phi and psi angles freely and independently rotatable,
3. Unequivocal visual indication of van der Waals collisions, such as those 
great red baskets in KiNG.

These two below are much less important than 1-3 above.
4. Visualization in browser rather than stand-alone application.
5. Works on OSX and linux as well as Windows.

Please let me know of resources with any of these capabilities.

The closest I have found is the kinemage 2literacy.kin by Simon Lovell at
http://www.bioinf.man.ac.uk/~lovell/kins.shtml
This has 1 and 2 above, but neither 3 nor 4. Is there some way to turn on 
the red collision baskets in this kinemage? Could it be shown in KiNG, or 
would that sacrifice the slider controls?

Other useful resources I've found are

  - An animated gif at
http://speedy.st-and.ac.uk/~naismith/teaching/lectures/3014/lecture/Rama_animationhtm.htm
that shows separate, side by side "canned" rotations, by J.H. Naismith. 
Meets none of 1-4 above, but does convey the general idea clearly and quickly.

  - A rather nice quicktime movie from Univ. Wisc. La Crosse
http://visu.uwlax.edu/BioChem/Rotate.mov
This partially meets #1 above (via the quicktime slider) but the 
non-standard element colors make it very confusing.

Thanks, -Eric

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