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

Mario Valle mvalle at cscs.ch
Wed Jun 7 11:15:36 EDT 2006


Take a look at "The Ramachandran Plot Explorer" 
<http://www.dillgroup.ucsf.edu/~bosco/rama.html>
Does not do exactly what you want, but it is worth a look.
Ciao!
			mario

Eric Martz wrote:
> [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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-- 
Ing. Mario Valle
Visualization Group                              | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
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