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

Jon R. Stoltzfus stoltzfu at msu.edu
Mon Jun 12 09:14:19 EDT 2006

You're probably already aware of it, but the the Ramachandran Plot Explorer
does the first two things on your list.  I tried to use it in a large
lecture, but it wasn't as effective as I'd hoped.  However, it is quite
useful in smaller group settings.  I believe it is open source and you may
even be able to get the person who wrote it to add feature 3.  It would be
much more effective if it showed the van der Waal's collisions, but I've
gotten busy and haven't pursued it.

You can download the Ramachandran Plot Explorer from
http://www.dillgroup.ucsf.edu/~bosco/rama.html.  If you come up with
anything better, I'd be interested.


Jon R. Stoltzfus, Ph.D.
Michigan State University
Biochemistry and Molecular Biology
Office: 305 Biochemistry
e-mail: stoltzfu at msu.edu
Phone: 517 432-8775

-----Original Message-----
From: molvis-list-bounces+stoltzfu=msu.edu at bioinformatics.org
[mailto:molvis-list-bounces+stoltzfu=msu.edu at bioinformatics.org] On Behalf
Of Eric Martz
Sent: Wednesday, June 07, 2006 11:05 AM
To: molvis-list at bioinformatics.org
Subject: [Molvis-list] Interactive visualization of phi/psi?

[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
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
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

  - A rather nice quicktime movie from Univ. Wisc. La Crosse
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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