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

[Fox, Kristin]

All,
	Although I am a big fan of using computer visualization in the  
classroom and lab for macromolecules, I really think that this is one  
case where using models the students can hold in their hands is  
preferable.
	I require them to bring a prebuilt peptide to class when we discuss  
phi/psi angles and they can also use it on the exam.  Nothing beats  
having the atoms actually crash into each other to give students the  
idea of what steric conflict means.  Once they have that obvious  
example down (like phi=0,psi=0), we can discuss the idea of atoms  
having an electron cloud and the areas of the Ramachandran plot with  
conformations that are energetically unfavorable, but not as bad as 0,0.
	We use the Darling models (http://www.darlingmodels.com/ccp51/cgi- 
bin/cp-app.cgi) and I bring tape to class so that they can fix the  
trans orientation of the peptide bond.  Darling also makes a special  
peptide bond model (http://www.darlingmodels.com/ccp51/cgi-bin/cp- 
app.cgi? 
usr=51F562948&rnd=198151&rrc=N&affl=&cip=149.106.224.2&act=&aff=&pg=prod 
&ref=kit_15b&cat=kit_specialized&catstr=HOME:kit_specialized) that  
can be used and is only $2.  Our students use these models in organic  
chemistry so they already have the kits.

Kristin

On Jun 7, 2006, at 11:05 AM, 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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Kristin Fox
Associate Professor of Chemistry
Director of Biochemistry
Union College
807 Union Street
Schenectady, NY 12308
Phone: (518) 388-6250
Fax: (518) 388-6796
foxk at union.edu