[Proteopedia] New Tutorial: Ramachandran Principle & Clashes

[Eric Martz]

Dear Proteopedians,

For years, I have wanted to see protein phi and psi angles rotate 
smoothly, showing clashes dynamically as they occur between atoms at van 
der Waals radii. Sure enough, JSmol is quite capable of this. I have 
made a new tutorial available in three formats:

1. YouTube video (voice explaining):
https://tinyurl.com/RamachandranPrincipleYouTube

2. Slideshow: https://tinyurl.com/RamachandranPrinciple

The images in the above two formats are *animated*, showing translucent 
van der Waals-sized atoms rotating smoothly with clashes forming and 
going away. Those animated clashes are compared side by side with 
Ramachandran plots. Also included is an animated explanation of dihedral 
angles.

3. An interactive JSmol tutorial with checkboxes and buttons:
http://proteopedia.org/w/Tutorial:Ramachandran_principle_and_phi_psi_angles

Please pass this on to websites that will alert educators.

There is also a practice *Quiz* with immediate feedback:
http://proteopedia.org/w/Dihedral/Ramachandran_Principle_Quiz

Angel Herráez and I have also made an illustrated list of ten websites 
that illustrate the Ramachandran principle and plot, and phi/psi 
dihedral angles in various ways, mostly using JSmol:

http://proteopedia.org/w/Dihedral/Index

Several of these are available also in *Spanish*, as indicated there.

Thanks to Jaime Prilusky for installing this tutorial in Proteopedia, 
and for providing an easy mechanism for making quizzes.

-Eric


-- 
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
Martz.MolviZ.Org <http://Martz.MolviZ.Org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20180717/7b5a0a1c/attachment.html>