[Proteopedia] New Tutorial: Ramachandran Principle & Clashes (sent again)

[Eric Martz]

I sent this on July 17 but I think there have been problems with the 
Proteopedia email list, so I am re-sending it in case you missed it (and 
to see if it goes through promptly). -Eric

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