[Chimera-users] Cartoon: Helix appearance

[Elaine Meng]

Hi Michael,
Putting aside the philosophical issue of what ribbon orientation has  
more "truthiness," you can try using the Ribbon Style Editor (under  
Tools... Depiction):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ 
ribbonstyle.html

Take a look at the "Residue Class" section.  What you get for  
proteins by default is the "amino acid" definition of
- which atoms are mainchain (automatically disappear when you show  
ribbon): N,CA,C,O
- which atom is the "guide" (controls path, smoothed over 5  
residues): CA
- which atom is the "orientation" atom (controls orientation): O

You can make your own definition and name/save it.  Changing the  
mainchain set does not affect the ribbon appearance at all, so ignore  
those.  I note that O is already the orientation atom.  I tried  
changing the guide atom to N or C, but that didn't seem to tip the  
ribbon out very much.  However, using C and O does make the ribbon  
plane coincide with those bonds fairly well.  (too see this, I made  
the ribbon wider in the Scaling section of Ribbon Style Editor and  
opened another copy of the same structure and showed its backbone  
atoms as sticks)

There is also a "Rotate" option, but the only choice is 90 degrees.  
Maybe one of the programmers can provide advice on whether it would  
be easy to edit some number somewhere in the code to get different  
rotation angles...
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Oct 25, 2007, at 3:47 PM, <kroneml at hotmail.de> wrote:

> Hello,
>
> I observed that Chimera (like almost all other protein viewers)  
> aligns the
> ribbon of a helix in a way that the ribbon is parallel in every  
> twist (the
> ribbon virtually forms a cylinder).
> My question is: is this correct, strictly speaking? I thought that the
> ribbon should lie in the plane defined by two successive C-alpha  
> atoms and
> the associated O atom? (Mike Carson defines it that way in his  
> "Ribbons",
> following the instructions of Richardson's "The anatomy and  
> taxonomy of
> protein structure"). If you draw it that way, the ribbon forming  
> the helix
> will tilt slightly outwards.
> Is the alignment of the helix ribbon in Chimera done simply because  
> it looks
> better this way or is there another reason?
>
> I did some research on this topic via google and even asked a  
> certified
> biologist (scientific assistant), but the internet had not much to  
> say about
> it and the biologist only told me that cartoon drawings don't have  
> to be
> very accurate, since they are only a tool to get a general idea of the
> protein's structure.
>
> Best regards,
> Michael Krone