[Chimera-users] Cartoon: Helix appearance

[kroneml at hotmail.de]

Hi Elaine,

I didn't know that the ribbon structure/orientation and the
guide/orientation atoms can be modified, thank you!

But in fact it's exactly the philosophical issue of what ribbon orientation
has more "truthiness" that I'm basically interested in. I'm currently doing
some research on cartoon drawings of proteins for my student research
project.

Bye,
Michael


> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Friday, October 26, 2007 1:49 AM
> To: kroneml at hotmail.de
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Cartoon: Helix appearance
> 
> 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