[Chimera-users] Fwd: ribbon causes coordinates changing

[Elaine Meng]

Hi Francesco,
The ribbon is an smoothed interpolated path over several residues, and it does not pass exactly through the real backbone atom positions.  By default, and for display purposes only (calculations still use the real positions) the backbone atoms are projected to the ribbon location.  

If you want to see the "real" backbone atom positions in addition to the ribbon, use the command "ribbackbone":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>

Unfortunately, that will usually look ugly, as the atoms may be floating away from the ribbon position.

In the future we would like to add controls to force the ribbon closer to the real atom positions, but it hasn't been done yet.  I've figured out a workaround that works quite nicely for proteins if you don't mind having a "tube" ribbon:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

I don't think this workaround generalizes very well to nucleic acids, however.  I tried it on your session by changing to sticks, displaying all atoms, undisplaying ribbon, and generating a tube for @c5' (instead of @ca as in the workaround instructions).  If you didn't mind the tube shape other things you might want to consider would be making its radius bigger, not coloring to match atoms (bandLength keyword), undisplaying some of the backbone atoms.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#tube>

I hope this helps (or at least clarifies what is going on),
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 30, 2010, at 9:45 AM, Francesco Oteri wrote:

> Dear chimera users,
> 
> I've a problem with ribbon. I've a DNA molecule where the two last base
> pair is an uncommon T-T pair. When I select these bases to display the
> ribbon, the coordinateds of the last atoms are changed. Seem that the
> new position are the end of the ribbon.
> 
> The chimera version I'm using is 1.5rc1 on a windows7 PC.
> 
> I attacch the session that represent my problem. The session is saved
> such to visualize the problem:  look at the end of the blue and red
> ribbons to detect it.
> 
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