[Chimera-users] ribbon+atoms

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 25 15:17:58 PST 2003

  Dear Soren,
Thanks for the compliments - we're trying!  You're right that in recent
versions of Chimera , showing ribbon turns off the backbone atoms.

There is an easy workaround:  open two copies of the same molecule,
use one copy to show ribbon and the other copy to show atoms.

The reason for the behavior is when the ribbon is drawn as a smooth curve,
it does not exactly pass through the backbone atoms.  Often one wants
to show just the ribbon and certain side chains, and the current
behavior is to extend the side chain to meet the ribbon (even when
the backbone atoms are not on the ribbon) so that they are not floating
in space.  However, we agree that sometimes one will want to display
both the ribbon and the backbone atoms, and in the future there will
a preference to switch between:

  (a) show ribbon, not backbone atoms, and extend the side chains
    to meet the ribbon
  (b) show ribbon and whatever backbone atoms are displayed by the user,
    do not extend side chains to meet the ribbon

Until this switchable preference becomes available, we hope that the
suggested workaround will let you do what you want.
Elaine C. Meng, Ph.D.
Babbitt Lab and Computer Graphics Lab
meng at cgl.ucsf.edu

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