[Chimera-users] PDB: 3NZ4 (Chimera vs Pmol Visualization)

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 7 14:28:24 PDT 2015

Hi Kevin,
What you are seeing is weird-looking bonds between the ribbon and the residues named MDO.  It is an artifact caused by the default smoothing of the ribbon path, the amino acid derivation of MDO, and the default hiding of “backbone” atoms in Chimera when the ribbon is displayed.  More on that here, if anybody wants details...

As you found, you could just show atoms without ribbons to solve the problem.  However, if you really wanted to show ribbons at the same time, here are some choices as to what you could do in Chimera to make it look less deformed:

(1) enable display of all atoms of the MDO at the same time as the ribbon, for example with command: 

.. however, side effects you may not like are that this will also show backbone atoms of the other residues that are displayed, and MDO and these other residues may be obviously detached (as if “floating” away) from the smoothed ribbon.  You could try hiding the backbone atoms of the other residues with:
~disp @n,c,o & ~:mdo
… or you could go back to the original behavior of disabling simultaneous backbone-atom and ribbon display with:

(2) use a non-smoothed ribbon path that is forced to go through the CA atoms, for example with command: 
ribspline cardinal

… however, this is still ugly because the ribbon makes a sharp turn near this derived residue, and the methyl group comes off of the ribbon at a strange angle.  You can go back to the default ribbon path with:
ribspline b

Sorry, neither makes a beautiful picture.  But I hope this helps to explain what is going on.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

Pictures before and after using “ribbackbone” command:

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