VMD-L Mailing List

From: JT (JTibbitt_at_odu.edu)
Date: Sun Nov 29 2009 - 02:59:31 CST

Hi all,
I just noticed some unexpected behavior when coloring a protein by
position (radial). I colored the entire cartoon protein using
position (radial). This generated a very nice image with the protein
color smoothly blending from blue on one side to white in the middle
to red on the other side. Then, another representation containing
just a few residues (drawn as licorice) was added and also colored by
position (radial). Since these residues were located on the 'red
side' of the protein, I expected the color of this representation to
remain red. However, it was actually colored blue and white. I did
not check, but maybe the 'position' is based only on the atoms in the
representation selection. Anyway, I'm not sure if adjusting the
behavior to match my expectation would be an improvement or an
unnecessary (and unwanted) complication. I just wanted to point it out.
Good day,
Jeff Tibbitt