Hi:
I am trying to use the Alignment Objects (i.e., lines between the paired
aligned atoms) created by using the OBJECT argument of the ALIGN command to
illustrate domain movement between the superimposed ligand-bound and
unbound forms of an enzyme.
I successfully made the basic aligned image, and now I want to tweak it.
Is it possible to change the color of the Alignment Object lines between
paired atoms? For me, they display only in yellow. From what I have read
online these lines are CGO objects with the color hardwired in upon
creation, and so it can’t be changed in PyMol latter on. However, I haven’t
been able to find a way to assign a color upon creation. Is there a way to
assign a specific color?
Additionally, I have seen this type of image where the lines between the
paired aligned atoms are two colors, with half of the line in one color
(say blue) and the other half another color (say red) to better illustrate
which protein is the origin of each end of the connecting line. I haven’t
discovered a way to make these bi-colored lines in ALIGN. Any ideas?
I have tried the open source version 1.8.0, plus several earlier versions
from various origins (all on Macs) with similar results.
Thanks much for any ideas.
Tim
Tim Umland, Ph.D.
Hauptman-Woodward Institute
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