#10 Request finer control of coloring and more export options
I am using pymol to create stereo images of a protein for
publication. For purposes of the paper it is necessary
that only certain amino atoms and bonds be shown. This
is the easy part. The hard part is in color coding these
items. Here is an real example of my problem to illustrate
my request:
I am displaying real and _possible_ disulfide
bonds within a protein molecule and need to be able to
color the sulfur atom in each cysteine as a separate
color from the disulfide bond that connects them. The
bond on each pair displayed must be a different color
from the rest as well. The editing system permits me to
only alter the color of the sulfur atoms which, in turn,
changes the color of the disulfide bond line between
them. Alternatively, I tried to use the measure wizard
instead since the dashed line between atoms can have
its color individually changed - I would then simply
change the parameters of the dashed line so that the gap
between dashes was 0.0 (a straight, unbroken line with
the color of my choosing). The problem is that changing
the parameters of the dashed line affects ALL dashed
lines so it is impossible to have both dashed lines and
solid lines made from dashed lines without gaps.
This sort of control is necessary to illustrate the
information about my protein but I am having to go
through contortions to get to the end point: export to png
(how about an eps/ps/illustrator export option?), import
into a graphics app, draw appropriately-colored lines on
top of those produced by pymol. This is especially
difficult to pull off well when stereo images are required,
as they are for me.
My request is that disulfide bond colors be editable
individually, that the nature of the dashed line produced
by the measure wizard be alterable on an individual line
basis, and that the export capabilities of pymol be
expanded to include vector-based images to make any
additional graphics editing easier.
Discussion
set_bond line_color, white, elem c, elem o
set_bond stick_color, white, elem s
etc.
At this point, vector-based export from PyMOL is a long ways off.