A variety of cartoon options
This section draws heavily on material also present on the PyMOLwiki.
The simplest illustration you can make of a protein is to provide a
cartoon diagram of the tertiary and/or quaternary structure. Working
from 1HHO, let's look at some of the options. But first let's color the
two different chains what we like (the full range of colors you can use
is under the Settings menu).
color yellow, chain a
color cyan, chain b
Impress me and choose other colors than those, but this is what you'll
see.
If you like an orientation you've found, you can save it as a view:
view 1, store
which can be restored at any future point (first rotate the image to a
new orientation) by typing
view 1
For some fun, you can play with the different cartoon options under the
Setting/Cartoon
menu. Personally, I like Round and Fancy helices
selected.
For publication purposes, you need to (a) create a white background,
(b) increase the image size and (c) raytrace the image, which will
create a high resolution picture suitable for framing. I recommend
working with a image size that's larger than what you need as
well. For this one, I'll use 600x600 pixels. Type
bg_color white
viewport 600, 600
ray
Note the improved image you get by typing "ray". Before is left, after is right.
Now you can play with the styles of ray tracing for fun. There are three modes:
set ray_trace_mode, 0 (or 1 or 2)
ray
Zero is the default, but 1 and 2 are shown left and right below.
OK, you can go ahead and start playing on your own with your own
proteins and your own color scheme. Also, if you're working with
some nucleic acid structures, there's a whole range of things you can
do with those. See the PyMOLwiki!