[PyMOL] Questions about ray-tracing

[Zach <kam...@mi...>]

Hello to all,

I am trying to ray trace a picture using pymol and I have a couple of questions:

a) I am using a cylindrical helix representation. Some of these helices have side
chains sticking out of them represented as sticks. The connection between the
alpha carbon (within the helix) and the beta atom (the first on the side chain) 
is
not connected and the residue seems to float. I know I can change the radius
of the cylinders through the cartoon_helix_radius setting but this would imply
making my helices fatter and I do not want to do this. As a matter of fact, what
I would like to do is to decrease the radii of the helices so that I can unclutter
the
picture but this would make the problem of floating residues even worse.
What can I do?

b) I would like to know how I can know the position of my light source with respect
to the object I am trying to render. I know I can change the position through the
light setting but I am not sure where it is located or what effect I will get by
changing
the coordinates of the light source. Trial and error is proving to be a difficult
choice
as I am not sure what I am doing.

Any help is really appreciated!

Zach