Unfortunately, there is currently no good solution to problem (a). PyMOL
doesn't yet support automatic repositioning of CA coordinates to reflect the
Regarding (b), the PyMOL light source is directional, not positional. The
direction is controlled using the light setting which has a default value of
[ -0.40000, -0.40000, -1.00000 ], which means that the light appears to come
downward over the right shoulder of the observer. It's a direction vector.
[0,-1,0] is straight down
[0,0,-1] is straight forward
[1,0,0] is from the left
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
400 Oyster Pt. Blvd., Ste 213
South San Francisco, CA 94080
> -----Original Message-----
> From: pymol-users-admin@...
> [mailto:pymol-users-admin@...] On Behalf Of Zach
> Sent: Tuesday, October 05, 2004 9:53 AM
> To: pymol-users@...
> Subject: [PyMOL] Questions about ray-tracing
> 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!
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