[PyMOL] how to outline as in ray_trace_mode=2

2008-08-21 Thread O. J. Ganesh
Hey once again everyone, This is along the lines as my previous questions... When I do: set ray_trace_mode, 2; It produces a 'black and white image', however this really is of the outlines of the objects in the model. Is there a way I can manually make certain objects into this outline

Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3

2008-08-18 Thread O. J. Ganesh
Hey again everyone, I've working with a model in pymol which needs to end up as a greyscale image (for a journal). The model is fairly complicated, and contains several molecules - some represented as spheres, some as sticks, etc. I was working with: set ray_trace_mode, 2; To produce a

[PyMOL] sheared spheres for dots in dot representation

2008-08-12 Thread O. J. Ganesh
Hello again. I'm having a bit of trouble with the dot representation again. When I use the dot representation on an object, the sphere on which the dots reside ends up sheared; that is, I do not get a nice round sphere to hold up the dots. I've adjusted vdw of the object I'd like to have

[PyMOL] dots representation

2008-07-29 Thread O. J. Ganesh
Hello, everyone. I'm having a hard time understanding the different properties of the dots representation in pymol. I just updated the wiki with what I've been able to piece together, but I still have many questions: 1) Why is the difference between dot_radius and dot_width (other than