[PyMOL] how to outline as in ray_trace_mode=2
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 representation? That is, not filled in with color, but outlined instead? Or just control the thickness of the edges of objects in the picture? This is outline view is fairly different than the other representations... Thanks.
Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3
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 black and white image after raytracing. I realize that this option is supposed to produce a black outline only... Now I'd like all the parts of the image that are in stick representation to be outlined in gray (40% black), with the rest being black outline and white. Is there a nice way to get the 'set ray_trace_mode, 2' effect with all stick representations being gray outline? Thanks. winmail.dat
[PyMOL] sheared spheres for dots in dot representation
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 in the dot representation, however no matter how small (or large) I make the spheres, the spheres are always sheared. I also played with the slab settings, and it doesn't matter how far back I move the 'camera' the spheres are still sheared. Is there some setting that I'm missing? I'd like to end up with round spheres for the dots, as in: http://www.pymolwiki.org/index.php/Image:Dots_ex.png I've uploaded an example of my problem to the wiki as: http://www.pymolwiki.org/index.php/Image:Sheared_dots.png Thanks!
[PyMOL] dots representation
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 dot_radius takes precedence over dot_width, and dot_radius is only apparent after ray tracing)? What are the scales on both dot_radius and dot_width? 2) Is dot_density the only way to adjust how many dots are on a 'sphere'? It only accepts integer values from 1 to 4... Is there some other way to control this parameter, since sometimes I'd love to use a value between dot_density=3 and dot_density=4..? 3) Speaking of dot_density and spheres, is there a good way to adjust the size of the sphere that the dot representation uses? I adjustable this through using alter, and changing the vdw setting for a selection (or object)... (then a rebuild)... Is this the best way? Thanks.
