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?
These arise from differences between OpenGL rasterization and ray tracing. PyMOL line and dot widths have the name meaning as their underlying OpenGL primitives (pixel widths), and they dominate over line and dot radii settings such that you get WYSIWYG raytracing output which is faithful to the OpenGL view in terms of cross-sectional area. If you set the radii values explicitly (Angstroms), then the ray tracer will be affected, but not the OpenGL viewer. 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..? No. The existing dot densities arise from successive cycles of isocosohedral interpolation. The code would need to be changed to support alternate sphere discretiziation topologies. 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? Yes. Cheers, Wawrren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of O. J. Ganesh Sent: Tuesday, July 29, 2008 1:32 PM To: pymol-users@lists.sourceforge.net Subject: [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. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
