> > I have two points that I think should be improved in > following pymol versions, and one question. > 1) Secondary structure can be viewed as cartoons, or as > colors. The problem is the boundaries are not the same. If I > color a strand by secondary structure, it seems that the > following loop is a strand as well. I'm attaching a figure to > make the point clear.
set cartoon_discrete_colors, on > 2) When viewing proteins as spheres, and then zooming into > them, the spheres seem hollow. This is can be very perplexing. Yes. Unfortunately this is a hard thing to fix -- basicially we would need to draw a circle right on the front clipping plane that would mask each sphere that intersects the front clipping plane. > The question is regarding plugins. I'm using MacPymol Version > 0.98beta27 , on a G3 mac with OS10.2.8. Although there are > plugins in the right directory, I can't activate them. What > am I doing wrong? Mixing apples & oranges. Plugins only work with Tcl/Tk-based versions of PyMOL, such as the pure X11 and Hybrid X11 builds. MacPyMOL is written in Cocoa, not Tcl/Tk. Cheers, Warren
