On Wed, April 16, 2008 6:32 am, Brian McMahon wrote: > Bob > snip > > I doubt that it's Jmol's job to distinguish between "main residue" and > "small moiety", so I would suggest allowing an optional colour scheme > that maps ellipsoid colour to maximum/minimum main axis ADP ratio > that runs something like this: > > max/min ratio > 6.0 colour ellipsoid RED > max/min ratio > 5.0 colour ellipsoid ORANGE > max/min ratio > 4.0 colour ellipsoid GREEN > max/min ratio > 3.0 colour ellipsoid BLUE > max/min ratio > 2.0 colour ellipsoid INDIGO > max/min ratio > 1.0 colour ellipsoid VIOLET > max/min ratio > 0.0 colour ellipsoid GREY > > and if non-positive definite, colour ellipsoid YELLOW.
But how do we tell, at a glance, the difference between a bad hydroxyl O and an OK one if they are both red (for just being oxygen)? I think something other than colour needs to be the cue for bad ADP ratios so they don't get mistaken for a normal atom-type display. For NDP atoms I like mercury's choice of displaying a cube. Rich ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
