For a long time now, it's been a bit bothersome to have lots of options 
on the Jmol menu that didn't make sense in Sage.  I've posted a patch 
and spkg that greatly simplifies the menu (but leaves the old menu 
available through an "Advanced" submenu, in case someone has grown fond 
of coloring molecular bonds :).

The spkg and patch are up at http://trac.sagemath.org/sage_trac/ticket/2873

The simplified menu looks like:

View:
   Positive octant
   XY plane
   XZ plane
   YZ plane
Style:
   Perspective Depth
   Boundbox
   Axes
   ----
   Stereographic
     (current submenu)
   Axes
     Hide
     Dotted
     ------
     Pixel width
     Width
   Boundbox
     Hide
     Dotted
     ------
     Pixel width
     Width
Color
   Background
   Axes
   Boundbox
---
Zoom
   (current submenu)
Spin
   (current submenu)
---
Advanced
   (current full menu)
---
About Jmol
   (current submenu)


What do people think?  (You can also apply the patch and install the 
spkg to see the menu).  Are there any other options you use that you'd 
like to see on the menu?  Note that I took off some of the animation and 
picking options since we don't currently use them, but it'd be cool to 
use them and put them back on the menu!

Incidentally, when doing this, I realized that the default view for a 3d 
object is not looking at the first octant, which would see more 
standard.  Is there a reason why we are not looking in the first octant 
when a 3d image is first displayed?

Also, I'll take this opportunity to ask for reviews of 
http://trac.sagemath.org/sage_trac/ticket/3106, which implements a "Get 
Image" link next to every Jmol plot.  Clicking this link pops up a 
static image of whatever is in the jmol applet, which you can then copy 
and do whatever with.

Thanks,

Jason


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