I have figured out how to use "isosurface" with "lobe" commands to
generate and orient the cartoon orbital lobes.
For example: isosurface sp2a color [97 173 62] center (atomno=2) lobe
{1 1 -1 0.8}; color $sp2a translucent 4 on;
I can even add electron pair dots using "draw circle" and place them
within the lobe.
For example:
draw dot1 circle {@2} {z} scale 0.03 color black offset {0.77 0.60 -0.6}
draw dot2 circle {@2} {z} scale 0.03 color black offset {0.60 0.60 -0.6}
My dots are "rigidly" positioned, and in some orientations of the model
they eclipse each other.
However, the "lcaoCartoo lonepair" generated dots always stay the same
distance apart (adjust their relative position) as the model is
manipulated.
How can I reproduce that "lonepair" behavior?
Thanks,
PM
On 12/5/2012 2:47 PM, Pshemak Maslak wrote:
The lcaoCartoon command run on CO2 structure (spartan):
select @2
lcaoCartoon scale 2.0 color [97 173 62] translucent
lcaoCartoon create "sp2b"
creates a lobe that is collinear with the O-C-O axis (rather than
about 120 degrees from it). "lonepair" creates similarly positioned
pair of dots.
Is there a way to adjust that position to its "proper" angle? I
presume that the problem is common to all linear molecules. The sp3
lobes (or lone pairs) are created essentially in one plane (for
example for fluorines in XeF2).
Any suggestions would be appreciated,
PM
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