(using Jmol scripting here....) Three atoms @1, @2, and @3, define a plane.Then
*var n = cross(@1.xyz - @2.xyz, @3.xyz - @2.xyz)* is a vector normal to that plane. Two atoms, @4, @5, define the bond. Then *var b = @5.xyz - @4.xyz* is the vector from atom 4 to atom 5. Then *var a = angle(n, 0, b)* is the angle between those two vectors, and *var x = 90 - a* is the desired angle to the plane rather than to the normal. Could be some sign issue here. Experiment. Bob On Mon, Jul 7, 2014 at 11:42 AM, Victor Rosas Garcia <rosas.vic...@gmail.com > wrote: > Hello everybody, > > I have defined a solvated system, and I have defined a plane using three > hydrogen atoms on separate water molecules. Now I have my solute and one of > its bonds is almost perpendicular to the defined plane. How can I find out > the bond-plane angle? Is such a measurement possible in Jmol? >
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