Friday, 25 January 2013


Arrows in molecular graphics are always pretty. So what can you do?

For molecular vibrations, I prefer Jmol. Turning on the "vectors" can simply be done in the context menu. For the scaling it is usually best to use the console (as described here), e.g.

 vector SCALE 0.03

The result looks something like this (more details about the molecule in this paper):

Another nice feature is that you can export transparent pngs using "PNGT"

write IMAGE width height PNGT n "fileName"

Then you can play around with it a little bit and create more fancy graphics (coming from this paper):

If you have any other kind of arrows you want to draw, like for example (transition) dipole moments, you can just set it up yourself in VMD. For example:
draw delete all

draw color red
draw cylinder {0 0 0} {19.28 -1.42 0.0} radius 0.4
draw cone {19.28 -1.42 0.0} {21.200001 -1.560000 0.000000} radius 0.8

draw color blue
draw cylinder {0 0 0} {-5.60 0.60 0.0} radius 0.4
draw cone {-5.600000 0.600000 0.000000} {-6.160000 0.660000 0.000000} radius 0.8
The nice thing compared to doing it in an external editor is that it also works well in 3D (assuming that you entered proper coordinates for the vector)

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