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Are there standards for density cutoffs, colours and colour mappings for electrostatic potential surfaces?

I observe that people use many different values. For instance, this article (in Fig. 1a) uses 0.001 au density cutoffs with colours ranging from blue (< 0 kcal/mol) to red (> 20 kcal/mol).

I understand that not every colour/energy range will work every time, but other publications/websites even switch the colour range. This website, for instance, uses red for negative energies and blue for most positive ones. Furthermore, the same website suggests a .02 au cutoff.

Are there recommendations on this? Which values are more commonly used by textbooks?

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You have probably found out from playing around that there are many options. For coloring there is no standard, blue and red are common because they are the easiest to see since they contrast well. As far as the density cutoff, there are some papers that recommend values but the main idea is to choose a value that gets close to the Van Der Waals radius for the atoms. This is after all what is typically is of interest in a chemical sense. The electron density at the Van Der Walls surface is what others atoms/molecules "see". Typically I will just plot both the Van Der Waals and electrostatic surface and modify the electrostatic cutoff to make them close. Then you can set the limits for positive and negative colors.

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  • $\begingroup$ Since it is then a matter of surface accessibility, would you recommend colouring the van der Waals surface instead of an electron density isosurface? $\endgroup$ – Felipe S. S. Schneider Jan 17 '17 at 23:18
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    $\begingroup$ It depends on what you are interested in. If you want to know where there is an excess/depletion of electron density the electron density surface is good for that. If you just want an idea of the bulk and access ability of a part of a molecule the Van der Waals surface is a good idea. In the case of the Van der Walls surface, you might want to consider the Connolly molecular surface or something like that, check Wikipedia for "Accessible surface area" for an idea of what it is. $\endgroup$ – brose Jan 18 '17 at 2:34

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