Using the +n parameter overrides the existing set solvent / set radius status.It is a crude rendering but calculates quickly, and has better visibility than dots.Hence, the syntax is the same as for dots. ![]() Draws a geodesic surface using the result of dots as vertices.(note: geoSurface off will also hide the dots). The expansion of spheres (probe radius) will be 1.2 unless otherwise stated by a previous set radius. Dots color is inherited from current color atoms and may be overrided by using color dots.Using the +n parameter overrides the existing set solvent and set radius status.Draws a dotted surface, using expanded dotted spheres (but only surface dots, no dots in the enclosed volume).Color is according to previous color atoms command (CPK scheme by default). ![]() 1.2 and 1.4 (Å for probe radius) are the commonly used values, but you can use any other.Since the rendering uses the atoms, it is incompatible with showing atoms and bonds inside the "surface".Draws atoms as expanded van der Waals spheres, giving the impression of a solid surface.(images of dots 100% and spacefill 100% shown as a reference) It is larger (more external) than the "molecular" surface.Sort of an expanded van der Waals surface. Corresponds to using an extended sphere around each atom (at a distance from the atom centre equal to the sum of the atom and probe radii), and eliminating those points that lie within neighbour spheres.Described by the center of the probe as it rolls along the atoms vdW spheres.solvent-excluded surfaces or molecular surfacesġ) Solvent-accessible surfaces (or Lee-Richards surfaces). ![]() The probe radius can be defined using the set radius command. Jmol, as Rasmol, uses a sphere with 1.2 Å radius for water Chime uses 1.2 Å for dots and 1.4 Å for surfaces. The mix of lower- and uppercase in the commands is for better readability, but Jmol is not case-sensitive.ĭefinition: probe (solvent probe) is a sphere that approximates the effective size of the solvent molecule. Syntax used: a command in the script language a parameter description that must be filled in with a value. For details, go to the official interactive scripting documentation for each command. This documentation does not detail all the options, but aims to collect the different ways to render surfaces, and clarify their differences. There is a testing / demo page including a Jmol applet to see results.
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