![]() This figure shows how the electrostatic potential superimposed on the 0.002 au isodensity surface can be used to rationalize why cis-HO(H)C=C(H)OH is more stable than trans-HO(H)C=C(H)OH, while the opposite is true for CH3(H)C=C(H)CH3. (click on the picture for a bigger version).įrom Molecular Modeling Basics CRC Press, May 2010. In both cases, the maximum potential value is 0.05 au. (a) RHF/6-31G(d) 0.002 au isodensity surface with superimposed electrostatic potential for (a) cis-HO(H)C=C(H)OH and (b) cis-CH3(H)C=C(H)CH3 and. The default surface is a solvent accessible surface, which is slightly larger than the van der Waals surface.Ī static and interactive version of the Avogadro and Jmol electrostatic potential map, respectively, can be found here.įigure 3.5. Isosurface solvent color range -0.05 0.05 map mepĪnd this set of commands can thus be used to control the color range and the nature of the surface. The electrostatic potential option in the Jmol menu corresponds to the following set of commands (as far as I can determine): Jmol is not able to determine the charges, but the information can be transferred from Avogadro by saving a mol2 file. It is currently not possible to alter the color range as far as I can see. #Jmol color scheme iso#An Iso Value of 0 seems to correspond to the van der Waals sphere surface. It is possible to change the surface using the so-called "Iso Value" but I could not find any documentation on how that actually works. #Jmol color scheme how to#The screencast above shows how to make such electrostatic potential maps using Avogadro and Jmol.Īvogadro uses an empirical method to determine the atomic charges (an integral part of the MMFF force field). Similarly, the electrostatic potential due to atomic charges can be a reasonable substitute for the electrostatic potential due to the electronic density. Previous posts ( such as this one) have demonstrated that the van der Waals surface is a reasonable substitute for the 0.002 isodensity surface. Depending on the input file format, not all fields may be defined.In a previous post I showed how to compute an electrostatic potential map superimposed on the 0.002 isodensity surface of a molecule based on data computed using quantum chemical methods such as RHF/6-31G(d). Used to specify the options of a GLModel. If set, only display in this frame of an animation How to orient the label w/respect to position: topLeft (default), topCenter, topRight, centerLeft, center, centerRight, bottomLeft, bottomCenter, bottomRight Position is in screen (not model) coordinates which are pixel offsets from upper left corner.Īn element to draw into the label. Sets the label to change with the model when zooming Show background rounded rectangle, default true Line width of border around label, default 0 Label type specification Properties: Name If true, user can click on object to trigger callback Volumetric data for vertex coloring, can be VolumeData object or raw data if volformat is specifiedĬoloring scheme for mapping volumetric data to vertex color, if not a Gradient object, show describe a builtin gradient one by providing an object with gradient, min, max, and (optionally) mid fields.įormat of voldata if not a $3Dmol.VolumeData object Width of line for wireframe rendering No longer supported by most browsersĬoordinates around which to include data use lectedAtoms() to convert an AtomSelectionSpec to coordinatesĭistance around coords to include data Specifies the isovalue to draw surface at Isosurface style specification Properties: Name Overloaded to select number of bonds, e.g. Reverse indexing is allowed (-1 specifies last added model). Can also specify by numerical creation order. Integer numerical ranges are supported as strings.Ī single model or list of models from which atoms should be selected. Properties: NameĪny field from AtomSpec, values may be singletons or lists. If valuesĪre provided as a list, then only one value of the list must match. Can includeĪny field from AtomSpec in which case atoms must equal the specified value.Īll fields must match for the selection to hold. Used to specify what atoms should be selected. ![]()
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