Jmol color scheme how to#

The default Y rate is 30 and 0 for X and Z rates. Mouse button > Spin > Set X (Y or Z) Rate > XX). > Spin > Off). You can try this in an open JmolĪpplication or by clicking the link in figure 2 to convert it to a liveĪbout axes other than Y select the rate (degrees per step)įor rotation about the X or Z axis. The spinning of the molecule use the pop-up menuĪgain (Right mouse button, control-click on one button mice, Using the default spin settings use the pop-up menu in both theĪpplication and the applet (Right mouse button, control-click on oneīutton mice, > Spin > On). You can try this inĪn open Jmol application or by clicking the link in figure 2 to convert

Jmol color scheme how to#

- Electrostatic Potential: how to compute electrostatic potentials in SwissPDB Viewer or open potentials computed by other programs.View of staggered ethane ( ethane-staggered-3-21G.log).- MSMS package for calculating molecular surfaces.Runs the calculation on the web server, the surface can be obtained in the form of a PDB file with oxygen atoms. You can derive volume information from any PDB file.Volume calculator web tools also downloadable. Using the Richards' rolling probe method, - Solvent-Accessible Surfaces (part 5 of Molecular Surfaces: A Review, by Michael L.Images generated by Angel Herráez or Bob Hanson. Information was obtained through testing, from jmol-users and jmol-developers e-mail distribution list, and from Bob Hanson's Interactive Scripting Documentation and example pages. This page was written by Angel Herráez, Universidad de Alcalá, in Spain. Seek more information on the official Interactive Scripting Documentation. Isosurfaces can also be colored in gradients according to a 'map', including by distance, by molecular electrostatic potential, etc. Remember you can use translucent or opaque in addition to the color. If the isosurface was assigned an id, then use color $ id color specification. Use color dots, color geoSurface, color isoSurface, color pMesh, etc. Same syntax as loading from a JVXL file (above).Surface input from Gaussian Cube format file If the file contains data for several isosurfaces or the isosurface data is within the same file as the coordinates, look up the interactive scripting documentation.If required while writing the page with JavaScript, you can use isoSurface ' filename '. Double quotes are mandatory around the filename (path, name and extension).Simple way: isoSurface ' filename ' or isoSurface file ' filename '.This renders the surface in almost no time (much less than the calculation needed to generate the surface the first time).Save the file (any extension will do, but. Copy the (long) result from the console and paste it into a text editor.From script: console on show isoSurface.Equivalent: pop-up menu > Show > Isosurface JVXL data (will open the console and output the data to it).If you are working in the console, use show isoSurface.Suggestion: clear the console (this facilitates copying the complete text later).First, generate and render the surface ( isoSurface saSurface or isoSurface solvent or any other isosurface).More details in the isoSurface documentation and in detailed specification of the JVXL format (PDF).Further, it can be generated by Jmol, while Cube is only generated by Gaussian (a commercial program). Briefly: JVXL is specific to Jmol and is a much more compact alternative to Cube format, containing only the information for one or a few surfaces.Other options, more advanced (see the interactive scripting documentation): isoSurface planeĦ) Saving and loading surface data Surface output to and input from JVXL (Jmol Voxel) format file The optional id assigns a name to the surface, so that later one can turn it on and off selectively, change its color or translucency.size: apart from changing cx cy cz, the size of the ellipsoid can also be changed using the scale n keyword (before the ellipsoid keyword).[ 100) or shrinks (size1: ellipsoid is shortened along the main axis (disk shape).