![jmol color scheme jmol color scheme](https://cbm.msoe.edu/markMyweb/jmolWebsite/images/glossaryImages/colorChains1.jpg)
Select :a isosurface A solvent delay 1 color isosurface red delay 1 select :b isosurface B solvent color isosurface blue move 0 360 0 0 0 0 0 0 4 delay 2 isosurface A off delay 2 isosurface A on isosurface B off delay 2 isosurface A on isosurface B on delay 2 isosurface A off isosurface B off ĭisplay a pre-calculated surface ("dnasurface.jvxl"). Note: naming the isosurfaces when you create them allows for displaying and manipulating multiple isosurfaces. Rotate 360 degrees, then turn one of these isosurfaces off, then the other off, then display both. Select nucleic isosurface dna1 solvent delay 1 color isosurface red delay 1 color isosurface blue delay 1 color isosurface translucent move 0 360 0 0 0 0 0 0 4 Ĭalculate two separate isosurfaces (named A and B) for the A and B chains. Rotate 360 degrees around y axis in 4 seconds.
![jmol color scheme jmol color scheme](https://cbm.msoe.edu/markMyweb/jmolCreatorStonyBrook/images/contentImages/help3.jpg)
JmolRadio(' Jmol scripts here', "", false ) Ĭalculate a surface (default color is gold, name of surface = dna1), color surface red, then blue, then white, then set as translucent. Molecular Electrostatic Potential surfaces are described below.Cavities may be depicted ('isosurface cavity').The solvent accessible surface ('isosurface sasurface') is a contour of the center of the probe as it is rolled on the molecule of interest.'isosurface molecular' sets a probe radius of 1.4. Radius of the spherical probe (in Angstroms) may be specified (default is 1.2). The solvent excluded surface ('isosurface solvent') is determined by rolling a probe solvent atom on the molecule at the distance of the van der Waals radii of the atoms.Use 'isosurface "filename.jvxl" ' to load the surface.ĭifferent types of surfaces may be specified (for more detail, see the Jmol Interactive Scripting Docs):.Copy the Jvxl file into the directory of the web page you are building so that the path to the Jvxl file can be easily linked.Use the 'write isosurface filename.jvxl' command to save the surface in a Jvxl file (this will save into the directory of your Jmol applet).Use one of the 'isosurface' commands (see below) to calculate the molecular surface of the selected molecule/s.Select the portion of your molecule you wish to display the surface of (e.g., "select nucleic" or "select ligand").Open the scripting window of the applet for command entry.
#Jmol color scheme full#
Versions 11.2 and up are recommended for full implementation of features below.