The isosurface command is similar to the pmesh command in terms of options. By naming these individual surfaces with unique identifiers you can control display settings and color for each of the surfaces independently. cube files, you can construct different isosurfaces with different shapes and sizes. cube file more than once with different parameters, or by reading different. Any number of display characteristics (such as "DOTS MESH NOFILL") may be included in a single isosurface command. Parameters to the isosurface command control the cutoff value and the display characteristics of the surface. You can give them distinct names and control their display properties independently. Note that positive and negative surfaces are created separately. Inside the surface, values are greater or equal to a specified positive cutoff or less than or equal to a specified negative cutoff. This surface represents the points in space where scalar values cross a specified "cutoff" value. cube file.Ī separate isosurface command is used to read the scalar field data and construct the isosurface. The load command reads only the atom position data from the. cube format, which contains both atom positions and scalar data. Jmol can generate isosurfaces from scalar field data in files of the gaussian. If you put an opaque object behind a translucent object, then you will see the object in the back.But if you put a translucent object behind another translucent object, then you will not see the translucent object in the back. Rather, translucent objects are "screened" so that every other pixel is painted. Note that the implementation of 'translucent' is not as an alpha channel. The level of 'translucent' cannot be controlled it is set at 50%. But if you 'color bonds opaque' or 'color bonds red' and also 'color atoms translucent' only the atoms will be translucent. If you simply 'color atoms translucent', then both the atoms and the bonds will be translucent. For example, by default a bond will inherit the two colors+translucencies of its endpoint atoms. Many objects inherit both color and opacity from the underlying associated atom (which, themselves "inherit" their color by default from their associated chemical element). In that case, however, the result is complicated by color inheritance, discussed next.Ĭolor Inheritance. Translucent and opaque can also be used alone with an object, even without specifying a color:
Thus, 'color atoms red' and 'color atoms opaque red' are synonymous. Setting a color sets the translucency to 'opaque' by default. The color command allows an optional color modifier of 'translucent' or 'opaque', which can be used with any object. Following that can be a rather wide variety of one- or two-word options, described below and dependent upon the kind of object being colored. If no object is given, then 'color atom' is assumed, and the currently selected atoms are colored. The first parameter of the color command specifies the object of that command. In general, the color command takes the following syntax: In addition, a page is in construction that lays out the. This will help us prioritize future development.Īdditional information external to this documentation can be found in relation to and. Please give us feedback on what features you use and that are currently That supports a larger number of file formats on a wider variety of This will provideĪ migration path for those who wish to move to an open source solution
#Color residues jmol full#
Goal is to eventually provide full script support. Jmol currently supports many of the RasMol/Chime scripting commands. The current URL for extended chime scripting commands Various extensions were added, including additional scriptingĬommands. The Chime web browser plug-in was based upon the RasMol source code. The current URL for full RasMol documentation Jmol supports the RasMol scripting language defined by RasMol. Supply feedback in case of bugs and/or unexpected behavior and/or As of this writing it should be considered *alpha test* code. The scripting engine has been completely rewritten for Jmol ReleaseĦ.
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