Jmol 10.x.19+ working document on isosurface. Last updated 4:01 PM 7/4/2006
see http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm for details.

The isosurface command is proving to be quite rich in its
generality. The basic sequence of all isosurface commands is:

  isosurface [id] [construction-parameters] [surface-object]
    [mapping-object] [display-parameters]

Here is a quick rundown of what these options involve. I realize it's
quite a large collection of options. Not all are compatible with each
other. See
<http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm>
for details. 

" " indicates a string INCLUDING the quotation marks
(a) indicates some atom expression INCLUDING the parentheses
{ } indicates a three or four coordinate set INCLUDING the braces
[ ] indicates an optional parameter -- don't include the brackets
 |  indicates "or"
 $  indicates a dollar sign, which would be followed by an object name
 

[id]

 is an optional name for this object


[surface-parameters]

 anisotropy {ax ay az}
 center (a)|{x y z}|$name
 color <color1> [<color2>]
 color absolute <min(red)> <max(blue)>
 colorScheme ["roygb"|"rwb"|"low"|"high"]
 contour <n> (number of contours)
 contour <-n> (negative indicates just the specified contour)
 cutoff <value>
 debug|nodebug            (voluminous details to Java console)
 eccentricity {cx cy cz f_ab}
 fixed|modelbased         (not attached|attached to the current model)
 gridpoints         (shows grid points used to construct the surface)
 insideout     (use if illumination is backward)
 phase ["x"|"y"|"z"|"xy"|"xz"|"yz"|"x2-y2"|"z2"] (optional type)
 resolution <pts_per_angstrom>
 reverseColor  (switch direction of coloring)
 scale <value>
 sign [<color1> [<color2>]] (color by the +/- sign of the value) 

 
[surface-object]

 "cube or jvxl file name" [<integer>] (optional surface index, starting with 1)
 "" [<integer>] (use the currently loaded file if CUBE or JVXL itself)
 ellipsoid {cx cy cz f_ab}
 functionXY "function-name-to-call" {xyz origin} {ni ix iy iz} {nj jx jy jz} {nk kx ky kz}
 lcaoCartoon [-]"<type(see below)>" (a)|{x y z} 
 lobe {cx cy cz f_ab}
 mo <index>  (a specified ab initio molecular orbital contained in an SMOL or WebMO file)
 atomicOrbital n l m [Zeff]
 plane {a b c d}
 sasurface [<radius>]
 solvent [<radius>]
 sphere <radius>


[mapping-object]
 
 map "cube or jvxl file name" [<integer>] (optional index)
 map "" [<integer>] (use the CUBE or JVXL file currently opened using "load")

 (the MAP keyword is only required if no surface object is indicated)

[display-parameters]
 
 dots|nodots
 fill|nofill
 mesh|nomesh
 translucent|opaque


lcaoCartoon notes
-----------------

lcaoCartoon types include the following. Note that specific lobes can be
targeted. This may take some experimentation to get the desired lobe, as
the lobe drawn depends upon the order of atoms attached to the central atom.
A minus sign prior to the type flips the direction of the lobe 180 degrees.
Note that each lobe of a p orbital is its own isosurface. 

 "s" (s orbital)
 "px"|"py"|"pz" (two lobes)
 "pxa"|"pxb"|"pya"|"pyb"|"pza"|"pzb" (single p orbital lobe)
 "sp2" (trigonal planar-directed lobe)
 "sp2a"|"sp2b"|"sp2c" (specific sp2 lobe)
 "sp3" (tetrahedrally-directed lobe)
 "sp3a"|"sp3b"|"sp3c"|"sp3d" (specific sp3 lobe)


note to current isosurface users (7/06)
---------------------------------------

You will find that isosurface behaves essentially as it always did. There are
many new keywords, of course, and the COLOR keyword has a much broader meaning.
Previously, COLOR simply introduced the word "absolute" or the filename of the 
mapping file, but since there is so much more we can do now than just mapping,
the COLOR keyword is no longer necessary for that purpose. Instead, it is only
necessary for "COLOR ABSOLUTE" or "COLOR <color name>". The keyword MAP introduces
a mapping data file when there is no surface object indicated.