Other possible ways:

1) use a script file, so you can reload the coloring in one go

2) use javascript, e.g.:

var nrRes = 800
var c = ["FF0000", "FF3300", "FF6600",  (etc.)  ]
/* array with 800 colors, but this could be autogenerated using 
javascript too; see e.g. 
http://wiki.jmol.org:81/index.php/Recycling_Corner#Molecule_color_pick
er
where 125 colors are generated using javascript
*/
var scr = ""
for (var i=1; i<=nrRes; i++)
{
  scr += "select resno=" + i + "; color [x" + c[i-1] + "]; "
}

function userColorJmol()
{
        jmolScript(scr)
}

In fact, I'm quite sure that method (2) can be implemented in Jmol 
script, but I don't master that yet.



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