Anthony, I know that it is possible (but I cannot script it straight away) to
read atom
properties, put them into a Jmol variable and use them, in your case, to draw
the spheroids.
But there may be a simpler solution:
Would the radius of the atom spheres be enough for representing your error? I
mean, do
you need to display the atom as a small sphere plus a spheroid around it, or
just a sphere
would do? When you say a spheroid, is that not a sphere?
If so, there is
spacefill temperature
that will size the atoms according to the "temperature" or "B-factor" field in
pdb file
(originally, a measure of atom mobility, or inaccuracy in the XYZ values). That
goes in
columns 61 to ?? in the pdb file (the decimal dot goes at column 64). **see NOTE
That sould be easy to do in Excel.
Then you just say "spacefill temperature" and you have the balls is assorted
sizes.
Some other advice:
1. Don't insert the applet manually. Use Jmol.js capabilities. It's easier and
you will have
less trouble across browsers.
2. Rathen than "C" for carbon, use "Xx" to tell Jmol these are chemically
unknown atoms.
Shouldn't make a difference in practice, but it's cleaner.
3. Avoid Jmol trying to render bonds: better than "wireframe 0.0", use
connect (*)(*) delete
Difference: not too significant, but e.g. if a user tries the pop-up menu and
changes the
rendering style, if won't spoil your plot with bonds.
NOTE: I checked the PDB:
61 - 66 Real(6.2) tempFactor Temperature factor.
that means columns 61 to 66, with 6 figures before and 2 adter the decimal
point.
BTW, Jmol will use those as angstroms for the spacefill, so you'd better use
small error
values or increase the separaton between your atoms. Both are easy in Excel.
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