Dear Bob,
thank you very much for fixing this problem so quickly. The mapping now
seems correct. Are the units of potential the same as the CASTEP
potential file (e.g. Hartree)?
>>> Not sure of the additional parameters you are adding there.
The reason I have loaded a {3 3 1} supercell and cropped around the
central unit is to display the solvent-accessible surface with periodic
boundary conditions.
I have noticed that the color range for the mapped electrostatic
potential must be specified in order not to over-emphasize small
differences in top and bottom surfaces.
Another point: the correct periodic boundary conditions are used when
the EP is displayed for planes inside the unit cell, e.g:
$ load "molybdenite_001_01.castep" {1 1 1}
$ isosurface plane z=15 map "molybdenite_001_01.pot_fmt"
Once again, thank you for the help and for the great capabilities of Jmol!
Otello
> This is fixed for Jmol 13.0.9 and 13.1.9. When mapping CASTEP cube
> data, Jmol was not resetting the origin to (0,0,0) at the start of
> mapping. So it was pulling mapped data from the wrong place in the
> cube file.
> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
> Thank you very much, Otello, for spotting this.
> Bob
--
Otello M. Roscioni
Dipartimento di Chimica Industriale "Toso Montanari"
Università di Bologna
Viale Risorgimento 4
40136 Bologna, Italy
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