Otello,
On Fri, Nov 16, 2012 at 7:50 AM, Otello Maria Roscioni <
otellomaria.rosci...@unibo.it> wrote:
> 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)?
>
>
Yes -- Jmol just takes whatever units are presented in the file. No
conversions. Note that you can use
set drawHover TRUE
and then hover over the surface to inspect numbers. Also,
set isosurfaceKey TRUE
is one of the newer additions to Jmol you might appreciate.
> >>> 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.
>
>
Yes, that is right. It is common when showing MEP to use a fixed range of
colors. For example:
color isosurface range -0.5 0.5
so that different models are represented on the same scale.
> 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
>
>
My pleasure! I'm very interested in seeing what the solid-state community
does with Jmol. Keep us posted!
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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