[Jmol-users] MEP Display

[Otis R. <ot...@ch...>]

Hello-

I need some advice on MEP display script. When I use the following script:

isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6
MOLECULAR color map mep;isosurface translucent;delay 2; echo;


I get proper MEP's for most molecules, but some molecules present
problems. For example, m-nitrophenol's MEP is completely blue (colors
= "roygb") even though the partial charges in the file are reasonable.


If I use the following script, which inserts "range all," then the
above problem disappears, but the simple sequence ethane, ethene,
ethyne is a bit disappointing - colorful, but disappointing:

isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6
MOLECULAR color range all map mep;isosurface translucent;delay 2;
echo;

The "point" is still captured in these latter hydrocarbon displays,
but this raises two questions:

1) I thought "range all" was default, but there must be another
default. What is the default range in the above script context?

2) I think my first line of script above comes close to the Jmol left
click menu script of "isosurface delete resolution 0 molecular map MEP
translucent." Indeed, the menu produces the same blue m-nitrophenol (o
and p as well). What is the current recommendation for a MEP script?

Again, the partial charges in the files are reasonable, and they can
be read by a direct call to:

select; wireframe 0.03; spacefill 1%; spacefill 1%;label
\"%-8.3[partialcharge]\";

Otis

-- 
Otis Rothenberger
http://chemagic.org