Thank you again, Bob, for your help. The trick is to use Jmol's
calculated values for surface MEP as the defining points for the
coloring scale, and not the partial charges values in the coordinate
file. (Maybe not so much of a trick if I knew what I was doing to
start with!) These values appear in the console when you set
debugscript on, which is very handy Bob!
I have posted a page with a grid for comparing the results of
"... color range all ... " with "... color range [defined] ..."
and
calculating the MEP over the side chain only vs. calculating for the
whole amino acid., i.e., the option including "select {*}" that Bob
outlines below.
http://moleculesinmotion.com/patterson_aas2/aminoacids/index.htm
The isosurface command used is listed above each column, and the data
calculated by Jmol are listed in a table below the applets. I hope
this may be useful to others pondering some of the options for MEP
display.
To me, for teaching about polar and non-polar side chains, calculating
over the side chain alone looks like the way to go, and restricting
the color range creates a very non-polar looking surface for valine,
contrasting with a nice charge level for asp. I am not sure I can
figure out what is going on with valine with 'color range all' and
calculating only over the side chain. (Top row, third column).
I'll be using this to make a page that will enable students to compare
the MEP of any two amino acid side chains and hopefully also
nucleotide bases and a few other small molecules. When it's finished I
will post the URL to the list, hope it may be of interest to some for
teaching purposes.
Best,
Frieda
On Aug 6, 2008, at 2:25 AM, Bob Hanson wrote:
> I think you want
>
> isosurface select {xxxx} molecular map select {*} mep
>
> That is, when you run the mep, you want to indicate that for THAT part
> of the calculation, you want all atoms selected. I hadn't realized
> myself that two selects work here -- I suppose it could be useful.
> Or not.
//////////////////////////////////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//////////////////////////////////////
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