I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In
Spartan, I see MEP mapped on a density surface that correspond to the
expectation of ionic sizes (Na+ small, Cl- big). In Jmol, MEP is mapped
on what appears to be a molecular surface matching atomic sizes (Na big,
Cl
Hi,
there is an IONIC radius option for the isosurface comand, have you tried
that?
http://chemapps.stolaf.edu/jmol/docs/#isosurface
Alex
- Ursprüngliche Mail -
Von: Pshemak Maslak n...@psu.edu
An: jmol-users@lists.sourceforge.net
Gesendet: Dienstag, 11. Februar 2014 16:19:44
load nacl.mol
{_Na}.formalcharge = 1
{_Cl}.formalcharge = -1
isosurface ionic
The Spartan reader does not assign formal charges, and you need those for
ionic
Bob
On Tue, Feb 11, 2014 at 9:30 AM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
there is an IONIC radius option for the
To whom it may concern:
I load the following 2 xyz files to Jmol:
one is :
17
!ZX Y Z
60.71255210 -0.00198305 -0.00038352
6 -0.71255210 -0.00198305 -0.00038352
11.211618320.18106610 -0.95074020
1 -1.21161832
RMSD is root mean square deviation. That's what you did?
x = {1.1}
y = {2.1}[1][17]
s = 0.0
for (var i = 1; i = 17; i++) { d = (x[i].xyz - y[i].xyz).distance(0); s +=
d * d }
print Sqrt(s / 17)
0.09403623
or
x = {1.1}.xyz.all
y = {2.1}[1][17].xyz.all
d2 = (x.sub(y)).mul(x.sub(y))
script
better:
x = {1.1}.xyz.all
y = {2.1}[1][17].xyz.all
print sqrt(x.sub(y).mul(x.sub(y)).sum/17)
(Iforgot about array.sum)
On Tue, Feb 11, 2014 at 8:35 PM, Robert Hanson hans...@stolaf.edu wrote:
RMSD is root mean square deviation. That's what you did?
x = {1.1}
y = {2.1}[1][17]
s = 0.0
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