Ah, ok. That makes sense. The COSMO file itself must be reloaded, not the
mol file. I don't know where the COSMO file comes from, but it appears not
to have come from 1-chlorobutane.mol. (Or, if it did, then some program is
messing with that file! You need to load the COSMO file itself along with
the JVXL file. Here's a revised function. Just call it as
loadCosmo("xxx.cos", false) before issuing the JVXL file. It's not clear to
me, if you have the COSMO file, why you would want to create a JVXL file.
Bob
function loadCosmo(fname, withSurface) {
if ("" + withSurface == "") { withSurface = true } # default TRUE
print "reading " + fname
Var fdata = load(fname).split(" DATA")
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata = "" + n + "\ndata are from " + fname + "\n"
print "nAtoms = " + atoms.length + " nSegments = " + segments.length
for (Var i = 1; i <=atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + " - " + radius + "\n"
}
if (withSurface) {
for (Var i = 1; i <=segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += "Xx " + (segments[i])[17][52] + sigma + "\n"
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme "rwb"
delete _Xx
} else {
load inline @fdata
}
}
On Thu, Feb 24, 2011 at 6:46 PM, Eduardo Oliveira <eduardo...@gmail.com>wrote:
> Hi Bob,
>
> I do the following steps:
>
> 1) I load 1-CHLOROBUTANE.mol
> 2) I open the console and enter this:
>
> function loadCosmo(fname) {
> print "reading " + fname
> Var fdata = load(fname).split(" DATA")
> Var atoms = fdata[2].lines[3][-2]
> Var segments = fdata[3].lines[3][0]
> Var n = atoms.length + segments.length
> fdata = "" + n + "\ndata are from " + fname + "\n"
> print "nAtoms = " + atoms.length + " nSegments = " + segments.length
> for (Var i = 1; i <=atoms.length; i++) {
> Var radius = (atoms[i])[52][63]
> fdata += (atoms[i])[6][51] + " - " + radius + "\n"
> }
> for (Var i = 1; i <=segments.length; i++) {
> Var sigma = (segments[i])[77][88]
> fdata += "Xx " + (segments[i])[17][52] + sigma + "\n"
> }
> load inline @fdata
>
> isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
> {_XX} ignore {not _XX} property partialcharge colorscheme "rwb"
>
> delete _Xx
> }
>
> loadCosmo "1-CHLOROBUTANE.cos"
>
> 3) I obtain picture nº 1
> 4) I right click File>Save jvxl surface
> 5) I obtain nº 2
> 6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
> "2.jvxl" colorscheme "rwb" and i get nº3.
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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