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 <eduardoydo@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 nš 1
4) I right click File>Save jvxl surface
5) I obtain nš 2
6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
"2.jvxl" colorscheme "rwb" and i get nš3.

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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