Thanks Bob for all your answers ! I'd need another life to test all your
suggestions but here is what I did to solve my problem :
- I updated my applet to todays version. It did not solve the problem. But it
requested less minimization/add hydrogens steps to work
- I used the filter '2d' settind with the load data script command, and it
works beautifully. Minimization happens in the background (no wriggling shaking
quaking molecule) which suits me perfectly.
I encountered another problem when I transferred back the model from Jmol to
chemdoodle and then transferred it again from chemdoodle to Jmol : as 3D
coordinates were included, when I loaded the new model in Jmol, the hydrogens
were not calculated.
So I wrote a little script to zero the Z coordinates, and it now works as
expected.
For the record, here is how I get the mol file from chemdoodle sketcher :
1st: I need to set an io object. I called it writeMOL...
writeMol = new ChemDoodle.io.MOLInterpreter();
2nd: my doodle to Jmol function looks like this :
function doodle2Jmol() {
var molFile = writeMol.write(sketcher.getMolecule());
//Let's 2D the 3D !
var tab = molFile.split("\n");
for (i in tab) {
if (tab[i].indexOf(" ")==0) { //that line has coordinates !
var tab2 = tab[i].split(" ");
tab2[3] = "0.0000";
tab[i]=tab2.join(" ");
}
}
molFile = tab.join("\n");
var spt = "load DATA \"model\"\n" + molFile + " \"model\" " + "filter
'2D'";
jmolScript(spt);
}
-Paul
------------------------------------------------------------------------------
Magic Quadrant for Content-Aware Data Loss Prevention
Research study explores the data loss prevention market. Includes in-depth
analysis on the changes within the DLP market, and the criteria used to
evaluate the strengths and weaknesses of these DLP solutions.
http://www.accelacomm.com/jaw/sfnl/114/51385063/
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