Bob,
This might be useful, but I'm frustrated that I blew getting the JmolScript
history. Formerly, this text could simply be copied. Did something change in
Java security related to this?
Anyway, here's the point of possible interest: While trying to cause this
error, I kept my eye on the Java console. After one successful click of the MEP
100 link, I noticed the appended Java console error even though the MEP was
displayed. The reason for this is that this model already has charges (mol2).
We don't kick auto charge calculation in until an model edit takes place. It
looks like I have a double dot code error. My problem is that I don't see it in
my code. I'll keep looking for it.
By the way, the expression e_x_p_r_e_s_s_i_o_n = e_x_p_r_e_s_s_i_o_n appears
also in the JmolScript history that wiped out while trying to copy. I think the
expression in question comes from my JavaScript mep() function:
function mep(num) {
if (num == 6) { doClean(); mepOn = false; objColor("mep3", "#ffc0cb");
objColor("mep2", "#ffffcc"); objColor("mep1", "#ffffcc"); return; }
setJsState(); var scpt = ""; var rng = "-.07 .07";
if (num == 3) { doClean(); calcPartial(); jmolScript('color {*}
partialCharge;color label yellow;label %-8.4[partialcharge]'); return; }
if (num == 4) { doClean(); jmolScript('dipole bonds on; dipole calculate
bonds; dipole molecular off'); return; }
if (num == 5) { doClean(); jmolScript('dipole molecular on; dipole
calculate molecular'); return; }
if (num == 2) { rng = "-.16 .16"; }
if (jmolEvaluate("{*}.partialCharge.sum") > .9 ||
jmolEvaluate("{*}.partialCharge.sum") < -.9) { rng = "all"; }
if (num == 1) { mepOn = true; objColor("mep1", "#ffc0cb"); objColor("mep2",
"#ffffcc"); objColor("mep3", "#ffffcc"); calcPartial(); scpt = "select {*};
isosurface resolution 0 vdw color range " + rng + " map mep translucent;"; }
if (num == 2) { mepOn = true; objColor("mep2", "#ffc0cb"); objColor("mep1",
"#ffffcc"); objColor("mep3", "#ffffcc"); calcPartial(); scpt = "select {*};
isosurface resolution 6 vdw 65% color range " + rng + " map MEP opaque;"; }
jmolScript(scpt);
}
Otis
JAVA CONSOLE
FileManager opening
http://chemistry.illinoisstate.edu/osrothen/models/2-chlorobutane_(R).txt
script 15 started
Error evaluating: {*}.partialCharge.sum
java.lang.StringIndexOutOfBoundsException: String index out of range: 44
eval ERROR: invalid argument
----
e_x_p_r_e_s_s_i_o_n = e_x_p_r_e_s_s_i_o_n { all } . partialCharge
partialCharge . >> . << sum
script ERROR: invalid argument
----
e_x_p_r_e_s_s_i_o_n = e_x_p_r_e_s_s_i_o_n { all } . partialCharge
partialCharge . >> . << sum
Script completed
Jmol script terminated
script 16 started
Script completed
Jmol script terminated
script 17 started
14 atoms selected
27 SMARTS matches used
Script completed
Jmol script terminated
script 18 started
14 atoms selected
isosurface resolution 0 vdw color range -.07 .07 map mep translucent;
solvent probe radius set to 100%
solvent-accessible surface with radius 0.0
Using surface reader org.jmol.jvxl.readers.IsoSolventReader@b0a168
14 atoms will be used in the surface calculation
isosurface resolution for axis 1 set to 3.898546 points/Angstrom; 35 voxels
isosurface resolution for axis 2 set to 3.9683704 points/Angstrom; 28 voxels
isosurface resolution for axis 3 set to 3.926425 points/Angstrom; 27 voxels
reading data progressively -- yzCount = 756
solvent surface time: 31 ms
boundbox corners {-3.8552752 -2.5683076 -2.478205} {3.8535705 3.2247012
3.131318}
Using surface reader org.jmol.jvxl.readers.AtomPropertyMapper@34e67d
14 atoms will be used in the surface calculation
0 contour lines; separation = 0.14
isosurface1 created with cutoff=0.0; isosurface count: 1
isosurface full data range -0.08323054 to 0.08682171 with color scheme spanning
-0.07 to 0.07
Script completed
Jmol script terminated
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jun 22, 2012, at 5:46 PM, Otis Rothenberger wrote:
> Bob, I'm in Tampa right now.I have the entire console report at home, and
> I'll send it when I get back to Anna Maria Island. For what it's worth now,
> I'm pretty sure that I was repeatedly clicking the Load ethane link on the
> VMK Edit screen. I noticed the hang up when I clicked the MEP 100 link on the
> Edit screen, thus turning on (NOT!) the auto MEP. In other words, either Load
> ethane link or MEP100 link broke it. I can send the code for these links when
> I get home. Otis
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
