I've scanned through the state for these particular settings (and anything
else that seemed like a likely candidate, and measurementLabels is fine (on)
while I cannot find measurementNumbers reported. I tried manually setting
it to "on", it was successfully accepted in the console window, but the
behavior did not change. Here is the full show state output:
*show state;*
pending
# Jmol state version 11.4.0 2007-12-20 06:37;
# fullName = "jmolApplet0[409194794598446]";
# documentBase = "
http://comte/structures3/bin-release/xray_vision_beta3.html";;
# codeBase = "http://comte/jmol/";;
function _setWindowState();
# height 512;
# width 512;
stateVersion = 1104000;
backgroundColor = "[xffffff]";
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
ambientPercent = 45;
diffusePercent = 84;
specular = true;
specularPercent = 22;
specularPower = 40;
specularExponent = 6;
statusReporting = true;
end function;
function _setFileState();
allowEmbeddedScripts = false;
set autoBond true;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultDirectory "";
set defaultLattice {0.0 0.0 0.0};
set defaultLoadScript "";
set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set forceAutoBond false;
set minBondDistance 0.4;
set percentVdwAtom 20;
set smartAromatic true;
load /*file*/"http://comte/struct/redacted.pdb";;
end function;
function _setVariableState();
set defaultanglelabel "%VALUE %UNITS";
set defaultcolorscheme "Jmol";
set defaultdirectory "";
set defaultdistancelabel "%VALUE %UNITS";
set defaultdrawarrowscale 0.5;
set defaultlattice "{0 0 0}";
set defaultloadscript "";
set defaulttorsionlabel "%VALUE %UNITS";
set defaulttranslucent 0.5;
set allowembeddedscripts true;
set allowrotateselected false;
set appletproxy "";
set applysymmetrytobonds false;
set autobond true;
set autofps false;
set axes window;
set axesmode 0;
set axesscale 2.0;
set bondmodeor false;
set bondradiusmilliangstroms 150;
set bondtolerance 0.45;
set cartoonrockets false;
set chaincasesensitive false;
set dataseparator "~~~";
set dipolescale 1.0;
set disablepopupmenu false;
set displaycellparameters true;
set dotsselectedonly false;
set dotsurface true;
set drawpicking false;
set dynamicmeasurements false;
set forceautobond false;
set greyscalerendering false;
set hbondsbackbone false;
set hbondssolid false;
set helppath "http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm
";
set hermitelevel 0;
set hidenameinpopup false;
set hidenavigationpoint false;
set highresolution false;
set historylevel 0;
set hoverdelay 0.5;
set isosurfacepropertysmoothing true;
set justifymeasurements false;
set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set measureallmodels false;
set measurementlabels true;
set minbonddistance 0.4;
set navigationperiodic false;
set navigationspeed 5.0;
set percentvdwatom 20;
set pickingspinrate 10;
set propertyatomnumberfield 0;
set propertycolorscheme "roygb";
set propertydatafield 0;
set rangeselected false;
set ribbonaspectratio 16;
set ribbonborder false;
set rocketbarrels false;
set selecthetero true;
set selecthydrogen true;
set sheetsmoothing 1.0;
set showhiddenselectionhalos false;
set showhydrogens true;
set showmeasurements true;
set showmultiplebonds true;
set shownavigationpointalways false;
set smartaromatic true;
set solventprobe false;
set solventproberadius 1.2;
set ssbondsbackbone false;
set stereodegrees 5;
set strandcountformeshribbon 7;
set strandcountforstrands 5;
set testflag1 false;
set testflag2 false;
set testflag3 false;
set testflag4 false;
set tracealpha true;
set usenumberlocalization true;
set vectorscale 1.0;
set vibrationperiod 1.0;
set vibrationscale 1.0;
set wireframerotation false;
set zoomlarge true;
set zshade false;
#user-defined variables;
natoms = 30;
# label defaults;
select none;
color label none;
background label none;
set labelOffset 4 4;
set labelAlignment left;
set labelPointer off;
font label 13 SansSerif Plain;
end function;
function _setModelState();
structure sheet ({0:38}) # model=1.1 & (83 - 87);
structure sheet ({66:114}) # model=1.1 & (91 - 96);
structure sheet ({123:135}) # model=1.1 & (98 - 100);
structure sheet ({156:229}) # model=1.1 & (103 - 112);
structure sheet ({241:324}) # model=1.1 & (115 - 125);
structure helix ({361:494}) # model=1.1 & (131 - 146);
structure sheet ({495:524}) # model=1.1 & (147 - 149);
structure sheet ({540:577}) # model=1.1 & (152 - 155);
structure sheet ({587:604}) # model=1.1 & (157 - 159);
structure sheet ({620:706}) # model=1.1 & (162 - 172);
structure helix ({733:792}) # model=1.1 & (177 - 183);
structure helix ({840:992}) # model=1.1 & (190 - 209);
structure sheet ({1092:1122}) # model=1.1 & (222 - 225);
structure sheet ({1146:1174}) # model=1.1 & (229 - 232);
structure sheet ({1205:1224}) # model=1.1 & (257 - 259);
structure helix ({1270:1303}) # model=1.1 & (265 - 269);
structure sheet ({1326:1352}) # model=1.1 & (272 - 274);
structure helix ({1353:1479}) # model=1.1 & (275 - 290);
structure helix ({1577:1646}) # model=1.1 & (302 - 310);
structure sheet ({1664:1715}) # model=1.1 & (313 - 318);
structure helix ({1744:1835}) # model=1.1 & (323 - 333);
structure sheet ({1886:1914}) # model=1.1 & (340 - 342);
structure helix ({1915:2018}) # model=1.1 & (343 - 355);
structure helix ({2027:2061}) # model=1.1 & (357 - 361);
select ({2083:2085 2087:2089 2091 2093 2095:2100 2102 2104:2106
2108:2110});
color atoms opaque [x32cd32];
measures delete;
measure({2097})({2100})({2099}); # angle 118.205696 118.2 °
[086]1:Z.C6 #4204 [086]1:Z.C1 #4209 [086]1:Z.C2 #4208;
measure({2095})({2098})({2099}); # angle 119.720146 119.7 °
[086]1:Z.C4 #4202 [086]1:Z.C3 #4206 [086]1:Z.C2 #4208;
measure({2098})({2096})({2093}); # angle 89.00548 89.0 °
[086]1:Z.C3 #4206 [086]1:Z.C5 #4203 [086]1:Z.C7 #4199;
measure({2095})({2100}); # distance 2.8421364 2.84 Å
[086]1:Z.C4 #4202 [086]1:Z.C1 #4209;
set measures angstroms;
font measures 15 SansSerif Plain;
select measures ({null});
isosurface ligZsurface ignore(protein or solvent) vdw -80% select(:Z)
SASURFACE RESOLUTION 50.0 translucent on;# ({2082:2111}) ({0:2081
2112:2297});
isosurface ligzsurface fill noMesh noDots notFrontOnly frontlit;
color $ligzsurface translucent 128 [xffa500];
boundBox off;
unitcell off;
hover "%U";
frank on;
font frank 16 SansSerif Bold;
end function;
function _setPerspectiveState();
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth true;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {-28.810001 -36.101997 -20.220001} {29.064 27.810997
23.829002} # volume = 162932.89;
center {0.4246333 -11.243336 4.615134};
moveto 0.0 { -144 720 -679 135.12} 677.95 0.0 0.0 {0.4246333 -11.243336
4.615134} 39.86 {0.0 0.0 0.0} 3.8366377 -38.057495 50.0;;
slab 55;depth 45;slab on;
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30;
end function;
function _setSelectionState();
select ({2083:2085 2087:2089 2091 2093 2095:2100 2102 2104:2106
2108:2110});
set hideNotSelected false;
end function;
function _setState();
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setVariableState;
_setModelState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
end function;
_setState;
Script completed
Jmol script terminated
Thanks very much for your help!
-Tom
On Sat, Apr 19, 2008 at 1:05 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> OK, well, this report looks a lot better -- at least it is the expected
> report. The only thing I can think of is that you somehow have
>
> set measurementLabels off
>
> or
>
> set measurementNumbers off
>
> Please send what you get from
>
> show state
>
> There's something simple wrong, but I don't think it's with the applet
> itself.
>
> Bob
>
>
>
> Thomas Stout wrote:
>
> >
> > As a follow-up (if means anything): I get exactly the same behavior
> > when I type the commands into the console: the dotted lines for the
> > angles are drawn, but /*the value of the angle is not drawn in the
> > applet*/. In this case the angle value is actually calculated and
> > reported in the console output (it wasn't from my html link activation):
> >
> > set pickingStyle MEASURE;set picking MEASURE ANGLE;
> > Script completed
> > Jmol script terminated
> > pending
> > Atom #1:[086]1:Z.C6 #4204
> > Atom #2:[086]1:Z.C1 #4209
> > Atom #3:[086]1:Z.C2 #4208
> > Angle [086]1:Z.C6 #4204 - [086]1:Z.C1 #4209 - [086]1:Z.C2 #4208 :
> > 118.205696
> > measureCompleted: [3, 2097, 2100, 2099, 118.2 °]
> > Script completed
> >
> > -Tom
> >
> > On Sat, Apr 19, 2008 at 12:24 PM, Thomas Stout <[EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> >
> > OK - thanks -- I've probably been distracted by the fact that the
> > Distance and Torsion measurements are working fine & that the
> > Angle appears to be working but just doesn't draw the
> > value....I'll parse my full page more carefully and see if I can
> > find where things are going wonky.....
> >
> > -Tom
> >
> >
> > On Sat, Apr 19, 2008 at 12:10 PM, Bob Hanson <[EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>> wrote:
> >
> > I don't think so. It is measuring angles from the measure
> > reports. And
> > when I try these commands they work great. Try those commands
> > from the
> > Jmol console; I'm guessing something is still wrong with your
> > JavaScript.
> >
> > Thomas Stout wrote:
> >
> > >
> > > Hmmm. Thanks Bob -- That seemed like my obvious mistake, but
> > > correcting it didn't seem to help. Here is the output from
> the
> > > console history when I activate the Angle measuring versus
> > Distance
> > > measuring:
> > >
> > > set pickingStyle MEASURE;set picking MEASURE ANGLE;
> > > measure (atomIndex=2097) (atomIndex=2100) (atomIndex=2099)
> > > measure (atomIndex=2100) (atomIndex=2102) (atomIndex=2097)
> > > measure (atomIndex=2097) (atomIndex=2096) (atomIndex=2095)
> > > Script completed
> > > Jmol script terminated
> > > Script completed
> > > Jmol script terminated
> > > Atom #1:[086]1:Z.C15 #4211
> > > Atom #2:[086]1:Z.N3 #4195
> > > Distance [086]1:Z.C15 #4211 - [086]1:Z.N3 #4195 : 4.8738594
> > > measureCompleted: [2, 2102, 2090, 4.87 Å]
> > > Script completed
> > > Jmol script terminated
> > >
> > > Jmol seems to actually not be measuring the angle, while it
> does
> > > measure the Distance (or torsion). Am I still not properly
> > activating
> > > the Angle measurement somehow?
> > >
> > > Thank you very much,
> > > Tom
> > >
> > > On Sat, Apr 19, 2008 at 4:58 AM, Bob Hanson
> > <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> > > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>
> wrote:
> > >
> > > Tom, I think it's your links. The command is
> > >
> > > set pickingStyle MEASURE
> > >
> > > not
> > >
> > > set pickingStyle MEASURE ON
> > >
> > > Bob
> > >
> > > Thomas Stout wrote:
> > >
> > > >
> > > > Hmmm.....is anyone else using interactive
> > measurements? I've just
> > > > added links to a web page to turn "on" and "off" the
> > > measurements mode
> > > > (so that someone could interactively measure
> > > distances/angles/torsions
> > > > of interest and then turn it off again). Distance and
> > Torsions work
> > > > just fine, but I find that Angles -- while displaying
> > the dotted
> > > lines
> > > > of the two "arms" of the selected angle -- do not
> > display the actual
> > > > measurement (ie, 109.5 degrees). Here are my links:
> > > >
> > > > <a href="javascript:jmolScript('set picking MEASURE
> > DISTANCE;set
> > > > pickingStyle MEASURE ON;set measurements
> > angstroms;');">Activate
> > > > Distance Measuring</b></a> <a
> > href="javascript:jmolScript('set
> > > > pickingStyle MEASURE OFF;');">Off</a><br>
> > > > <a href="javascript:jmolScript('set picking MEASURE
> > ANGLE;set
> > > > pickingStyle MEASURE ON;');"><b>Activate Angle
> > Measuring</b></a> <a
> > > > href="javascript:jmolScript('set pickingStyle MEASURE
> > > OFF;');">Off</a><br>
> > > > <a href="javascript:jmolScript('set picking MEASURE
> > TORSION;set
> > > > pickingStyle MEASURE ON;');"><b>Activate Torsion
> > > Measuring</b></a> <a
> > > > href="javascript:jmolScript('set pickingStyle MEASURE
> > > OFF;');">Off</a><br>
> > > >
> > > > I'm using Jmol version 11.4.0 and the behavior is the
> > same in IE6 on
> > > > WindowsXP and in Firefox 2.0.0.4 <http://2.0.0.4>
> > <http://2.0.0.4>
> > > <http://2.0.0.4> on linux.
> > > >
> > > > Any thoughts about what I may be missing here?
> > > > Thanks!
> > > > -Tom
> > > >
> > >
> >
> >------------------------------------------------------------------------
> > > >
> > >
> >
> >-------------------------------------------------------------------------
> > > >This SF.net email is sponsored by the 2008 JavaOne(SM)
> > Conference
> > > >Don't miss this year's exciting event. There's still
> > time to save
> > > $100.
> > > >Use priority code J8TL2D2.
> > >
> > >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > > >
> > >
> >
> >------------------------------------------------------------------------
> > > >
> > > >_______________________________________________
> > > >Jmol-users mailing list
> > > >[email protected]
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > > >https://lists.sourceforge.net/lists/listinfo/jmol-users
> > > >
> > > >
> > >
> > >
> > > --
> > > Robert M. Hanson
> > > Professor of Chemistry
> > > St. Olaf College
> > > Northfield, MN
> > > http://www.stolaf.edu/people/hansonr
> > >
> > >
> > > 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
> > >
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------
> > > This SF.net email is sponsored by the 2008 JavaOne(SM)
> > Conference
> > > Don't miss this year's exciting event. There's still
> > time to save
> > > $100.
> > > Use priority code J8TL2D2.
> > >
> >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > > _______________________________________________
> > > Jmol-users mailing list
> > > [email protected]
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > > https://lists.sourceforge.net/lists/listinfo/jmol-users
> > >
> > >
> >
> >------------------------------------------------------------------------
> > >
> >
> >-------------------------------------------------------------------------
> > >This SF.net email is sponsored by the 2008 JavaOne(SM)
> Conference
> > >Don't miss this year's exciting event. There's still time to
> > save $100.
> > >Use priority code J8TL2D2.
> > >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > >
> >
> >------------------------------------------------------------------------
> > >
> > >_______________________________________________
> > >Jmol-users mailing list
> > >[email protected]
> > <mailto:[email protected]>
> > >https://lists.sourceforge.net/lists/listinfo/jmol-users
> > >
> > >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > 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
> >
> >
> >
> >
> -------------------------------------------------------------------------
> > This SF.net email is sponsored by the 2008 JavaOne(SM)
> Conference
> > Don't miss this year's exciting event. There's still time to
> > save $100.
> > Use priority code J8TL2D2.
> >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > <mailto:[email protected]>
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> >Don't miss this year's exciting event. There's still time to save $100.
> >Use priority code J8TL2D2.
> >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
>
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
-------------------------------------------------------------------------
This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
Don't miss this year's exciting event. There's still time to save $100.
Use priority code J8TL2D2.
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
