Thomas, sorry for putting you through all that. The state script did the trick, though. That's just what I needed. It was a bug in Jmol going back at least to version 9.0 -- four years ago.
Bug: measurement labels for angles specifically do not appear when slabbing. Fixed for 11.5.30 and 11.4.2, to be released soon. Bob Thomas Stout wrote: > > 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] > <mailto:[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]> > > <mailto:[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]> > > <mailto:[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]>> > > > <mailto:[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> > > > <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]>> > > > <mailto:[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]>> > > > <mailto:[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]> > > <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
