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Re: [Jmol-users] interactive measurements mode -- Angles don't report?
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From: Bob H. <ha...@st...> - 2008-04-20 18:53:39
|
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 <ha...@st...
> <mailto:ha...@st...>> 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
> <tho...@gm... <mailto:tho...@gm...>
> > <mailto:tho...@gm... <mailto:tho...@gm...>>>
> 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
> <ha...@st... <mailto:ha...@st...>
> > <mailto:ha...@st... <mailto:ha...@st...>>> 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
> > <ha...@st... <mailto:ha...@st...>
> <mailto:ha...@st... <mailto:ha...@st...>>
> > > <mailto:ha...@st... <mailto:ha...@st...>
> <mailto:ha...@st... <mailto:ha...@st...>>>> 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)
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> > >
> >
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> > > >
> > >
> >
> >------------------------------------------------------------------------
> > > >
> > > >_______________________________________________
> > > >Jmol-users mailing list
> > > >Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>
> > > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>>
> > >
> >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
> > > Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>
> > > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>>
> > >
> 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
> > >Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>
> > >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
> > Jmo...@li...
> <mailto:Jmo...@li...>
> > <mailto:Jmo...@li...
> <mailto:Jmo...@li...>>
> > 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
> >Jmo...@li...
> <mailto:Jmo...@li...>
> >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
> Jmo...@li...
> <mailto:Jmo...@li...>
> 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
>Jmo...@li...
>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
|