[Jmol-users] State script measurementunits bug

Eric Martz Wed, 16 Apr 2008 20:15:05 -0700

It appears to me that the state script does not maintain "set measurementunits angstroms".
The following is an example (for PDB 2rd0).
The four distance monitors were definitely in Angstroms when the state script was saved.
Rerunning it, the monitor labels are in nm.
I see the line "set measures angstroms" in the script below, but evidently something else is neutralizing it?

# Jmol state version 11.5.24 2008-03-31 02:46;
# fullName = "jmolApplet1__550759578123689__";
# documentBase = " http://proteopedia.org/wiki/index.php/2rd0#Figures_From_The_Publication ";
# codeBase = "" href="http://proteopedia.org/wiki/extensions/Jmol/" eudora="autourl"> http://proteopedia.org/wiki/extensions/Jmol/";

function _setWindowState();
# height 550;
# width 550;
stateVersion = 1105024;
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();

set 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 defaultVDW Jmol;
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://proteopedia.org/cgi-bin/getpdbz?2rd0";

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 0.0 0.0}";
   set defaultloadscript "";
   set defaulttorsionlabel "%VALUE %UNITS";
   set defaulttranslucent 0.5;
   set defaultvdw "Jmol";
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 delaymaximumms 0;
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 true;
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;
@~anomalous_atoms ({});
@~backbone_invisible ({});
@~fig2c ({2731 2734:2737 3527 3530:3534 9086 9089:9092 9122 9125:9128});
@~hydroxy_unchained_nucs ({});
@~nobackbone_aas ({});
@~nophosphorus_nucs ({});
@~protein ({0:9364});
@~unbondable_aas ({});
@~unchained_aas ({});
@~unchained_nucs ({});
isspinning = true;
loadedfileprev = "2RD0";
reloadfile = true;
spinflag = true;

# label defaults;
select none;
color label none;
background label none;
set labelOffset 4 4;
set labelAlignment left;
set labelPointer off;
font label 13.0 SansSerif Plain;

end function;

function _setModelState();

structure sheet ({213:269})           # model=1.1 & (19 - 25);
structure sheet ({305:357})           # model=1.1 & (31 - 37);
structure helix ({383:490})           # model=1.1 & (41 - 53);
structure helix ({491:522})           # model=1.1 & (54 - 56);
structure helix ({530:572})           # model=1.1 & (58 - 62);
structure helix ({582:622})           # model=1.1 & (64 - 68);
structure sheet ({623:668})           # model=1.1 & (69 - 74);
structure sheet ({692:740})           # model=1.1 & (78 - 82);
structure helix ({787:827})           # model=1.1 & (88 - 92);
structure sheet ({874:916})           # model=1.1 & (98 - 102);
structure helix ({952:1013})          # model=1.1 & (108 - 114);
structure helix ({1034:1073})         # model=1.1 & (117 - 122);
structure helix ({1154:1250})         # model=1.1 & (133 - 143);
structure helix ({1251:1352})         # model=1.1 & (144 - 156);
structure helix ({1367:1432})         # model=1.1 & (159 - 166);
structure helix ({1545:1597})         # model=1.1 & (181 - 186);
structure sheet ({1611:1693})         # model=1.1 & (189 - 198);
structure sheet ({1723:1809})         # model=1.1 & (203 - 212);
structure helix ({1834:1954})         # model=1.1 & (216 - 230);
structure helix ({1985:2039})         # model=1.1 & (235 - 241);
structure helix ({2070:2094})         # model=1.1 & (246 - 248);
structure sheet ({2104:2147})         # model=1.1 & (250 - 254);
structure sheet ({2181:2203})         # model=1.1 & (260 - 261);
structure helix ({2242:2271})         # model=1.1 & (266 - 269);
structure helix ({2272:2363})         # model=1.1 & (270 - 280);
structure sheet ({2390:2434})         # model=1.1 & (284 - 289);
structure helix ({2435:2484})         # model=1.1 & (290 - 295);
structure sheet ({2636:2703})         # model=1.1 & (333 - 341);
structure sheet ({2832:2873})         # model=1.1 & (357 - 361);
structure sheet ({2930:2944})         # model=1.1 & (370 - 371);
structure sheet ({3021:3132})         # model=1.1 & (382 - 392);
structure sheet ({3192:3230})         # model=1.1 & (401 - 405);
structure sheet ({3309:3336})         # model=1.1 & (425 - 428);
structure sheet ({3419:3460})         # model=1.1 & (439 - 444);
structure sheet ({3665:3715})         # model=1.1 & (472 - 477);
structure helix ({3795:3847})         # model=1.1 & (487 - 493);
structure helix ({3848:3899})         # model=1.1 & (494 - 499);
structure helix ({4023:4060})         # model=1.1 & (538 - 542);
structure helix ({4069:4168})         # model=1.1 & (544 - 554);
structure helix ({4169:4214})         # model=1.1 & (555 - 559);
structure helix ({4222:4245})         # model=1.1 & (561 - 563);
structure helix ({4246:4307})         # model=1.1 & (564 - 571);
structure helix ({4346:4458})         # model=1.1 & (576 - 589);
structure helix ({4511:4574})         # model=1.1 & (596 - 603);
structure helix ({4608:4738})         # model=1.1 & (608 - 623);
structure helix ({4739:4805})         # model=1.1 & (624 - 631);
structure helix ({4806:4869})         # model=1.1 & (632 - 639);
structure helix ({4870:4899})         # model=1.1 & (640 - 642);
structure helix ({4937:5036})         # model=1.1 & (647 - 658);
structure helix ({5044:5173})         # model=1.1 & (660 - 673);
structure helix ({5201:5351})         # model=1.1 & (677 - 695);
structure helix ({5356:5566})         # model=1.1 & (697 - 721);
structure helix ({5611:5720})         # model=1.1 & (727 - 739);
structure helix ({5732:5797})         # model=1.1 & (741 - 748);
structure sheet ({5811:5835})         # model=1.1 & (751 - 753);
structure sheet ({5851:5897})         # model=1.1 & (756 - 761);
structure sheet ({5961:5979})         # model=1.1 & (770 - 771);
structure sheet ({6032:6083})         # model=1.1 & (779 - 783);
structure sheet ({6191:6251})         # model=1.1 & (797 - 803);
structure helix ({6272:6455})         # model=1.1 & (807 - 827);
structure sheet ({6534:6565})         # model=1.1 & (838 - 842);
structure sheet ({6580:6615})         # model=1.1 & (845 - 849);
structure sheet ({6649:6671})         # model=1.1 & (854 - 856);
structure helix ({6672:6728})         # model=1.1 & (857 - 863);
structure helix ({6763:6804})         # model=1.1 & (870 - 874);
structure helix ({6830:6887})         # model=1.1 & (878 - 883);
structure helix ({6918:7106})         # model=1.1 & (888 - 912);
structure sheet ({7170:7201})         # model=1.1 & (921 - 924);
structure sheet ({7231:7259})         # model=1.1 & (929 - 931);
structure helix ({7389:7454})         # model=1.1 & (957 - 964);
structure helix ({7519:7708})         # model=1.1 & (974 - 994);
structure helix ({7709:7789})         # model=1.1 & (995 - 1004);
structure helix ({7894:7961})         # model=1.1 & (1019 - 1026);
structure helix ({7992:8145})         # model=1.1 & (1031 - 1048);
structure helix ({8187:8653})         # model=1.1 & (447 - 499);
structure helix ({8782:9199})         # model=1.1 & (525 - 573);
structure helix ({9200:9266})         # model=1.1 & (574 - 580);

select ({3942:5351});
color atoms opaque [xffff00];
select ({1628:2452});
color atoms opaque [x0000cd];
select ({8154:9364});
color atoms opaque [xff0000];
select ({5352:8153});
color atoms opaque [xff00ff];
select ({0:125 963:1627 2453:2613 3749:3941});
color atoms opaque [xc0c0c0];
select ({0:9364});
Spacefill 0.0;
select ({126:962});
color atoms opaque [x32cd32];
select ({2614:3748});
color atoms opaque [x00bfff];
select BONDS ({241:243 247 276:278 282 5947:5950 5953 6766:6769});
wireframe 0.3;
select BONDS ({0:240 244:246 248:275 279:281 283:5946 5951 5952 5954:6765 6770:9565});
wireframe 0.0;
select BONDS ({241:243 276:278 5947:5950 6766:6768});
color bonds opaque cpk;

select ({2735});
label "N345";
select ({3532});
label "E453";
select ({9090});
label "D560";
select ({9126});
label "N564";
select ({2735 3532 9090 9126});
font label 22.0 SansSerif Bold;
measures delete;
measure({9127})({2737}); # distance   2.8378172       0.284 nm        [ASN]564:B.OD1 #9129    [ASN]345:A.ND2 #2738;
measure({2737})({9092}); # distance   2.9767447       0.298 nm        [ASN]345:A.ND2 #2738    [ASP]560:B.OD2 #9094;
measure({9127})({9091}); # distance   3.4433522       0.344 nm        [ASN]564:B.OD1 #9129    [ASP]560:B.OD1 #9093;
set measures angstroms;
font measures 15.0 SansSerif Plain;
select measures ({null});

select ({2677:2873 2884:2900 2916:3045 3192:3328 3440:3603 3610:3687 4575:4580 5201:5224 7328:7337 7798:7901 8244:8251 8259:8506 8974:9254});
Cartoon on;
select ({0:9364});
color Cartoon translucent 160 none;

boundBox off;

unitcell off;

set echo off;

hover "%n %r, Chain=%c, Element=%e";

frank on;
font frank 16.0 SansSerif Bold;
set fontScaling false
;
end function;

function _setPerspectiveState();
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth true;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {20.587006 12.039993 38.852997} {133.33301 118.862 135.65001} # volume = 1165799.4;
center {81.3824 31.217398 87.58761};
moveto 0.0 { 946 314 -81 121.84} 1192.38 22.55 -6.36 {81.3824 31.217398 87.58761} 97.47658 {0.0 0.0 0.0} -7489.981 -4175.049 50.0;;
slab 100;depth 0;
set spinX 0; set spinY 5; set spinZ 0; set spinFps 30;
end function;

function _setSelectionState();
select ({2734:2737 3530:3534 9089:9092 9125:9128});
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;

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[Jmol-users] State script measurementunits bug

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