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Sandbox 50

From Proteopedia

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Line 1: Line 1:
-
<!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
+
# Jmol state version 12.0.41 2011-02-04 14:47;
-
{{Template:Oberholser_Sandbox_Reservation}}
+
# fullName = "jmolApplet0__836949901642189__";
-
<StructureSection load='1dq8' size='500' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1hpl]])' scene=''>
+
# documentBase = "http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1HPL&params.annotationsStr=DSSP,SCOP,Protein%20Modification&params.showJmol=true";
-
= Horse Pancreatic Lipase =
+
# codeBase = "http://www.pdb.org/pdb/Viewers/jmol-12.0.41/";
-
Lipase, which is produced primarily in the pancreas, functions as a catalyst in the hydrolysis of ester bonds in lipid substrates. This makes lipases an essential molecule for fat digestion.
+
-
Horse pancreatic lipase’s function is to convert triacylglycerols into 2-monoacylglycerols and free fatty acids. These monomers are then able to be shuttled into the small intestine to be absorbed into the lymphatic system.
+
-
== hydrophobic residues ==
 
-
=== test ===
 
-
<scene name='Sandbox_50/Hphobic_residues/1'>hydrophobic residues</scene>
 
-
<scene name='Sandbox_50/Polar_residues/1'>Polar Residues</scene>
+
function _setWindowState() {
 +
# height 300;
 +
# width 300;
 +
stateVersion = 1200041;
 +
background [xffffff];
 +
axis1Color = "[xff0000]";
 +
axis2Color = "[x008000]";
 +
axis3Color = "[x0000ff]";
 +
set ambientPercent 45;
 +
set diffusePercent 84;
 +
set specular true;
 +
set specularPercent 22;
 +
set specularPower 40;
 +
set specularExponent 6;
 +
set zShadePower 1;
 +
statusReporting = true;
 +
}
-
<scene name='Sandbox_50/Nonpolar_residues/1'>Non-polar residues</scene>
+
function _setFileState() {
-
<scene name='Sandbox_50/Nonpolar_and_polar_combined/1'>Polar (purple) and nonpolar (green) residues</scene>
+
set allowEmbeddedScripts false;
 +
set appendNew true;
 +
set appletProxy "";
 +
set applySymmetryToBonds false;
 +
set autoBond true;
 +
set bondRadiusMilliAngstroms 150;
 +
set bondTolerance 0.45;
 +
set defaultLattice {0.0 0.0 0.0};
 +
set defaultLoadFilter "";
 +
set defaultLoadScript "";
 +
set defaultVDW Auto;
 +
set forceAutoBond false;
 +
#set defaultDirectory "";
 +
#set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";
 +
#set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";
 +
#set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";
 +
#set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]";
 +
set legacyAutoBonding false;
 +
set minBondDistance 0.4;
 +
set minimizationCriterion 0.0010;
 +
set minimizationSteps 100;
 +
set pdbGetHeader false;
 +
set pdbSequential false;
 +
set percentVdwAtom 23;
 +
set smallMoleculeMaxAtoms 40000;
 +
set smartAromatic true;
 +
load /*file*/"http://www2.rcsb.org/pdb/files/1HPL.pdb";
-
<scene name='Sandbox_50/Helix/1'>helix in purple</scene>
+
}
-
<scene name='Sandbox_50/Active_site/1'>TextToBeDisplayed</scene>
+
function _setVariableState() {
-
</StructureSection>
+
set defaultanglelabel "%VALUE %UNITS";
 +
set defaultcolorscheme "Jmol";
 +
set defaultdistancelabel "%VALUE %UNITS";
 +
set defaultdrawarrowscale 0.5;
 +
set defaultlattice "{0 0 0}";
 +
set defaultloadfilter "";
 +
set defaultloadscript "";
 +
set defaulttorsionlabel "%VALUE %UNITS";
 +
set defaulttranslucent 3.0;
 +
set defaultvdw "Auto";
 +
set allowembeddedscripts true;
 +
set allowrotateselected false;
 +
set appletproxy "";
 +
set applysymmetrytobonds false;
 +
set atompicking true;
 +
set atomtypes "";
 +
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 cartoonbaseedges false;
 +
set cartoonrockets false;
 +
set chaincasesensitive false;
 +
set dataseparator "[[User:Student|Student]]";
 +
set defaultstructuredssp true;
 +
set delaymaximumms 0;
 +
set dipolescale 1.0;
 +
set disablepopupmenu false;
 +
set displaycellparameters true;
 +
set dotdensity 3;
 +
set dotscale 1;
 +
set dotsselectedonly false;
 +
set dotsurface true;
 +
set dragselected false;
 +
set drawhover false;
 +
set drawpicking false;
 +
set dsspcalculatehydrogenalways true;
 +
set dynamicmeasurements false;
 +
set ellipsoidarcs false;
 +
set ellipsoidaxes false;
 +
set ellipsoidaxisdiameter 0.02;
 +
set ellipsoidball true;
 +
set ellipsoiddotcount 200;
 +
set ellipsoiddots false;
 +
set ellipsoidfill false;
 +
set forceautobond false;
 +
set fractionalrelative false;
 +
set gestureswipefactor 1.0;
 +
set greyscalerendering false;
 +
set hbondsangleminimum 90.0;
 +
set hbondsbackbone false;
 +
set hbondsdistancemaximum 3.25;
 +
set hbondsrasmol true;
 +
set hbondssolid false;
 +
set helixstep 1;
 +
set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm";
 +
set hermitelevel 0;
 +
set hidenameinpopup false;
 +
set hidenavigationpoint false;
 +
set highresolution false;
 +
set historylevel 0;
 +
set hoverdelay 0.5;
 +
set imagestate true;
 +
set iskiosk false;
 +
set isosurfacepropertysmoothing true;
 +
set justifymeasurements false;
 +
set loadatomdatatolerance 0.01;
 +
set measureallmodels false;
 +
set measurementlabels true;
 +
set messagestylechime false;
 +
set minbonddistance 0.4;
 +
set minimizationcriterion 0.0010;
 +
set minimizationrefresh true;
 +
set minimizationsilent false;
 +
set minimizationsteps 100;
 +
set monitorenergy false;
 +
set multiplebondradiusfactor 0.0;
 +
set multiplebondspacing -1.0;
 +
set navigatesurface false;
 +
set navigationperiodic false;
 +
set navigationspeed 5.0;
 +
set pdbgetheader false;
 +
set pdbsequential false;
 +
set percentvdwatom 23;
 +
set pickingspinrate 10;
 +
set picklabel "";
 +
set pointgroupdistancetolerance 0.2;
 +
set pointgrouplineartolerance 8.0;
 +
set propertyatomnumbercolumncount 0;
 +
set propertyatomnumberfield 0;
 +
set propertycolorscheme "roygb";
 +
set propertydatacolumncount 0;
 +
set propertydatafield 0;
 +
set quaternionframe "p";
 +
set rangeselected false;
 +
set ribbonaspectratio 16;
 +
set ribbonborder false;
 +
set rocketbarrels false;
 +
set saveproteinstructurestate true;
 +
set selectallmodels true;
 +
set selecthetero true;
 +
set selecthydrogen true;
 +
set sheetsmoothing 1.0;
 +
set showhiddenselectionhalos false;
 +
set showhydrogens true;
 +
set showkeystrokes true;
 +
set showmeasurements true;
 +
set showmultiplebonds true;
 +
set shownavigationpointalways false;
 +
set slabbyatom false;
 +
set slabbymolecule false;
 +
set smallmoleculemaxatoms 40000;
 +
set smartaromatic true;
 +
set solventprobe false;
 +
set solventproberadius 1.2;
 +
set ssbondsbackbone false;
 +
set stereodegrees -5;
 +
set strandcountformeshribbon 7;
 +
set strandcountforstrands 5;
 +
set strutdefaultradius 0.3;
 +
set strutlengthmaximum 7.0;
 +
set strutsmultiple false;
 +
set strutspacing 6;
 +
set testflag1 false;
 +
set testflag2 false;
 +
set testflag3 false;
 +
set testflag4 false;
 +
set tracealpha true;
 +
set usearcball false;
 +
set useminimizationthread true;
 +
set usenumberlocalization true;
 +
set vectorscale 1.0;
 +
set vibrationscale 1.0;
 +
set wireframerotation false;
 +
set zoomlarge 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;
 +
 
 +
}
 +
 
 +
function _setModelState() {
 +
 
 +
select ({7002 7003});
 +
Spacefill 0.5;
 +
select ({0:7001 7004:7708});
 +
Spacefill 0.0;
 +
select BONDS ({1510 1512 1514:1519 1535:1544 1554:1560 1576:1582});
 +
wireframe 0.5;
 +
select BONDS ({0:1509 1511 1513 1520:1534 1545:1553 1561:1575 1583:7200});
 +
wireframe 0.0;
 +
 
 +
measures delete;
 +
select *; set measures nanometers;
 +
font measures 15.0 SansSerif Plain;
 +
 
 +
select ({0:7001});
 +
Cartoon 0.0;
 +
color Cartoon opaque chain;
 +
 
 +
select ({1449:1457 1473:1483 1492:1499 1513:1520});
 +
Strands 0.0;
 +
select ({0:1448 1458:1472 1484:1491 1500:1512 1521:7001});
 +
Strands on;
 +
select ({0:7001});
 +
color Strands opaque [x808080];
 +
 
 +
set echo off;
 +
set echo bottom left; echo "Protein Modification: calcium ion (Metal coordination) 325_crosslink4";
 +
font echo 10.0 SansSerif Bold; color echo [x000000];
 +
 
 +
boundBox off;
 +
font boundBox 14.0 SansSerif Plain;
 +
boundBox off;
 +
 
 +
unitcell off;
 +
font unitcell 14.0 SansSerif Plain;
 +
unitcell off;
 +
 
 +
hover "%U";
 +
 
 +
frank off;
 +
font frank 16.0 SansSerif Bold;
 +
select *;
 +
 
 +
}
 +
 
 +
function _setPerspectiveState() {
 +
set perspectiveModel 11;
 +
set scaleAngstromsPerInch 0.0;
 +
set perspectiveDepth true;
 +
set visualRange 5.0;
 +
set cameraDepth 3.0;
 +
boundbox corners {-2.2789993 13.026001 -19.830002} {81.053 74.486 82.824} # volume = 525751.1;
 +
center {38.646023 47.94447 -6.8159995};
 +
moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {39.387 43.756 31.496998} 58.66127 {0.0 0.0 0.0} 0.0 0.0 0.0;
 +
save orientation "default";
 +
moveto 0.0 { 35 -107 -994 123.82} 200.0 0.0 0.0 {38.646023 47.94447 -6.8159995} 58.66127 {0.0 0.0 0.0} -31.404827 -98.16444 0.0;;
 +
slab 100;depth 0;
 +
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10;
 +
}
 +
 
 +
function _setSelectionState() {
 +
select ({1449:1457 1473:1483 1492:1499 1513:1520});
 +
set hideNotSelected false;
 +
}
 +
 
 +
function _setState() {
 +
initialize;
 +
set refreshing false;
 +
_setWindowState;
 +
_setFileState;
 +
_setVariableState;
 +
_setModelState;
 +
_setPerspectiveState;
 +
_setSelectionState;
 +
set refreshing true;
 +
set antialiasDisplay true;
 +
set antialiasTranslucent true;
 +
set antialiasImages true;
 +
}
 +
 
 +
_setState;

Revision as of 20:51, 7 November 2011

  1. Jmol state version 12.0.41 2011-02-04 14:47; 
 # fullName = "jmolApplet0__836949901642189__";
 # documentBase = "http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1HPL&params.annotationsStr=DSSP,SCOP,Protein%20Modification&params.showJmol=true";
 # codeBase = "http://www.pdb.org/pdb/Viewers/jmol-12.0.41/";


function _setWindowState() {

  1. height 300;
  2. width 300; 
 stateVersion = 1200041;
 background [xffffff];
 axis1Color = "[xff0000]";
 axis2Color = "[x008000]";
 axis3Color = "[x0000ff]";
 set ambientPercent 45;
 set diffusePercent 84;
 set specular true;
 set specularPercent 22;
 set specularPower 40;
 set specularExponent 6;
 set zShadePower 1;
 statusReporting  = true;

}

function _setFileState() { 

 set allowEmbeddedScripts false;
 set appendNew true;
 set appletProxy "";
 set applySymmetryToBonds false;
 set autoBond true;
 set bondRadiusMilliAngstroms 150;
 set bondTolerance 0.45;
 set defaultLattice {0.0 0.0 0.0};
 set defaultLoadFilter "";
 set defaultLoadScript "";
 set defaultVDW Auto;
 set forceAutoBond false;
 #set defaultDirectory "";
 #set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";
 #set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";
 #set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";
 #set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]";
 set legacyAutoBonding false;
 set minBondDistance 0.4;
 set minimizationCriterion  0.0010;
 set minimizationSteps  100;
 set pdbGetHeader false;
 set pdbSequential false;
 set percentVdwAtom 23;
 set smallMoleculeMaxAtoms 40000;
 set smartAromatic true;
 load /*file*/"http://www2.rcsb.org/pdb/files/1HPL.pdb";

}

function _setVariableState() { 

  set defaultanglelabel "%VALUE %UNITS";
  set defaultcolorscheme "Jmol";
  set defaultdistancelabel "%VALUE %UNITS";
  set defaultdrawarrowscale 0.5;
  set defaultlattice "{0 0 0}";
  set defaultloadfilter "";
  set defaultloadscript "";
  set defaulttorsionlabel "%VALUE %UNITS";
  set defaulttranslucent 3.0;
  set defaultvdw "Auto";
 set allowembeddedscripts true;
 set allowrotateselected false;
 set appletproxy "";
 set applysymmetrytobonds false;
 set atompicking true;
 set atomtypes "";
 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 cartoonbaseedges false;
 set cartoonrockets false;
 set chaincasesensitive false;
 set dataseparator "Student";
 set defaultstructuredssp true;
 set delaymaximumms 0;
 set dipolescale 1.0;
 set disablepopupmenu false;
 set displaycellparameters true;
 set dotdensity 3;
 set dotscale 1;
 set dotsselectedonly false;
 set dotsurface true;
 set dragselected false;
 set drawhover false;
 set drawpicking false;
 set dsspcalculatehydrogenalways true;
 set dynamicmeasurements false;
 set ellipsoidarcs false;
 set ellipsoidaxes false;
 set ellipsoidaxisdiameter 0.02;
 set ellipsoidball true;
 set ellipsoiddotcount 200;
 set ellipsoiddots false;
 set ellipsoidfill false;
 set forceautobond false;
 set fractionalrelative false;
 set gestureswipefactor 1.0;
 set greyscalerendering false;
 set hbondsangleminimum 90.0;
 set hbondsbackbone false;
 set hbondsdistancemaximum 3.25;
 set hbondsrasmol true;
 set hbondssolid false;
 set helixstep 1;
 set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm";
 set hermitelevel 0;
 set hidenameinpopup false;
 set hidenavigationpoint false;
 set highresolution false;
 set historylevel 0;
 set hoverdelay 0.5;
 set imagestate true;
 set iskiosk false;
 set isosurfacepropertysmoothing true;
 set justifymeasurements false;
 set loadatomdatatolerance 0.01;
 set measureallmodels false;
 set measurementlabels true;
 set messagestylechime false;
 set minbonddistance 0.4;
 set minimizationcriterion 0.0010;
 set minimizationrefresh true;
 set minimizationsilent false;
 set minimizationsteps 100;
 set monitorenergy false;
 set multiplebondradiusfactor 0.0;
 set multiplebondspacing -1.0;
 set navigatesurface false;
 set navigationperiodic false;
 set navigationspeed 5.0;
 set pdbgetheader false;
 set pdbsequential false;
 set percentvdwatom 23;
 set pickingspinrate 10;
 set picklabel "";
 set pointgroupdistancetolerance 0.2;
 set pointgrouplineartolerance 8.0;
 set propertyatomnumbercolumncount 0;
 set propertyatomnumberfield 0;
 set propertycolorscheme "roygb";
 set propertydatacolumncount 0;
 set propertydatafield 0;
 set quaternionframe "p";
 set rangeselected false;
 set ribbonaspectratio 16;
 set ribbonborder false;
 set rocketbarrels false;
 set saveproteinstructurestate true;
 set selectallmodels true;
 set selecthetero true;
 set selecthydrogen true;
 set sheetsmoothing 1.0;
 set showhiddenselectionhalos false;
 set showhydrogens true;
 set showkeystrokes true;
 set showmeasurements true;
 set showmultiplebonds true;
 set shownavigationpointalways false;
 set slabbyatom false;
 set slabbymolecule false;
 set smallmoleculemaxatoms 40000;
 set smartaromatic true;
 set solventprobe false;
 set solventproberadius 1.2;
 set ssbondsbackbone false;
 set stereodegrees -5;
 set strandcountformeshribbon 7;
 set strandcountforstrands 5;
 set strutdefaultradius 0.3;
 set strutlengthmaximum 7.0;
 set strutsmultiple false;
 set strutspacing 6;
 set testflag1 false;
 set testflag2 false;
 set testflag3 false;
 set testflag4 false;
 set tracealpha true;
 set usearcball false;
 set useminimizationthread true;
 set usenumberlocalization true;
 set vectorscale 1.0;
 set vibrationscale 1.0;
 set wireframerotation false;
 set zoomlarge true;
  1. 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;

}

function _setModelState() { 

 select ({7002 7003});
 Spacefill 0.5;
 select ({0:7001 7004:7708});
 Spacefill 0.0;
 select BONDS ({1510 1512 1514:1519 1535:1544 1554:1560 1576:1582});
 wireframe 0.5;
 select BONDS ({0:1509 1511 1513 1520:1534 1545:1553 1561:1575 1583:7200});
 wireframe 0.0;

 measures delete;
 select *; set measures nanometers;
 font measures 15.0 SansSerif Plain;

 select ({0:7001});
 Cartoon 0.0;
 color Cartoon opaque chain;

 select ({1449:1457 1473:1483 1492:1499 1513:1520});
 Strands 0.0;
 select ({0:1448 1458:1472 1484:1491 1500:1512 1521:7001});
 Strands on;
 select ({0:7001});
 color Strands opaque [x808080];

 set echo off;
 set echo bottom left; echo "Protein Modification: calcium ion (Metal coordination) 325_crosslink4";
 font echo 10.0 SansSerif Bold; color echo [x000000];

 boundBox off;
 font boundBox 14.0 SansSerif Plain;
 boundBox off;

 unitcell off;
 font unitcell 14.0 SansSerif Plain;
 unitcell off;

 hover "%U";

 frank off;
 font frank 16.0 SansSerif Bold;
 select *;

}

function _setPerspectiveState() { 

 set perspectiveModel 11;
 set scaleAngstromsPerInch 0.0;
 set perspectiveDepth true;
 set visualRange 5.0;
 set cameraDepth 3.0;
 boundbox corners {-2.2789993 13.026001 -19.830002} {81.053 74.486 82.824} # volume = 525751.1;
 center {38.646023 47.94447 -6.8159995};
 moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {39.387 43.756 31.496998} 58.66127 {0.0 0.0 0.0} 0.0 0.0 0.0;
 save orientation "default";
 moveto 0.0 { 35 -107 -994 123.82} 200.0 0.0 0.0 {38.646023 47.94447 -6.8159995} 58.66127 {0.0 0.0 0.0} -31.404827 -98.16444 0.0;;
 slab 100;depth 0;
 set spinX 0; set spinY 30; set spinZ 0; set spinFps 30;  set navX 0; set navY 0; set navZ 0; set navFps 10;

}

function _setSelectionState() { 

 select ({1449:1457 1473:1483 1492:1499 1513:1520});
 set hideNotSelected false;

}

function _setState() { 

 initialize;
 set refreshing false;
 _setWindowState;
 _setFileState;
 _setVariableState;
 _setModelState;
 _setPerspectiveState;
 _setSelectionState;
 set refreshing true;
 set antialiasDisplay true;
 set antialiasTranslucent true;
 set antialiasImages true;

}

_setState;

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_50"
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