Clicked several times. Saw the single carbon atom. Selected all text. Here’s the file. Frieda |
JSmol is an HTML5/Java-switchable version of Jmol. For a zip file containing all the files in this directory, see http://chemapps.stolaf.edu/jmol/zip/Jmol.zip. This page demonstrates Jmol using HTML5, Java, or WebGL. Credits: WebGL interface written by Takanori Nakane. Java2Script written by Zhou Renjian, et al. Jzlib written by Atsuhiko Yamanaka. Jmol._Canvas2D (Jmol) "jmolApplet0"[x] loading... ./j2s/core/package.js loading... ./j2s/core/core.z.js -- required by ClazzNode Jmol JavaScript applet jmolApplet0__708249813877046__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript true AppletRegistry.checkIn(jmolApplet0__708249813877046__) new matrix rotate! vwrOptions: { "name":"jmolApplet0","allowJavaScript":true,"applet":true,"documentBase":"http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__708249813877046__","codePath":"http://chemapps.stolaf.edu/jmol/jsmol/./j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"708249813877046","bgcolor":"#FFFFFF" } setting document base to "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm"; (C) 2012 Jmol Development Jmol Version: 14.1.15 2014-05-06 15:22 java.vendor: Java2Script (HTML5) java.version: JSmol 14.1.14 Apr 27, 2014 os.name: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/35.0.1916.114 Safari/537.36 Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet0 (signed) setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.initializeModel resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.setAxesOrientationRasmol resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.setBooleanPropertyTok resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] Jmol getValue emulate null defaults = "Jmol" setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.setAxesOrientationRasmol resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.setBooleanPropertyTok resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] Jmol getValue boxbgcolor null Jmol getValue bgcolor #FFFFFF backgroundColor = "#FFFFFF" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet0__708249813877046__ ready loading... ./j2s/core/corescript.z.js script 1 started antialiasDisplay = true FileManager.getAtomSetCollectionFromFile(data/caffeine.mol) setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.initializeModel resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] FileManager opening 1 http://chemapps.stolaf.edu/jmol/jsmol/data/caffeine.mol The Resolver thinks Mol C8H10N4O2 APtclcactv10291122543D 0 0.00000 0.00000 Time for openFile(data/caffeine.mol): 74 ms reading 24 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 24 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation setScale1 0 JU.M3.setScale 1 JV.TransformManager.resetRotation 2 JV.TransformManager.homePosition 3 JV.Viewer.reset 4 JV.Viewer.initializeModel resetRotation [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to1 [ [1 0 0] [0 1 0] [0 0 1] ] matrixRotate set to2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] setScale1 0 JU.M3.setScale 1 JM.Orientation.construct 2 function (d,c) 3 function () 4 JV.StateManager.saveOrientation finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] Script completed Jmol script terminated finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] loading... ./j2s/core/coretext.z.js setStatusAtomPicked(2,C3 #3 1.7906 0.2081 0.001) C3 #3 1.7906 0.2081 0.001 finalize1 [ [1 0 0] [0 1 0] [0 0 1] ] finalize2 [ [1 0 0] [0 1 0] [0 0 1] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ] finalize1 [ [0 0 0] [0 0 0] [0 0 0] ] finalize2 [ [0 0 0] [0 0 0] [0 0 0] ]
Search
console image display faster sharper
platformSpeed: 8 7 6 5 4 3 2 1
info show clear hide
spacefill wire ball&stick cartoons fancy not flat
color atomno color cpk color structure
isosurface vdw off mep translucent opaque
labels on off echo larger smaller Try various buttons. If anything
doesn't work please let me know.
Enter "!" and a command into the search box and press ENTER or open the applet
console to execute a script command.
keyword searches
=caffeine? (RCSB)
=1blu? (RCSB)
=1crn? (RCSB)
JSmol/Java
JSmol/HTML5
JSmol/WebGL
this-domain calls
swipe gesture test
EDS map test
2.2MB EDM test
local file reading writing saving(PNGJ)
make a nanotube
minimize drag-minimize !quit
flexible fit
PyMOL session - dna PP 2
estron.cml vasp.xml water.xodydata
thread test
echo/surface test
pause resume
!quit !exit
moveto
delay/hover
animation
spin/vibration
mo homo SQUARED
load data/1hxw.png (image)
load data/square_planar.spartan
load data/water.xyz.gz
load data/no2_nbo.log.gz
pmesh "data/sage.pmesh"
load data/caffeine.mol
isosurface "caffeine.jvxl"
load data/1crn.pdb
load data/k04041.cif {1 1 1}
load data/cl2o.gamess
(load +) mo homo
mo lumo mesh fill
image x 0.5 x 1.0 x 2.0 off on front mid back
cyclflip2.spt !quit
direct database calls(unless MSIE)
load $caffeine (from NCI)
load =1blu (from RCSB)
load =1d66 (from RCSB)
load =4tra (from RCSB)
load :1983 (PubChem CID)
load :aspirin (PubChem name)
load :smiles:CC/C=C/CC (PubChem SMILES)
load $CC/C=C/CC (NCI SMILES)
load :caffeine (PubChem, with mep)
load $caffeine (NCI, with MMFF94 mep)
load ==HEM (RCSB ligand)
On May 27, 2014, at 5:03 PM, Robert Hanson <[email protected]> wrote:
|
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