jsmol/j2s/core/package.js
-- required by ClazzNode ajax=false async=true
jsmol/j2s/core/core.z.js
-- required by ClazzNode ajax=false async=true
jsmol/j2s/J/g3d/PixelatorT.js
-- required by J.g3d.Graphics3D ajax=false async=true
JSmol exec jmolApplet start applet null
Jmol JavaScript applet jmolApplet__8066101190824049__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue allowjavascript null
AppletRegistry.checkIn(jmolApplet__8066101190824049__)
vwrOptions:
{ "name":"jmolApplet","applet":true,"documentBase":"https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do;jsessionid=83977fd15ce3d913bce743543538?ddid=GELAT1R2&action=view","platform":"J.awtjs2d.Platform","fullName":"jmolApplet__8066101190824049__","codePath":"https://dyndom.cmp.uea.ac.uk/dyndom/jsmol/j2s/","display":"jmolApplet_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8066101190824049","bgcolor":"#FFFFFF" }
setting document base to "https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do;jsessionid=83977fd15ce3d913bce743543538?ddid=GELAT1R2&action=view"
(C) 2012 Jmol Development
Jmol Version: 14.2.12_2015.02.11 2015-02-11 06:00
java.vendor: Java2Script (HTML5)
java.version: 2014-12-19 08:17:57 (JSmol/j2s)
os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
Access: ALL
memory: 0.0/0.0
processors available: 1
useCommandThread: false
appletId:jmolApplet (signed)
jsmol/j2s/core/corescript.z.js
-- required by ClazzNode ajax=true async=false
Jmol getValue emulate null
defaults = "Jmol"
Jmol getValue boxbgcolor null
Jmol getValue bgcolor #FFFFFF
backgroundColor = "#FFFFFF"
Jmol getValue ANIMFRAMECallback null
Jmol getValue APPLETREADYCallback Jmol._readyCallback
APPLETREADYCallback = "Jmol._readyCallback"
callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY
Jmol getValue ATOMMOVEDCallback null
Jmol getValue CLICKCallback null
Jmol getValue DRAGDROPCallback 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 jmolApplet__8066101190824049__ ready
script 1 started
FileManager.getAtomSetCollectionFromFile(dyndommorphs/GELAT1R2_JSMOLSCRPT)
FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphs/GELAT1R2_JSMOLSCRPT
The Resolver thinks Pdb
jsmol/j2s/core/corebio.z.js
-- required by ClazzNode ajax=true async=false
jsmol/j2s/J/render/MeshRenderer.js
-- required by J.renderbio.BioShapeRenderer ajax=true async=false
jsmol/j2s/J/shape/Mesh.js
-- required by J.renderbio.BioShapeRenderer ajax=true async=false
jsmol/j2s/J/renderbio/RocketRenderer.js
-- required by J.renderbio.RocketsRenderer ajax=true async=false
#jmolScript: select all; color grey; background white;
#jmolScript: select 93- 98, 116- 142
#jmolScript: color [0 ,0 ,255]
#jmolScript: select 99- 115, 143- 149
#jmolScript: color [255,0 ,0 ]
#jmolScript: select 179- 192
#jmolScript: color [0 ,0 ,255]
#jmolScript: backbone 100;
#jmolScript: select 193- 206
#jmolScript: color [255,0 ,0 ]
#jmolScript: backbone 100;
#jmolScript: select 98- 99, 140- 143
#jmolScript: color [0 ,255,0 ]
#jmolScript: select 113- 117
#jmolScript: color [0 ,255,0 ]
#jmolScript: select all
#jmolScript: anim mode loop 0.5 0.5;anim on;
#jmolScript: set echo top left;color echo [x0D0D99];echo "DynDom"
#jmolScript: set antialiasDisplay ON
Time for openFile(dyndommorphs/GELAT1R2_JSMOLSCRPT): 1197 ms
reading 1682 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
2 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
Default Van der Waals type for model set to Babel
1682 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 14.2.12_2015.02.11 2015-02-11 06:00 DSSP analysis for model 1.1 - null
W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637
We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer for our purposes. At this point in time, we make no guarantee
that this code gives precisely the same analysis as the code available via license
from CMBI at http://swift.cmbi.ru.nl/gv/dssp
All bioshapes have been deleted and must be regenerated.
Jmol 14.2.12_2015.02.11 2015-02-11 06:00 DSSP analysis for model 1.2 - null
NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.
Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.
null
Adding embedded #jmolscript: select ({723:750});backbone only;select ({1654:1681});backbone only;select *; select all; color grey; background white; select 93- 98, 116- 142; color [0 ,0 ,255]; select 99- 115, 143- 149; color [255,0 ,0 ]; select 179- 192; color [0 ,0 ,255]; backbone 100; select 193- 206; color [255,0 ,0 ]; backbone 100; select 98- 99, 140- 143; color [0 ,255,0 ]; select 113- 117; color [0 ,255,0 ]; select all; anim mode loop 0.5 0.5;anim on; set echo top left;color echo [x0D0D99];echo "DynDom"; set antialiasDisplay ON
2 models
jsmol/j2s/J/thread/AnimationThread.js
-- required by ClazzNode ajax=true async=false
jsmol/j2s/J/g3d/HermiteRenderer.js
-- required by ClazzNode ajax=true async=false
jsmol/j2s/core/coretext.z.js
-- required by ClazzNode ajax=true async=false
DynDom
1qib (A)
jsmol/j2s/core/corescriptmath.z.js
-- required by ClazzNode ajax=true async=false
jsmol/j2s/JV/PropertyManager.js
-- required by ClazzNode ajax=true async=false
jsmol/j2s/core/coreprop.z.js
-- required by JV.PropertyManager ajax=true async=false
1gen
Script completed
Jmol script terminated
