loadScript /js/j2s/core/package.js
loadScript /js/j2s/core/corejmol.z.js
loadScript /js/j2s/J/translation/PO.js
loadScript /js/j2s/core/corescript.z.js
JSmol exec obie start applet null
Jmol JavaScript applet obie__539873716148287__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue allowjavascript null
AppletRegistry.checkIn(obie__539873716148287__)
vwrOptions:
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setting document base to "https://psnpbind.org/variant/425"
(C) 2015 Jmol Development
Jmol Version: 14.31.16 2020-11-03 04:42
java.vendor: Java2Script (HTML5)
java.version: 2019-06-08 00:17:46 (JSmol/j2s)
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processors available: 1
useCommandThread: false
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Jmol getValue emulate null
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Jmol getValue boxbgcolor null
Jmol getValue bgcolor #FFFFFF
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Jmol getValue ANIMFRAMECallback null
Jmol getValue APPLETREADYCallback Jmol._readyCallback
APPLETREADYCallback = "Jmol._readyCallback"
StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY
Jmol getValue ATOMMOVEDCallback null
Jmol getValue AUDIOCallback null
Jmol getValue CLICKCallback null
Jmol getValue DRAGDROPCallback null
Jmol getValue ECHOCallback null
Jmol getValue ERRORCallback null
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Jmol getValue HOVERCallback null
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Jmol getValue LOADSTRUCTCallback null
Jmol getValue MEASURECallback null
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Jmol getValue MINIMIZATIONCallback null
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Jmol getValue RESIZECallback null
Jmol getValue SCRIPTCallback null
Jmol getValue SYNCCallback null
Jmol getValue STRUCTUREMODIFIEDCallback null
Jmol getValue doTranslate null
language=en_US
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Jmol getValue load null
Jmol applet obie__539873716148287__ ready
script 1 started
FileManager.getAtomSetCollectionFromFile(https://psnpbind.org/files/3b5r/proteins/3b5r_protein_Repair_9/3b5r_protein_Repair_9_final.pdb)
FileManager opening url https://psnpbind.org/files/3b5r/proteins/3b5r_protein_Repair_9/3b5r_protein_Repair_9_final.pdb
The Resolver thinks Pdb
loadScript /js/j2s/core/corebio.z.js
Protein in water t= 22228.00000 step= 22228
Setting space group name to P 1
Time for openFile(https://psnpbind.org/files/3b5r/proteins/3b5r_protein_Repair_9/3b5r_protein_Repair_9_final.pdb): 514 ms
reading 4065 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
4065 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 14.31.16 2020-11-03 04:42 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 in Java for our purposes.
Second generation DSSP 2.0 is used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.
All bioshapes have been deleted and must be regenerated.
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.
Time for creating model: 150 ms
Protein in water t= 22228.00000 step= 22228
0 atoms deleted
1 atoms selected
loadScript /js/j2s/core/coretext.z.js
1 atoms selected
4065 atoms selected
11 atoms selected
specular = true
refreshing = false
refreshing = true
loadScript /js/j2s/J/g3d/HermiteRenderer.js
loadScript /js/j2s/J/renderbio/BioMeshRenderer.js
loadScript /js/j2s/J/render/MeshRenderer.js
loadScript /js/j2s/J/shape/Mesh.js
Script completed
Jmol script terminated
