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__4683499620434124__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue allowjavascript null
AppletRegistry.checkIn(obie__4683499620434124__)
vwrOptions:
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setting document base to "https://psnpbind.org/variant/88"
(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
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Jmol getValue ERRORCallback null
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Jmol getValue SYNCCallback null
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language=en_US
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Jmol getValue load null
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script 1 started
FileManager.getAtomSetCollectionFromFile(https://psnpbind.org/files/2y5h/proteins/2y5h_protein_Repair_2/2y5h_protein_Repair_2_final.pdb)
FileManager opening url https://psnpbind.org/files/2y5h/proteins/2y5h_protein_Repair_2/2y5h_protein_Repair_2_final.pdb
The Resolver thinks Pdb
loadScript /js/j2s/core/corebio.z.js
Protein in water t= 23260.00000 step= 23260
Setting space group name to P 1
Time for openFile(https://psnpbind.org/files/2y5h/proteins/2y5h_protein_Repair_2/2y5h_protein_Repair_2_final.pdb): 398 ms
reading 4425 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
4425 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: 155 ms
Protein in water t= 23260.00000 step= 23260
0 atoms deleted
1 atoms selected
loadScript /js/j2s/core/coretext.z.js
1 atoms selected
4425 atoms selected
14 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
