Class jalview.project.Jalview2xmlTests

File format identified as Jalview
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 110.0/187.7
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession12075698230354002131.tmp)
FileManager opening file /tmp/viewerSession12075698230354002131.tmp
Time for openFile(/tmp/viewerSession12075698230354002131.tmp): 63 ms
FileManager opening file /tmp/viewerSession12075698230354002131.tmp

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb9861987754025869160.txt)
FileManager opening file /tmp/jalview_pdb9861987754025869160.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb9861987754025869160.txt): 52 ms
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 62.3/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Time for creating model: 65 ms
unrecognized SET parameter in Jmol state script (set anyway): usearcball
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 69.9/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
registry.getSupportedServices: [RNAalifoldWS, AAConWS, MuscleWS, ClustalWS, ClustalOWS, DisemblWS, MSAprobsWS, MafftWS, GLprobsWS, IUPredWS, TcoffeeWS, GlobPlotWS, ProbconsWS, JronnWS]
Attempting to connect with MafftWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@9d2b3d6
Attempting to connect with MuscleWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@262e3ea1
Attempting to connect with ClustalWS...
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 86.7/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2e995b81
Attempting to connect with ClustalOWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3cc2fde3
Attempting to connect with TcoffeeWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3687d898
Attempting to connect with ProbconsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1918bba4
Attempting to connect with MSAprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4ddab23a
Attempting to connect with GLprobsWS...
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 89.8/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@e33824c
Attempting to connect with AAConWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@55d454b6
Attempting to connect with RNAalifoldWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@38fbc0b1
Attempting to connect with JronnWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2a9be895
Attempting to connect with DisemblWS...
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 93.2/187.7
processors available: 4
useCommandThread: false
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@413b71d5
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Attempting to connect with GlobPlotWS...
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5472ffab
Attempting to connect with IUPredWS...
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5206ab10
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 80.9/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 75.0/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 86.3/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 83.1/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 85.7/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 1866504708  Dataset for examples/uniref50.fa.xml
File format identified as Jalview
Per sequence colourscheme (Background) successfully applied and recovered.
Per sequence (Group) colourscheme successfully applied and recovered.
File format identified as Jalview
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 119.8/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 82.5/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 86.7/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 85.9/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 89.5/187.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
ALL CLOSED
File format identified as Jalview
File format identified as Jalview
ALL CLOSED
File format identified as Fasta
Writing jar entry 0uniref50.fa.xml
Writing jar entry 1uniref50.fa.xml
Writing jar entry 2uniref50.fa.xml
Writing jar entry 1299580705  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
File format identified as Stockholm
Writing jar entry RF00031_folded.stk.xml
Writing jar entry 1751989333  Dataset for examples/RF00031_folded.stk.xml
File format identified as Jalview
Read in same number of annotations as originally present (61)
File format identified as Fasta
Writing jar entry Copied From Clipboard.xml
Writing jar entry 915829339  Dataset for Copied From Clipboard.xml
File format identified as Jalview
ALL CLOSED
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 1512991814  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as Jalview
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 168.7/266.3
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession16887067123787792729.tmp)
FileManager opening file /tmp/viewerSession16887067123787792729.tmp
Time for openFile(/tmp/viewerSession16887067123787792729.tmp): 72 ms
FileManager opening file /tmp/viewerSession16887067123787792729.tmp

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb1503205283362276285.txt)
FileManager opening file /tmp/jalview_pdb1503205283362276285.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb1503205283362276285.txt): 56 ms
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 69.9/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Time for creating model: 77 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 70.4/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
unrecognized SET parameter in Jmol state script (set anyway): usearcball
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 81.9/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 85.9/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 90.7/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Writing jar entry viewer__jalview_pre2_4_512,285,363,365396702378797848224085276951090 (JMOL)
Writing jar entry 1A70 (1A70)
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
JMOL CREATE IMAGE
JMOL CREATE IMAGE
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_1.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_2.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_3.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_4.xml
Writing jar entry 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
ALL CLOSED
File format identified as Jalview
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 83.5/272.6
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession14787149138952417431.tmp)
FileManager opening file /tmp/viewerSession14787149138952417431.tmp
Time for openFile(/tmp/viewerSession14787149138952417431.tmp): 26 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 78.8/245.4
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 79.9/241.2
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 84.3/241.2
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 98.4/274.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
ALL CLOSED
File format identified as Fasta
Writing jar entry Copied From Clipboard.xml
Writing jar entry 1406543464  Dataset for Copied From Clipboard.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as Fasta
Writing jar entry 0uniref50.fa.xml
Writing jar entry 1uniref50.fa.xml
Writing jar entry 1121931889  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as PDB
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 142.2/259.0
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
ELECTRON TRANSPORT                      06-FEB-13   3W5V
CROSS-LINKED COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ R
found biomolecule 1: A, D
biomolecule 1: number of transforms: 1
found biomolecule 2: C, B
biomolecule 2: number of transforms: 1
FAD = FLAVIN-ADENINE DINUCLEOTIDE
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 1 21 1
3W5V
reading 6290 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 Jmol
6290 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 26 ms

blah
Writing jar entry 3W5V (3W5V)
Writing jar entry 3W5V.pdb.xml
Writing jar entry 427518901  Dataset for examples/3W5V.pdb.xml
ALL CLOSED
File format identified as Jalview
blah
ALL CLOSED
File format identified as Jalview
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 96.4/227.5
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession6304967046699429736.tmp)
FileManager opening file /tmp/viewerSession6304967046699429736.tmp
Time for openFile(/tmp/viewerSession6304967046699429736.tmp): 63 ms
FileManager opening file /tmp/viewerSession6304967046699429736.tmp

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb12662611628409489582.txt)
FileManager opening file /tmp/jalview_pdb12662611628409489582.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb12662611628409489582.txt): 61 ms
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 70.9/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Time for creating model: 75 ms
unrecognized SET parameter in Jmol state script (set anyway): usearcball
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 71.8/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 86.1/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 95.4/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 93.2/227.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Writing jar entry viewer__jalview_pre2_4_512,285,363,365396702378797848224085276956432 (JMOL)
Writing jar entry 1A70 (1A70)
Writing jar entry 0MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
JMOL CREATE IMAGE
JMOL CREATE IMAGE
Writing jar entry 1MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 2MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 3MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 4MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1299929225  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
ALL CLOSED
File format identified as Jalview
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 81.7/264.2
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession7877639782160518217.tmp)
FileManager opening file /tmp/viewerSession7877639782160518217.tmp
Time for openFile(/tmp/viewerSession7877639782160518217.tmp): 81 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 79.0/248.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 87.5/248.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 94.4/248.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 85.0/248.5
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 852156346  Dataset for examples/uniref50.fa.xml
File format identified as Jalview
T-Coffee score shading successfully recovered from project.
File format identified as Jalview
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 135.4/276.8
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 85.1/272.6
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 97.0/272.6
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 97.8/272.6
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 114.9/272.6
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 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 Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms

DEBUG - Firing service changed event for []
DEBUG - A MsaWS service called Muscle Multiple Protein Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS

DEBUG - A MsaWS service called MAFFT Multiple Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS

DEBUG - A MsaWS service called ClustalW Multiple Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS

DEBUG - A SecStrPred service called JPred Secondary Structure Prediction exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred

DEBUG - No service endpoints to use for service discovery.
DEBUG - Constructing news reader.
DEBUG - Filechooser init thread finished.
Aug 13, 2020 12:05:43 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276942710
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276942710
Aug 13, 2020 12:05:43 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
Aug 13, 2020 12:05:43 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
Aug 13, 2020 12:05:43 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Scanning news items: newsnew=false and lastDate is Thu Aug 13 13:05:42 BST 2020
DEBUG - Completed construction of reader.
DEBUG - Completed news thread.
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession12075698230354002131.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276942710
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276942710
Warning - overwriting a sequenceSetId for a viewport!
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Aug 13, 2020 12:05:43 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276942710
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276942710
Warning - overwriting a sequenceSetId for a viewport!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276942710
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276942710
Warning - overwriting a sequenceSetId for a viewport!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276942710
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276942710
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Warning - overwriting a sequenceSetId for a viewport!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:44 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:45 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:05:45 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276945206
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276945206
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@3cc2fde3, jalview.ws.jws2.jabaws2.Jws2Instance@4ddab23a, jalview.ws.jws2.jabaws2.Jws2Instance@e33824c, jalview.ws.jws2.jabaws2.Jws2Instance@2e995b81, jalview.ws.jws2.jabaws2.Jws2Instance@262e3ea1, jalview.ws.jws2.jabaws2.Jws2Instance@9d2b3d6, jalview.ws.jws2.jabaws2.Jws2Instance@1918bba4, jalview.ws.jws2.jabaws2.Jws2Instance@3687d898, jalview.ws.jws2.jabaws2.Jws2Instance@55d454b6, jalview.ws.jws2.jabaws2.Jws2Instance@413b71d5, jalview.ws.jws2.jabaws2.Jws2Instance@5472ffab, jalview.ws.jws2.jabaws2.Jws2Instance@5206ab10, jalview.ws.jws2.jabaws2.Jws2Instance@2a9be895, jalview.ws.jws2.jabaws2.Jws2Instance@38fbc0b1]
Rebuild WS Menu for service change
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276945206
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276945206
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276945206
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276945206
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276945206
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276945206
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276945206
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276945206
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 39308942
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 35314588546933
DEBUG - Setting viewport's view id : 353145885.109506356946933
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276947100
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276947100
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276947100
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276947100
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276947100
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276947100
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276947100
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276947100
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Scanning news items: newsnew=false and lastDate is Thu Aug 13 13:05:42 BST 2020
DEBUG - Saved last read date as 13 Aug 2020, 13:05:42
DEBUG - Scanning news items: newsnew=false and lastDate is Thu Aug 13 13:05:42 BST 2020
DEBUG - Saved last read date as 13 Aug 2020, 13:05:42
DEBUG - Scanning news items: newsnew=false and lastDate is Thu Aug 13 13:05:42 BST 2020
DEBUG - Saved last read date as 13 Aug 2020, 13:05:42
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276947100
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276947100
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with null is compatible with Jalview version null
Assuming project file with null is compatible with Jalview version 2.8.3
Assuming project file with 2.8.3 is compatible with Jalview version null
Assuming project file with Development Build is compatible with Jalview version null
Assuming project file with DEVELOPMENT BUILD is compatible with Jalview version null
Assuming project file with Development Build is compatible with Jalview version 2.8.3
Assuming project file with Test is compatible with Jalview version null
Assuming project file with TEST is compatible with Jalview version null
Assuming project file with Test is compatible with Jalview version 2.8.3
Assuming project file with Automated Build is compatible with Jalview version null
Assuming project file with Automated Build is compatible with Jalview version 2.8.3
Assuming project file with AUTOMATED BUILD is compatible with Jalview version 2.8.3
Invalid version format found: For input string: "3B1"
Invalid version format found: For input string: "3B1"
DEBUG - Created new dataset ds01 for alignment 405878402
DEBUG - Setting viewport's sequence set id : 177359188648768
DEBUG - Setting viewport's view id : 1773591886.33922690348768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG - Setting viewport's sequence set id : 150455325548768
DEBUG - Setting viewport's view id : 1504553255.22888345348768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 150455325548768
DEBUG - Setting viewport's view id : 1504553255.35455277048768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 150455325548768
DEBUG - Setting viewport's view id : 1504553255.143304329248768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 150455325548768
DEBUG - Setting viewport's view id : 1504553255.115655818348768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 203850517148768
DEBUG - Setting viewport's view id : 2038505171.164046979848768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 203850517148768
DEBUG - Setting viewport's view id : 2038505171.43400285648768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 203850517148768
DEBUG - Setting viewport's view id : 2038505171.129780277248768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 1567856105
DEBUG - Setting viewport's sequence set id : 150455325549278
DEBUG - Setting viewport's view id : 1504553255.115655818349278
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 150455325549278
DEBUG - Setting viewport's view id : 1504553255.22888345349278
DEBUG - Not enabling Google Tracking.
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 1384948621
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 1384948621
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 1737346498
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 138494862149798
DEBUG - Setting viewport's view id : 1384948621.167338901249798
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 138494862149798
DEBUG - Setting viewport's view id : 1384948621.61629828349798
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 138494862149798
DEBUG - Setting viewport's view id : 1384948621.83728813049798
Warning - overwriting a sequenceSetId for a viewport!
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: Index 2 out of bounds for length 2
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.paintTabArea(BasicTabbedPaneUI.java:897)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.paint(BasicTabbedPaneUI.java:860)
	at java.desktop/javax.swing.plaf.metal.MetalTabbedPaneUI.paint(MetalTabbedPaneUI.java:933)
	at java.desktop/javax.swing.plaf.metal.MetalTabbedPaneUI.update(MetalTabbedPaneUI.java:814)
	at java.desktop/javax.swing.JComponent.paintComponent(JComponent.java:797)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1074)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JLayeredPane.paint(JLayeredPane.java:590)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JLayeredPane.paint(JLayeredPane.java:590)
	at java.desktop/javax.swing.JComponent.paintToOffscreen(JComponent.java:5255)
	at java.desktop/javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:246)
	at java.desktop/javax.swing.RepaintManager.paint(RepaintManager.java:1323)
	at java.desktop/javax.swing.JComponent._paintImmediately(JComponent.java:5203)
	at java.desktop/javax.swing.JComponent.paintImmediately(JComponent.java:5013)
	at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:865)
	at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:848)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:848)
	at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:823)
	at java.desktop/javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:772)
	at java.desktop/javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1890)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
DEBUG - Created new dataset ds01 for alignment 1216360914
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 65332246550364
DEBUG - Setting viewport's view id : 653322465.213975837450364
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 117455992
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 59920220650768
DEBUG - Setting viewport's view id : 599202206.39103881750768
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 709662170
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 13234853150994
DEBUG - Setting viewport's view id : 132348531.5276499450994
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276951090
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276951090
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession16887067123787792729.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276951090
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276951090
Warning - overwriting a sequenceSetId for a viewport!
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276951090
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276951090
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276951090
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276951090
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276951090
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276951090
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> write STATE "/tmp/JMOL4804436988963397898.spt"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1684)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:812)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:688)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:620)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:572)
	at jalview.project.Jalview2xmlTests.__CLR4_4_1odp6yo3pq9(Jalview2xmlTests.java:433)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:412)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:132)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
	at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:412)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
	at java.base/java.lang.Thread.run(Thread.java:834)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1684)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:812)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:688)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:620)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:572)
	at jalview.project.Jalview2xmlTests.__CLR4_4_1odp6yo3pq9(Jalview2xmlTests.java:433)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:412)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:132)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
	at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:412)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
	at java.base/java.lang.Thread.run(Thread.java:834)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1684)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:812)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:688)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:620)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:572)
	at jalview.project.Jalview2xmlTests.__CLR4_4_1odp6yo3pq9(Jalview2xmlTests.java:433)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:412)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:132)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
	at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:412)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
	at java.base/java.lang.Thread.run(Thread.java:834)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 64601434  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1684)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:812)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:688)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:620)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:572)
	at jalview.project.Jalview2xmlTests.__CLR4_4_1odp6yo3pq9(Jalview2xmlTests.java:433)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:412)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:132)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
	at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
	at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:412)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
	at java.base/java.lang.Thread.run(Thread.java:834)
DEBUG - Created new dataset ds01 for alignment 1390185946
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695109053500
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2110744939670237879784822408527695109053500
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession14787149138952417431.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
eval ERROR: 
----
         load file <<<<"/tmp/viewerSession14787149138952417431.tmp"
Eval
 pc:0
1 statements
----
Token[keyword(1/0x8001401) value="load"]
Token[keyword(7/0x49401207) value="file"]
Token[string(4/0x4) value="/tmp/viewerSession14787149138952417431.tmp"]

END

Ignoring incomplete Jmol state for PDB ids: Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695109053500
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2090615939670237879784822408527695109053500
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695109053500
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.3082358739670237879784822408527695109053500
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695109053500
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.947217539670237879784822408527695109053500
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695109053500
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2230318039670237879784822408527695109053500
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - reusing DseqFor ID
DEBUG - Created new dataset ds01 for alignment 1123020176
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 180904256655393
DEBUG - Setting viewport's view id : 1809042566.171597087455393
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 353982865
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 1110259922
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 35398286555612
DEBUG - Setting viewport's view id : 353982865.28315470655612
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 35398286555612
DEBUG - Setting viewport's view id : 353982865.107447373855612
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 666376163
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 47858417456272
DEBUG - Setting viewport's view id : 478584174.27594213556272
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276956432
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276956432
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession6304967046699429736.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276956432
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276956432
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276956432
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276956432
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276956432
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276956432
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276956432
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276956432
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> write STATE "/tmp/JMOL1132319168571162956.spt"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Created new dataset ds01 for alignment 1132085507
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695643258510
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2230318039670237879784822408527695643258510
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession7877639782160518217.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
eval ERROR: 
----
         load file <<<<"/tmp/viewerSession7877639782160518217.tmp"
Eval
 pc:0
1 statements
----
Token[keyword(1/0x8001401) value="load"]
Token[keyword(7/0x49401207) value="file"]
Token[string(4/0x4) value="/tmp/viewerSession7877639782160518217.tmp"]

END

Ignoring incomplete Jmol state for PDB ids: Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695643258510
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.947217539670237879784822408527695643258510
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695643258510
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.3082358739670237879784822408527695643258510
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695643258510
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2090615939670237879784822408527695643258510
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527695643258510
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2110744939670237879784822408527695643258510
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 666593771
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 100183419060472
DEBUG - Setting viewport's view id : 1001834190.125759630260472
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276960582
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276960582
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276960582
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276960582
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276960582
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276960582
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276960582
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276960582
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276960582
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276960582
Warning - overwriting a sequenceSetId for a viewport!