Class jalview.ext.jmol.JmolViewerTest

all > jalview.ext.jmol > JmolViewerTest

tests

failures

ignored

3.134s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testAddStrToSingleSeqViewJMol	2.350s	passed
testSingleSeqViewJMol	0.784s	passed

Standard output

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: 420.0/499.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
reading 690 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
690 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 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@1c4d49c8
Attempting to connect with MuscleWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4a08e033
Attempting to connect with ClustalWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1f23bbe2
Attempting to connect with ClustalOWS...
(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: 114.4/308.3
processors available: 4
useCommandThread: false
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@15f6440c
Attempting to connect with TcoffeeWS...
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
Time for openFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt): 110 ms
reading 690 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
690 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: 94.1/308.3
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
reading 690 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
690 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2f196ec7
Attempting to connect with ProbconsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@73d72ba7
Attempting to connect with MSAprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4e0ca859
Attempting to connect with GLprobsWS...
Time for creating model: 133 ms
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ


Adding embedded #jmolscript: select ({0:689});backbone only;select *;
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: 94.9/308.3
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.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@7f322f1f
Default Van der Waals type for model set to Jmol
6290 atoms created
Attempting to connect with AAConWS...
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3d934837
Time for creating model: 26 ms
Attempting to connect with RNAalifoldWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5f6f9a7e
Attempting to connect with JronnWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@144dffd6
Attempting to connect with DisemblWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@63a066d
Attempting to connect with GlobPlotWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@69168265
Attempting to connect with IUPredWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6b9bb53b

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/3W5V.pdb)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/3W5V.pdb
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
Time for openFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/3W5V.pdb): 7 ms
reading 6290 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models 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
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: 118.7/308.3
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
reading 690 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
690 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: 108.3/308.3
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: 20 ms
Time for creating model: 210 ms
2 models

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: 99.7/308.3
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
reading 690 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
690 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
(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: 99.9/308.3
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
Time for openFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt): 79 ms
reading 690 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
690 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: 98.1/308.3
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ
reading 690 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
690 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Time for creating model: 131 ms
OXIDOREDUCTASE/ELECTRON TRANSPORT       08-MAY-00   1GAQ
1GAQ


Adding embedded #jmolscript: select ({0:689});backbone only;select *;

Standard error

DEBUG - (Re)-Initialising the discovery URL list.
DEBUG - Setting default services
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 - Firing service changed event for []
DEBUG - Firing service changed event for []
DEBUG - Firing service changed event for []
DEBUG - Firing service changed event for []
DEBUG - Filechooser init thread finished.
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Aug 13, 2020 12:06:15 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Aug 13, 2020 12:06:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Allocating Jmol Viewer: 
Aug 13, 2020 12:06:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES  "/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt"

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 - Waiting around for jmb notify.
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> 

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - >>Jmol>> model *; select backbone;restrict;cartoon;wireframe off;spacefill off
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> select 19-314:A/1.1;color[255,255,255]

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> loadingJalviewdata=true
load APPEND  "/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/3W5V.pdb"
loadingJalviewdata=null

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Waiting around for jmb notify.
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> select 19-314:A/1.1;color[255,255,255]

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Waiting around for jmb notify.
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@15f6440c, jalview.ws.jws2.jabaws2.Jws2Instance@4e0ca859, jalview.ws.jws2.jabaws2.Jws2Instance@7f322f1f, jalview.ws.jws2.jabaws2.Jws2Instance@1f23bbe2, jalview.ws.jws2.jabaws2.Jws2Instance@4a08e033, jalview.ws.jws2.jabaws2.Jws2Instance@1c4d49c8, jalview.ws.jws2.jabaws2.Jws2Instance@73d72ba7, jalview.ws.jws2.jabaws2.Jws2Instance@2f196ec7, jalview.ws.jws2.jabaws2.Jws2Instance@3d934837, jalview.ws.jws2.jabaws2.Jws2Instance@63a066d, jalview.ws.jws2.jabaws2.Jws2Instance@69168265, jalview.ws.jws2.jabaws2.Jws2Instance@6b9bb53b, jalview.ws.jws2.jabaws2.Jws2Instance@144dffd6, jalview.ws.jws2.jabaws2.Jws2Instance@5f6f9a7e]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@15f6440c, jalview.ws.jws2.jabaws2.Jws2Instance@4e0ca859, jalview.ws.jws2.jabaws2.Jws2Instance@7f322f1f, jalview.ws.jws2.jabaws2.Jws2Instance@1f23bbe2, jalview.ws.jws2.jabaws2.Jws2Instance@4a08e033, jalview.ws.jws2.jabaws2.Jws2Instance@1c4d49c8, jalview.ws.jws2.jabaws2.Jws2Instance@73d72ba7, jalview.ws.jws2.jabaws2.Jws2Instance@2f196ec7, jalview.ws.jws2.jabaws2.Jws2Instance@3d934837, jalview.ws.jws2.jabaws2.Jws2Instance@63a066d, jalview.ws.jws2.jabaws2.Jws2Instance@69168265, jalview.ws.jws2.jabaws2.Jws2Instance@6b9bb53b, jalview.ws.jws2.jabaws2.Jws2Instance@144dffd6, jalview.ws.jws2.jabaws2.Jws2Instance@5f6f9a7e]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@15f6440c, jalview.ws.jws2.jabaws2.Jws2Instance@4e0ca859, jalview.ws.jws2.jabaws2.Jws2Instance@7f322f1f, jalview.ws.jws2.jabaws2.Jws2Instance@1f23bbe2, jalview.ws.jws2.jabaws2.Jws2Instance@4a08e033, jalview.ws.jws2.jabaws2.Jws2Instance@1c4d49c8, jalview.ws.jws2.jabaws2.Jws2Instance@73d72ba7, jalview.ws.jws2.jabaws2.Jws2Instance@2f196ec7, jalview.ws.jws2.jabaws2.Jws2Instance@3d934837, jalview.ws.jws2.jabaws2.Jws2Instance@63a066d, jalview.ws.jws2.jabaws2.Jws2Instance@69168265, jalview.ws.jws2.jabaws2.Jws2Instance@6b9bb53b, jalview.ws.jws2.jabaws2.Jws2Instance@144dffd6, jalview.ws.jws2.jabaws2.Jws2Instance@5f6f9a7e]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@15f6440c, jalview.ws.jws2.jabaws2.Jws2Instance@4e0ca859, jalview.ws.jws2.jabaws2.Jws2Instance@7f322f1f, jalview.ws.jws2.jabaws2.Jws2Instance@1f23bbe2, jalview.ws.jws2.jabaws2.Jws2Instance@4a08e033, jalview.ws.jws2.jabaws2.Jws2Instance@1c4d49c8, jalview.ws.jws2.jabaws2.Jws2Instance@73d72ba7, jalview.ws.jws2.jabaws2.Jws2Instance@2f196ec7, jalview.ws.jws2.jabaws2.Jws2Instance@3d934837, jalview.ws.jws2.jabaws2.Jws2Instance@63a066d, jalview.ws.jws2.jabaws2.Jws2Instance@69168265, jalview.ws.jws2.jabaws2.Jws2Instance@6b9bb53b, jalview.ws.jws2.jabaws2.Jws2Instance@144dffd6, jalview.ws.jws2.jabaws2.Jws2Instance@5f6f9a7e]
DEBUG - Waiting around for jmb notify.
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
DEBUG - Waiting around for jmb notify.
Rebuild WS Menu for service change
Rebuild WS Menu for service change
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - >>Jmol>> model *; select backbone;restrict;cartoon;wireframe off;spacefill off
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> select 19-314:A/1.1|18-314:A/2.1;color[255,255,255]

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> select *; cartoons off; backbone

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
INFO - Couldn't align structures with the 'null' associated alignment panels.
java.lang.NullPointerException
	at java.base/java.util.ArrayList.addAll(ArrayList.java:701)
	at jalview.structures.models.AAStructureBindingModel.executeCommand(AAStructureBindingModel.java:1099)
	at jalview.structures.models.AAStructureBindingModel.executeCommands(AAStructureBindingModel.java:1065)
	at jalview.structures.models.AAStructureBindingModel.superposeStructures(AAStructureBindingModel.java:917)
	at jalview.gui.StructureViewerBase.alignStructsWithAllAlignPanels(StructureViewerBase.java:788)
	at jalview.gui.AppJmol$3.run(AppJmol.java:412)
	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)
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES  "/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1/examples/1gaq.txt"

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 - Waiting around for jmb notify.
DEBUG - Waiting around for jmb notify.
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> 

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> model *; select backbone;restrict;cartoon;wireframe off;spacefill off
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> select 19-314:A/1.1;color[255,255,255]

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending