Class jalview.ext.jmol.JmolViewerTest

2

tests

0

failures

0

ignored

4.056s

duration

100%

successful

Test Duration Result
testAddStrToSingleSeqViewJMol 3.267s passed
testSingleSeqViewJMol 0.789s passed
Java version: 11.0.25
Java Home: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
amd64 Linux 3.10.0-1160.24.1.el7.x86_64
CMD [-props test/jalview/ext/rbvi/chimera/testProps.jvprops] executed successfully!
loading services
Could not make Java version check
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 71.9/175.1
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: 9 ms
INFO: I18N missing: en_GB	label.jmol_help
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 117.4/175.1
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-JOB1/examples/1gaq.txt)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-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-GDB665-JOB1/examples/1gaq.txt): 82 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
Time for creating model: 6 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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 69.8/175.1
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: 5 ms
registry.getSupportedServices: [RNAalifoldWS, ClustalWS, ProbconsWS, ClustalOWS, DisemblWS, JronnWS, TcoffeeWS, IUPredWS, MSAprobsWS, GlobPlotWS, MafftWS, GLprobsWS, MuscleWS, AAConWS]
Attempting to connect with MafftWS...
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 87.1/175.1
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
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@552f4eda
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
Attempting to connect with MuscleWS...
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 48 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@489bd347
Attempting to connect with ClustalWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@244156c2
Attempting to connect with ClustalOWS...

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-JOB1/examples/3W5V.pdb)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-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-GDB665-JOB1/examples/3W5V.pdb): 19 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.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@19560534
Default Van der Waals type for model set to Jmol
6290 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Attempting to connect with TcoffeeWS...
Time for creating model: 43 ms
2 models

Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 75.0/175.1
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: 10 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6ed7bc6
Attempting to connect with ProbconsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4a457d2
Attempting to connect with MSAprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@39856832
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 81.7/175.1
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
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6f292f28
Time for creating model: 29 ms
Attempting to connect with AAConWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@742d5a81
Attempting to connect with RNAalifoldWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6cacfb73
Attempting to connect with JronnWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@35bc74db
Attempting to connect with DisemblWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@39878411
Attempting to connect with GlobPlotWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2c3a2acf
Attempting to connect with IUPredWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3bd8fb56
 atom 1 [VAL]313:A.CA/2.1 #2343	atom 2 [TYR]314:A.CA/1.1 #2344
 atom 1 [GLU]312:A.CA/2.1 #2334	atom 2 [VAL]313:A.CA/1.1 #2337
 atom 1 [VAL]311:A.CA/2.1 #2327	atom 2 [GLU]312:A.CA/1.1 #2328
 atom 1 [ASN]310:A.CA/2.1 #2319	atom 2 [VAL]311:A.CA/1.1 #2321
 atom 1 [TRP]309:A.CA/2.1 #2305	atom 2 [ASN]310:A.CA/1.1 #2313
 atom 1 [GLN]308:A.CA/2.1 #2296	atom 2 [TRP]309:A.CA/1.1 #2299
 atom 1 [ASP]307:A.CA/2.1 #2288	atom 2 [GLN]308:A.CA/1.1 #2290
 atom 1 [GLY]306:A.CA/2.1 #2284	atom 2 [ASP]307:A.CA/1.1 #2282
 atom 1 [ARG]305:A.CA/2.1 #2273	atom 2 [GLY]306:A.CA/1.1 #2278
 atom 1 [LYS]304:A.CA/2.1 #2264	atom 2 [ARG]305:A.CA/1.1 #2267
 atom 1 [LEU]303:A.CA/2.1 #2256	atom 2 [LYS]304:A.CA/1.1 #2258
 atom 1 [GLN]302:A.CA/2.1 #2247	atom 2 [LEU]303:A.CA/1.1 #2250
 atom 1 [LYS]301:A.CA/2.1 #2238	atom 2 [GLN]302:A.CA/1.1 #2241
 atom 1 [LYS]300:A.CA/2.1 #2229	atom 2 [LYS]301:A.CA/1.1 #2232
 atom 1 [TYR]299:A.CA/2.1 #2217	atom 2 [LYS]300:A.CA/1.1 #2223
 atom 1 [ASP]298:A.CA/2.1 #2209	atom 2 [TYR]299:A.CA/1.1 #2211
 atom 1 [PHE]297:A.CA/2.1 #2198	atom 2 [ASP]298:A.CA/1.1 #2203
 atom 1 [TRP]296:A.CA/2.1 #2184	atom 2 [PHE]297:A.CA/1.1 #2192
 atom 1 [ASP]295:A.CA/2.1 #2176	atom 2 [TRP]296:A.CA/1.1 #2178
 atom 1 [ILE]294:A.CA/2.1 #2168	atom 2 [ASP]295:A.CA/1.1 #2170
 atom 1 [GLY]293:A.CA/2.1 #2164	atom 2 [ILE]294:A.CA/1.1 #2162
 atom 1 [ASP]292:A.CA/2.1 #2156	atom 2 [GLY]293:A.CA/1.1 #2158
 atom 1 [LYS]291:A.CA/2.1 #2147	atom 2 [ASP]292:A.CA/1.1 #2150
 atom 1 [GLU]290:A.CA/2.1 #2138	atom 2 [LYS]291:A.CA/1.1 #2141
 atom 1 [ALA]289:A.CA/2.1 #2133	atom 2 [GLU]290:A.CA/1.1 #2132
 atom 1 [LEU]288:A.CA/2.1 #2125	atom 2 [ALA]289:A.CA/1.1 #2127
 atom 1 [SER]287:A.CA/2.1 #2119	atom 2 [LEU]288:A.CA/1.1 #2119
 atom 1 [VAL]286:A.CA/2.1 #2112	atom 2 [SER]287:A.CA/1.1 #2113
 atom 1 [MET]285:A.CA/2.1 #2104	atom 2 [VAL]286:A.CA/1.1 #2106
 atom 1 [ILE]284:A.CA/2.1 #2096	atom 2 [MET]285:A.CA/1.1 #2098
 atom 1 [ASP]283:A.CA/2.1 #2088	atom 2 [ILE]284:A.CA/1.1 #2090
 atom 1 [ASP]282:A.CA/2.1 #2080	atom 2 [ASP]283:A.CA/1.1 #2082
 atom 1 [ILE]281:A.CA/2.1 #2072	atom 2 [ASP]282:A.CA/1.1 #2074
 atom 1 [GLY]280:A.CA/2.1 #2068	atom 2 [ILE]281:A.CA/1.1 #2066
 atom 1 [LYS]279:A.CA/2.1 #2059	atom 2 [GLY]280:A.CA/1.1 #2062
 atom 1 [GLU]278:A.CA/2.1 #2050	atom 2 [LYS]279:A.CA/1.1 #2053
 atom 1 [MET]277:A.CA/2.1 #2042	atom 2 [GLU]278:A.CA/1.1 #2044
 atom 1 [GLY]276:A.CA/2.1 #2038	atom 2 [MET]277:A.CA/1.1 #2036
 atom 1 [LYS]275:A.CA/2.1 #2029	atom 2 [GLY]276:A.CA/1.1 #2032
 atom 1 [LEU]274:A.CA/2.1 #2021	atom 2 [LYS]275:A.CA/1.1 #2023
 atom 1 [GLY]273:A.CA/2.1 #2017	atom 2 [LEU]274:A.CA/1.1 #2015
 atom 1 [CYS]272:A.CA/2.1 #2011	atom 2 [GLY]273:A.CA/1.1 #2011
 atom 1 [MET]271:A.CA/2.1 #2003	atom 2 [CYS]272:A.CA/1.1 #2005
 atom 1 [TYR]270:A.CA/2.1 #1991	atom 2 [MET]271:A.CA/1.1 #1997
 atom 1 [VAL]269:A.CA/2.1 #1984	atom 2 [TYR]270:A.CA/1.1 #1985
 atom 1 [TYR]268:A.CA/2.1 #1972	atom 2 [VAL]269:A.CA/1.1 #1978
 atom 1 [THR]267:A.CA/2.1 #1965	atom 2 [TYR]268:A.CA/1.1 #1966
 atom 1 [ASN]266:A.CA/2.1 #1957	atom 2 [THR]267:A.CA/1.1 #1959
 atom 1 [ASP]265:A.CA/2.1 #1949	atom 2 [ASN]266:A.CA/1.1 #1951
 atom 1 [LYS]264:A.CA/2.1 #1940	atom 2 [ASP]265:A.CA/1.1 #1943
 atom 1 [LYS]263:A.CA/2.1 #1931	atom 2 [LYS]264:A.CA/1.1 #1934
 atom 1 [LEU]262:A.CA/2.1 #1923	atom 2 [LYS]263:A.CA/1.1 #1925
 atom 1 [LEU]261:A.CA/2.1 #1915	atom 2 [LEU]262:A.CA/1.1 #1917
 atom 1 [GLU]260:A.CA/2.1 #1906	atom 2 [LEU]261:A.CA/1.1 #1909
 atom 1 [TRP]259:A.CA/2.1 #1892	atom 2 [GLU]260:A.CA/1.1 #1900
 atom 1 [LEU]258:A.CA/2.1 #1884	atom 2 [TRP]259:A.CA/1.1 #1886
 atom 1 [GLU]257:A.CA/2.1 #1875	atom 2 [LEU]258:A.CA/1.1 #1878
 atom 1 [GLU]256:A.CA/2.1 #1866	atom 2 [GLU]257:A.CA/1.1 #1869
 atom 1 [LYS]255:A.CA/2.1 #1857	atom 2 [GLU]256:A.CA/1.1 #1860
 atom 1 [TYR]254:A.CA/2.1 #1845	atom 2 [LYS]255:A.CA/1.1 #1851
 atom 1 [GLU]253:A.CA/2.1 #1836	atom 2 [TYR]254:A.CA/1.1 #1839
 atom 1 [ALA]252:A.CA/2.1 #1831	atom 2 [GLU]253:A.CA/1.1 #1830
 atom 1 [MET]251:A.CA/2.1 #1823	atom 2 [ALA]252:A.CA/1.1 #1825
 atom 1 [ARG]250:A.CA/2.1 #1812	atom 2 [MET]251:A.CA/1.1 #1817
 atom 1 [THR]249:A.CA/2.1 #1805	atom 2 [ARG]250:A.CA/1.1 #1806
 atom 1 [GLN]248:A.CA/2.1 #1796	atom 2 [THR]249:A.CA/1.1 #1799
 atom 1 [ILE]247:A.CA/2.1 #1788	atom 2 [GLN]248:A.CA/1.1 #1790
 atom 1 [TYR]246:A.CA/2.1 #1776	atom 2 [ILE]247:A.CA/1.1 #1782
 atom 1 [MET]245:A.CA/2.1 #1768	atom 2 [TYR]246:A.CA/1.1 #1770
 atom 1 [ARG]244:A.CA/2.1 #1757	atom 2 [MET]245:A.CA/1.1 #1762
 atom 1 [GLU]243:A.CA/2.1 #1748	atom 2 [ARG]244:A.CA/1.1 #1751
 atom 1 [GLY]242:A.CA/2.1 #1744	atom 2 [GLU]243:A.CA/1.1 #1742
 atom 1 [ALA]241:A.CA/2.1 #1739	atom 2 [GLY]242:A.CA/1.1 #1738
 atom 1 [ALA]240:A.CA/2.1 #1734	atom 2 [ALA]241:A.CA/1.1 #1733
 atom 1 [ASN]239:A.CA/2.1 #1726	atom 2 [ALA]240:A.CA/1.1 #1728
 atom 1 [THR]238:A.CA/2.1 #1719	atom 2 [ASN]239:A.CA/1.1 #1720
 atom 1 [GLN]237:A.CA/2.1 #1710	atom 2 [THR]238:A.CA/1.1 #1713
 atom 1 [GLU]236:A.CA/2.1 #1701	atom 2 [GLN]237:A.CA/1.1 #1704
 atom 1 [ARG]235:A.CA/2.1 #1690	atom 2 [GLU]236:A.CA/1.1 #1695
 atom 1 [SER]234:A.CA/2.1 #1684	atom 2 [ARG]235:A.CA/1.1 #1684
 atom 1 [VAL]233:A.CA/2.1 #1677	atom 2 [SER]234:A.CA/1.1 #1678
 atom 1 [ALA]232:A.CA/2.1 #1672	atom 2 [VAL]233:A.CA/1.1 #1671
 atom 1 [TYR]231:A.CA/2.1 #1660	atom 2 [ALA]232:A.CA/1.1 #1666
 atom 1 [ASP]230:A.CA/2.1 #1652	atom 2 [TYR]231:A.CA/1.1 #1654
 atom 1 [VAL]229:A.CA/2.1 #1645	atom 2 [ASP]230:A.CA/1.1 #1646
 atom 1 [ARG]228:A.CA/2.1 #1634	atom 2 [VAL]229:A.CA/1.1 #1639
 atom 1 [PHE]227:A.CA/2.1 #1623	atom 2 [ARG]228:A.CA/1.1 #1628
 atom 1 [ASN]226:A.CA/2.1 #1615	atom 2 [PHE]227:A.CA/1.1 #1617
 atom 1 [GLU]225:A.CA/2.1 #1606	atom 2 [ASN]226:A.CA/1.1 #1609
 atom 1 [PRO]224:A.CA/2.1 #1599	atom 2 [GLU]225:A.CA/1.1 #1600
 atom 1 [ALA]223:A.CA/2.1 #1594	atom 2 [PRO]224:A.CA/1.1 #1593
 atom 1 [ARG]222:A.CA/2.1 #1583	atom 2 [ALA]223:A.CA/1.1 #1588
 atom 1 [GLU]221:A.CA/2.1 #1574	atom 2 [ARG]222:A.CA/1.1 #1577
 atom 1 [LYS]220:A.CA/2.1 #1565	atom 2 [GLU]221:A.CA/1.1 #1568
 atom 1 [MET]219:A.CA/2.1 #1557	atom 2 [LYS]220:A.CA/1.1 #1559
 atom 1 [LYS]218:A.CA/2.1 #1548	atom 2 [MET]219:A.CA/1.1 #1551
 atom 1 [GLY]217:A.CA/2.1 #1544	atom 2 [LYS]218:A.CA/1.1 #1542
 atom 1 [PHE]216:A.CA/2.1 #1533	atom 2 [GLY]217:A.CA/1.1 #1538
 atom 1 [GLU]215:A.CA/2.1 #1524	atom 2 [PHE]216:A.CA/1.1 #1527
 atom 1 [GLU]214:A.CA/2.1 #1515	atom 2 [GLU]215:A.CA/1.1 #1518
 atom 1 [LYS]213:A.CA/2.1 #1506	atom 2 [GLU]214:A.CA/1.1 #1509
 atom 1 [TYR]212:A.CA/2.1 #1494	atom 2 [LYS]213:A.CA/1.1 #1500
 atom 1 [LEU]211:A.CA/2.1 #1486	atom 2 [TYR]212:A.CA/1.1 #1488
 atom 1 [LEU]210:A.CA/2.1 #1478	atom 2 [LEU]211:A.CA/1.1 #1480
 atom 1 [SER]209:A.CA/2.1 #1472	atom 2 [LEU]210:A.CA/1.1 #1472
 atom 1 [SER]208:A.CA/2.1 #1466	atom 2 [SER]209:A.CA/1.1 #1466
 atom 1 [SER]207:A.CA/2.1 #1460	atom 2 [SER]208:A.CA/1.1 #1460
 atom 1 [THR]206:A.CA/2.1 #1453	atom 2 [SER]207:A.CA/1.1 #1454
 atom 1 [PRO]205:A.CA/2.1 #1446	atom 2 [THR]206:A.CA/1.1 #1447
 atom 1 [VAL]204:A.CA/2.1 #1439	atom 2 [PRO]205:A.CA/1.1 #1440
 atom 1 [GLY]203:A.CA/2.1 #1435	atom 2 [VAL]204:A.CA/1.1 #1433
 atom 1 [LEU]202:A.CA/2.1 #1427	atom 2 [GLY]203:A.CA/1.1 #1429
 atom 1 [PHE]201:A.CA/2.1 #1416	atom 2 [LEU]202:A.CA/1.1 #1421
 atom 1 [LEU]200:A.CA/2.1 #1408	atom 2 [PHE]201:A.CA/1.1 #1410
 atom 1 [TRP]199:A.CA/2.1 #1394	atom 2 [LEU]200:A.CA/1.1 #1402
 atom 1 [GLY]198:A.CA/2.1 #1390	atom 2 [TRP]199:A.CA/1.1 #1388
 atom 1 [LEU]197:A.CA/2.1 #1382	atom 2 [GLY]198:A.CA/1.1 #1384
 atom 1 [GLY]196:A.CA/2.1 #1378	atom 2 [LEU]197:A.CA/1.1 #1376
 atom 1 [ASN]195:A.CA/2.1 #1370	atom 2 [GLY]196:A.CA/1.1 #1372
 atom 1 [PHE]194:A.CA/2.1 #1359	atom 2 [ASN]195:A.CA/1.1 #1364
 atom 1 [LYS]193:A.CA/2.1 #1350	atom 2 [PHE]194:A.CA/1.1 #1353
 atom 1 [TYR]192:A.CA/2.1 #1338	atom 2 [LYS]193:A.CA/1.1 #1344
 atom 1 [ASP]191:A.CA/2.1 #1330	atom 2 [TYR]192:A.CA/1.1 #1332
 atom 1 [ASP]190:A.CA/2.1 #1322	atom 2 [ASP]191:A.CA/1.1 #1324
 atom 1 [HIS]189:A.CA/2.1 #1312	atom 2 [ASP]190:A.CA/1.1 #1316
 atom 1 [LYS]188:A.CA/2.1 #1303	atom 2 [HIS]189:A.CA/1.1 #1306
 atom 1 [GLU]187:A.CA/2.1 #1294	atom 2 [LYS]188:A.CA/1.1 #1297
 atom 1 [PHE]186:A.CA/2.1 #1283	atom 2 [GLU]187:A.CA/1.1 #1288
 atom 1 [PHE]185:A.CA/2.1 #1272	atom 2 [PHE]186:A.CA/1.1 #1277
 atom 1 [MET]184:A.CA/2.1 #1264	atom 2 [PHE]185:A.CA/1.1 #1266
 atom 1 [LYS]183:A.CA/2.1 #1255	atom 2 [MET]184:A.CA/1.1 #1258
 atom 1 [TRP]182:A.CA/2.1 #1241	atom 2 [LYS]183:A.CA/1.1 #1249
 atom 1 [LEU]181:A.CA/2.1 #1233	atom 2 [TRP]182:A.CA/1.1 #1235
 atom 1 [PHE]180:A.CA/2.1 #1222	atom 2 [LEU]181:A.CA/1.1 #1227
 atom 1 [SER]179:A.CA/2.1 #1216	atom 2 [PHE]180:A.CA/1.1 #1216
 atom 1 [ARG]178:A.CA/2.1 #1205	atom 2 [SER]179:A.CA/1.1 #1210
 atom 1 [PHE]177:A.CA/2.1 #1194	atom 2 [ARG]178:A.CA/1.1 #1199
 atom 1 [PRO]176:A.CA/2.1 #1187	atom 2 [PHE]177:A.CA/1.1 #1188
 atom 1 [ALA]175:A.CA/2.1 #1182	atom 2 [PRO]176:A.CA/1.1 #1181
 atom 1 [ILE]174:A.CA/2.1 #1174	atom 2 [ALA]175:A.CA/1.1 #1176
 atom 1 [GLY]173:A.CA/2.1 #1170	atom 2 [ILE]174:A.CA/1.1 #1168
 atom 1 [THR]172:A.CA/2.1 #1163	atom 2 [GLY]173:A.CA/1.1 #1164
 atom 1 [GLY]171:A.CA/2.1 #1159	atom 2 [THR]172:A.CA/1.1 #1157
 atom 1 [THR]170:A.CA/2.1 #1152	atom 2 [GLY]171:A.CA/1.1 #1153
 atom 1 [ALA]169:A.CA/2.1 #1147	atom 2 [THR]170:A.CA/1.1 #1146
 atom 1 [LEU]168:A.CA/2.1 #1139	atom 2 [ALA]169:A.CA/1.1 #1141
 atom 1 [MET]167:A.CA/2.1 #1131	atom 2 [LEU]168:A.CA/1.1 #1133
 atom 1 [ILE]166:A.CA/2.1 #1123	atom 2 [MET]167:A.CA/1.1 #1125
 atom 1 [ILE]165:A.CA/2.1 #1115	atom 2 [ILE]166:A.CA/1.1 #1117
 atom 1 [THR]164:A.CA/2.1 #1108	atom 2 [ILE]165:A.CA/1.1 #1109
 atom 1 [ALA]163:A.CA/2.1 #1103	atom 2 [THR]164:A.CA/1.1 #1102
 atom 1 [ASN]162:A.CA/2.1 #1095	atom 2 [ALA]163:A.CA/1.1 #1097
 atom 1 [PRO]161:A.CA/2.1 #1088	atom 2 [ASN]162:A.CA/1.1 #1089
 atom 1 [ASP]160:A.CA/2.1 #1080	atom 2 [PRO]161:A.CA/1.1 #1082
 atom 1 [LYS]159:A.CA/2.1 #1071	atom 2 [ASP]160:A.CA/1.1 #1074
 atom 1 [PRO]158:A.CA/2.1 #1064	atom 2 [LYS]159:A.CA/1.1 #1065
 atom 1 [MET]157:A.CA/2.1 #1056	atom 2 [PRO]158:A.CA/1.1 #1058
 atom 1 [LEU]156:A.CA/2.1 #1048	atom 2 [MET]157:A.CA/1.1 #1050
 atom 1 [MET]155:A.CA/2.1 #1040	atom 2 [LEU]156:A.CA/1.1 #1042
 atom 1 [GLU]154:A.CA/2.1 #1031	atom 2 [MET]155:A.CA/1.1 #1034
 atom 1 [LYS]153:A.CA/2.1 #1022	atom 2 [GLU]154:A.CA/1.1 #1025
 atom 1 [GLY]152:A.CA/2.1 #1018	atom 2 [LYS]153:A.CA/1.1 #1016
 atom 1 [VAL]151:A.CA/2.1 #1011	atom 2 [GLY]152:A.CA/1.1 #1012
 atom 1 [PRO]150:A.CA/2.1 #1004	atom 2 [VAL]151:A.CA/1.1 #1005
 atom 1 [GLY]149:A.CA/2.1 #1000	atom 2 [PRO]150:A.CA/1.1 #998
 atom 1 [THR]148:A.CA/2.1 #993	atom 2 [GLY]149:A.CA/1.1 #994
 atom 1 [ILE]147:A.CA/2.1 #985	atom 2 [THR]148:A.CA/1.1 #987
 atom 1 [GLN]146:A.CA/2.1 #976	atom 2 [ILE]147:A.CA/1.1 #979
 atom 1 [VAL]145:A.CA/2.1 #969	atom 2 [GLN]146:A.CA/1.1 #970
 atom 1 [ASN]144:A.CA/2.1 #961	atom 2 [VAL]145:A.CA/1.1 #963
 atom 1 [ASP]143:A.CA/2.1 #953	atom 2 [ASN]144:A.CA/1.1 #955
 atom 1 [GLY]142:A.CA/2.1 #949	atom 2 [ASP]143:A.CA/1.1 #947
 atom 1 [PRO]141:A.CA/2.1 #942	atom 2 [GLY]142:A.CA/1.1 #943
 atom 1 [GLN]140:A.CA/2.1 #933	atom 2 [PRO]141:A.CA/1.1 #936
 atom 1 [LEU]139:A.CA/2.1 #925	atom 2 [GLN]140:A.CA/1.1 #927
 atom 1 [ASP]138:A.CA/2.1 #917	atom 2 [LEU]139:A.CA/1.1 #919
 atom 1 [CYS]137:A.CA/2.1 #911	atom 2 [ASP]138:A.CA/1.1 #911
 atom 1 [LEU]136:A.CA/2.1 #903	atom 2 [CYS]137:A.CA/1.1 #905
 atom 1 [PHE]135:A.CA/2.1 #892	atom 2 [LEU]136:A.CA/1.1 #897
 atom 1 [ASN]134:A.CA/2.1 #884	atom 2 [PHE]135:A.CA/1.1 #886
 atom 1 [SER]133:A.CA/2.1 #878	atom 2 [ASN]134:A.CA/1.1 #878
 atom 1 [CYS]132:A.CA/2.1 #872	atom 2 [SER]133:A.CA/1.1 #872
 atom 1 [VAL]131:A.CA/2.1 #865	atom 2 [CYS]132:A.CA/1.1 #866
 atom 1 [GLY]130:A.CA/2.1 #861	atom 2 [VAL]131:A.CA/1.1 #859
 atom 1 [LYS]129:A.CA/2.1 #852	atom 2 [GLY]130:A.CA/1.1 #855
 atom 1 [VAL]128:A.CA/2.1 #845	atom 2 [LYS]129:A.CA/1.1 #846
 atom 1 [ILE]127:A.CA/2.1 #837	atom 2 [VAL]128:A.CA/1.1 #839
 atom 1 [GLU]126:A.CA/2.1 #828	atom 2 [ILE]127:A.CA/1.1 #831
 atom 1 [GLY]125:A.CA/2.1 #824	atom 2 [GLU]126:A.CA/1.1 #822
 atom 1 [ALA]124:A.CA/2.1 #819	atom 2 [GLY]125:A.CA/1.1 #818
 atom 1 [ASP]123:A.CA/2.1 #811	atom 2 [ALA]124:A.CA/1.1 #813
 atom 1 [ASN]122:A.CA/2.1 #803	atom 2 [ASP]123:A.CA/1.1 #805
 atom 1 [THR]121:A.CA/2.1 #796	atom 2 [ASN]122:A.CA/1.1 #797
 atom 1 [TYR]120:A.CA/2.1 #784	atom 2 [THR]121:A.CA/1.1 #790
 atom 1 [ILE]119:A.CA/2.1 #776	atom 2 [TYR]120:A.CA/1.1 #778
 atom 1 [LEU]118:A.CA/2.1 #768	atom 2 [ILE]119:A.CA/1.1 #770
 atom 1 [ARG]117:A.CA/2.1 #757	atom 2 [LEU]118:A.CA/1.1 #762
 atom 1 [LYS]116:A.CA/2.1 #748	atom 2 [ARG]117:A.CA/1.1 #751
 atom 1 [VAL]115:A.CA/2.1 #741	atom 2 [LYS]116:A.CA/1.1 #742
 atom 1 [CYS]114:A.CA/2.1 #735	atom 2 [VAL]115:A.CA/1.1 #735
 atom 1 [LEU]113:A.CA/2.1 #727	atom 2 [CYS]114:A.CA/1.1 #729
 atom 1 [SER]112:A.CA/2.1 #721	atom 2 [LEU]113:A.CA/1.1 #721
 atom 1 [VAL]111:A.CA/2.1 #714	atom 2 [SER]112:A.CA/1.1 #715
 atom 1 [THR]110:A.CA/2.1 #707	atom 2 [VAL]111:A.CA/1.1 #708
 atom 1 [LYS]109:A.CA/2.1 #698	atom 2 [THR]110:A.CA/1.1 #701
 atom 1 [SER]108:A.CA/2.1 #692	atom 2 [LYS]109:A.CA/1.1 #692
 atom 1 [ASP]107:A.CA/2.1 #684	atom 2 [SER]108:A.CA/1.1 #686
 atom 1 [GLY]106:A.CA/2.1 #680	atom 2 [ASP]107:A.CA/1.1 #678
 atom 1 [PHE]105:A.CA/2.1 #669	atom 2 [GLY]106:A.CA/1.1 #674
 atom 1 [ASP]104:A.CA/2.1 #661	atom 2 [PHE]105:A.CA/1.1 #663
 atom 1 [GLY]103:A.CA/2.1 #657	atom 2 [ASP]104:A.CA/1.1 #655
 atom 1 [ILE]102:A.CA/2.1 #649	atom 2 [GLY]103:A.CA/1.1 #651
 atom 1 [ALA]101:A.CA/2.1 #644	atom 2 [ILE]102:A.CA/1.1 #643
 atom 1 [SER]100:A.CA/2.1 #638	atom 2 [ALA]101:A.CA/1.1 #638
 atom 1 [SER]99:A.CA/2.1 #632	atom 2 [SER]100:A.CA/1.1 #632
 atom 1 [ALA]98:A.CA/2.1 #627	atom 2 [SER]99:A.CA/1.1 #626
 atom 1 [ILE]97:A.CA/2.1 #619	atom 2 [ALA]98:A.CA/1.1 #621
 atom 1 [SER]96:A.CA/2.1 #613	atom 2 [ILE]97:A.CA/1.1 #613
 atom 1 [TYR]95:A.CA/2.1 #601	atom 2 [SER]96:A.CA/1.1 #607
 atom 1 [LEU]94:A.CA/2.1 #593	atom 2 [TYR]95:A.CA/1.1 #595
 atom 1 [ARG]93:A.CA/2.1 #582	atom 2 [LEU]94:A.CA/1.1 #587
 atom 1 [VAL]92:A.CA/2.1 #575	atom 2 [ARG]93:A.CA/1.1 #576
 atom 1 [LYS]91:A.CA/2.1 #566	atom 2 [VAL]92:A.CA/1.1 #569
 atom 1 [HIS]90:A.CA/2.1 #556	atom 2 [LYS]91:A.CA/1.1 #560
 atom 1 [PRO]89:A.CA/2.1 #549	atom 2 [HIS]90:A.CA/1.1 #550
 atom 1 [LYS]88:A.CA/2.1 #540	atom 2 [PRO]89:A.CA/1.1 #543
 atom 1 [GLY]87:A.CA/2.1 #536	atom 2 [LYS]88:A.CA/1.1 #534
 atom 1 [ASN]86:A.CA/2.1 #528	atom 2 [GLY]87:A.CA/1.1 #530
 atom 1 [LYS]85:A.CA/2.1 #519	atom 2 [ASN]86:A.CA/1.1 #522
 atom 1 [ASP]84:A.CA/2.1 #511	atom 2 [LYS]85:A.CA/1.1 #513
 atom 1 [VAL]83:A.CA/2.1 #504	atom 2 [ASP]84:A.CA/1.1 #505
 atom 1 [GLY]82:A.CA/2.1 #500	atom 2 [VAL]83:A.CA/1.1 #498
 atom 1 [ASP]81:A.CA/2.1 #492	atom 2 [GLY]82:A.CA/1.1 #494
 atom 1 [ALA]80:A.CA/2.1 #487	atom 2 [ASP]81:A.CA/1.1 #486
 atom 1 [ILE]79:A.CA/2.1 #479	atom 2 [ALA]80:A.CA/1.1 #481
 atom 1 [VAL]78:A.CA/2.1 #472	atom 2 [ILE]79:A.CA/1.1 #473
 atom 1 [GLY]77:A.CA/2.1 #468	atom 2 [VAL]78:A.CA/1.1 #466
 atom 1 [ILE]76:A.CA/2.1 #460	atom 2 [GLY]77:A.CA/1.1 #462
 atom 1 [SER]75:A.CA/2.1 #454	atom 2 [ILE]76:A.CA/1.1 #454
 atom 1 [GLN]74:A.CA/2.1 #445	atom 2 [SER]75:A.CA/1.1 #448
 atom 1 [GLY]73:A.CA/2.1 #441	atom 2 [GLN]74:A.CA/1.1 #439
 atom 1 [GLU]72:A.CA/2.1 #432	atom 2 [GLY]73:A.CA/1.1 #435
 atom 1 [ARG]71:A.CA/2.1 #421	atom 2 [GLU]72:A.CA/1.1 #426
 atom 1 [TYR]70:A.CA/2.1 #409	atom 2 [ARG]71:A.CA/1.1 #415
 atom 1 [PRO]69:A.CA/2.1 #402	atom 2 [TYR]70:A.CA/1.1 #403
 atom 1 [ILE]68:A.CA/2.1 #394	atom 2 [PRO]69:A.CA/1.1 #396
 atom 1 [LYS]67:A.CA/2.1 #385	atom 2 [ILE]68:A.CA/1.1 #388
 atom 1 [GLY]66:A.CA/2.1 #381	atom 2 [LYS]67:A.CA/1.1 #379
 atom 1 [GLU]65:A.CA/2.1 #372	atom 2 [GLY]66:A.CA/1.1 #375
 atom 1 [THR]64:A.CA/2.1 #365	atom 2 [GLU]65:A.CA/1.1 #366
 atom 1 [SER]63:A.CA/2.1 #359	atom 2 [THR]64:A.CA/1.1 #359
 atom 1 [PHE]62:A.CA/2.1 #348	atom 2 [SER]63:A.CA/1.1 #353
 atom 1 [VAL]61:A.CA/2.1 #341	atom 2 [PHE]62:A.CA/1.1 #342
 atom 1 [MET]60:A.CA/2.1 #333	atom 2 [VAL]61:A.CA/1.1 #335
 atom 1 [HIS]59:A.CA/2.1 #323	atom 2 [MET]60:A.CA/1.1 #327
 atom 1 [TRP]58:A.CA/2.1 #309	atom 2 [HIS]59:A.CA/1.1 #317
 atom 1 [THR]57:A.CA/2.1 #302	atom 2 [TRP]58:A.CA/1.1 #303
 atom 1 [GLU]56:A.CA/2.1 #293	atom 2 [THR]57:A.CA/1.1 #296
 atom 1 [GLY]55:A.CA/2.1 #289	atom 2 [GLU]56:A.CA/1.1 #287
 atom 1 [PRO]54:A.CA/2.1 #282	atom 2 [GLY]55:A.CA/1.1 #283
 atom 1 [ALA]53:A.CA/2.1 #277	atom 2 [PRO]54:A.CA/1.1 #276
 atom 1 [ASP]52:A.CA/2.1 #269	atom 2 [ALA]53:A.CA/1.1 #271
 atom 1 [ASP]51:A.CA/2.1 #261	atom 2 [ASP]52:A.CA/1.1 #263
 atom 1 [GLY]50:A.CA/2.1 #257	atom 2 [ASP]51:A.CA/1.1 #255
 atom 1 [THR]49:A.CA/2.1 #250	atom 2 [GLY]50:A.CA/1.1 #251
 atom 1 [ILE]48:A.CA/2.1 #242	atom 2 [THR]49:A.CA/1.1 #244
 atom 1 [LYS]47:A.CA/2.1 #233	atom 2 [ILE]48:A.CA/1.1 #236
 atom 1 [THR]46:A.CA/2.1 #226	atom 2 [LYS]47:A.CA/1.1 #227
 atom 1 [ASN]45:A.CA/2.1 #218	atom 2 [THR]46:A.CA/1.1 #220
 atom 1 [LEU]44:A.CA/2.1 #210	atom 2 [ASN]45:A.CA/1.1 #212
 atom 1 [LEU]43:A.CA/2.1 #202	atom 2 [LEU]44:A.CA/1.1 #204
 atom 1 [CYS]42:A.CA/2.1 #196	atom 2 [LEU]43:A.CA/1.1 #196
 atom 1 [ARG]41:A.CA/2.1 #185	atom 2 [CYS]42:A.CA/1.1 #190
 atom 1 [GLY]40:A.CA/2.1 #181	atom 2 [ARG]41:A.CA/1.1 #179
 atom 1 [VAL]39:A.CA/2.1 #174	atom 2 [GLY]40:A.CA/1.1 #175
 atom 1 [TYR]38:A.CA/2.1 #162	atom 2 [VAL]39:A.CA/1.1 #168
 atom 1 [PRO]37:A.CA/2.1 #155	atom 2 [TYR]38:A.CA/1.1 #156
 atom 1 [GLU]36:A.CA/2.1 #146	atom 2 [PRO]37:A.CA/1.1 #149
 atom 1 [LYS]35:A.CA/2.1 #137	atom 2 [GLU]36:A.CA/1.1 #140
 atom 1 [PRO]34:A.CA/2.1 #130	atom 2 [LYS]35:A.CA/1.1 #131
 atom 1 [LYS]33:A.CA/2.1 #121	atom 2 [PRO]34:A.CA/1.1 #124
 atom 1 [TYR]32:A.CA/2.1 #109	atom 2 [LYS]33:A.CA/1.1 #115
 atom 1 [LEU]31:A.CA/2.1 #101	atom 2 [TYR]32:A.CA/1.1 #103
 atom 1 [ASN]30:A.CA/2.1 #93	atom 2 [LEU]31:A.CA/1.1 #95
 atom 1 [THR]29:A.CA/2.1 #86	atom 2 [ASN]30:A.CA/1.1 #87
 atom 1 [VAL]28:A.CA/2.1 #79	atom 2 [THR]29:A.CA/1.1 #80
 atom 1 [VAL]27:A.CA/2.1 #72	atom 2 [VAL]28:A.CA/1.1 #73
 atom 1 [GLY]26:A.CA/2.1 #68	atom 2 [VAL]27:A.CA/1.1 #66
 atom 1 [GLU]25:A.CA/2.1 #59	atom 2 [GLY]26:A.CA/1.1 #62
 atom 1 [GLU]24:A.CA/2.1 #50	atom 2 [GLU]25:A.CA/1.1 #53
 atom 1 [GLN]23:A.CA/2.1 #41	atom 2 [GLU]24:A.CA/1.1 #44
 atom 1 [LYS]22:A.CA/2.1 #32	atom 2 [GLN]23:A.CA/1.1 #35
 atom 1 [LYS]21:A.CA/2.1 #23	atom 2 [LYS]22:A.CA/1.1 #26
 atom 1 [SER]20:A.CA/2.1 #17	atom 2 [LYS]21:A.CA/1.1 #17
 atom 1 [CYS]19:A.CA/2.1 #11	atom 2 [SER]20:A.CA/1.1 #11
 atom 1 [LYS]18:A.CA/2.1 #2	atom 2 [GLU]19:A.CA/1.1 #2
RMSD 31.29 --> 3.81 Angstroms
spinFPS is set too fast (30.0) -- can't keep up!
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 115.2/175.1
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: 6 ms
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 84.8/175.1
processors available: 4
useCommandThread: false
appConsole Linux

FileManager.getAtomSetCollectionFromFile(/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-JOB1/examples/1gaq.txt)
FileManager opening file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-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-GDB665-JOB1/examples/1gaq.txt): 67 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
Time for creating model: 5 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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 83.0/175.1
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: 5 ms
INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (29ms)
INFO - Discovering jws1 services
Could not load jar:file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-JOB1/build/clover/clover-classes/!/.build_properties
CMD [-noquestionnaire] executed successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Reloading services for jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
INFO - Reloading services for jalview.ws2.client.slivka.SlivkaWSDiscoverer
INFO - Fetching list of services from https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/
INFO - Fetching list of services from https://www.compbio.dundee.ac.uk/slivka/
Invalid or corrupt date in property 'JALVIEW_NEWS_RSS_LASTMODIFIED' : value was 'Apr 23, 2014 2:53:26 PM'
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$new$1(AlignFrame.java:986) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.fireServicesChanged(AbstractWebServiceDiscoverer.java:199) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.lambda$startDiscoverer$1(AbstractWebServiceDiscoverer.java:178) ~[clover-classes/:?]
	at java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:930) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:907) [?:?]
	at java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506) [?:?]
	at java.util.concurrent.CompletableFuture.postFire(CompletableFuture.java:610) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:910) [?:?]
	at java.util.concurrent.CompletableFuture$Completion.exec(CompletableFuture.java:479) [?:?]
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) [?:?]
	at java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$new$1(AlignFrame.java:986) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.fireServicesChanged(AbstractWebServiceDiscoverer.java:199) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.lambda$startDiscoverer$1(AbstractWebServiceDiscoverer.java:178) ~[clover-classes/:?]
	at java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:930) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:907) [?:?]
	at java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506) [?:?]
	at java.util.concurrent.CompletableFuture.postFire(CompletableFuture.java:610) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:910) [?:?]
	at java.util.concurrent.CompletableFuture$Completion.exec(CompletableFuture.java:479) [?:?]
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) [?:?]
	at java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$new$1(AlignFrame.java:986) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.fireServicesChanged(AbstractWebServiceDiscoverer.java:199) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.lambda$startDiscoverer$1(AbstractWebServiceDiscoverer.java:178) ~[clover-classes/:?]
	at java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:930) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:907) [?:?]
	at java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506) [?:?]
	at java.util.concurrent.CompletableFuture.postFire(CompletableFuture.java:610) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:910) [?:?]
	at java.util.concurrent.CompletableFuture$Completion.exec(CompletableFuture.java:479) [?:?]
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) [?:?]
	at java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
INFO - Reloading services for jalview.ws2.client.jpred4.JPred4WSDiscoverer
INFO - Fetching list of services from https://www.compbio.dundee.ac.uk/jpred4/
Feb 28, 2025 2:54:31 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.
Feb 28, 2025 2:54:31 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.
Feb 28, 2025 2:54:31 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.
Feb 28, 2025 2:54:31 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.
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Allocating Jmol Viewer: 
Feb 28, 2025 2:54:32 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
Feb 28, 2025 2:54:32 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:32 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:32 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:33 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:34 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:34 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Allocating Jmol Viewer: