Class jalview.ext.jmol.JmolViewerTest
|
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: