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: