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Hello, I have a project with 11 mgf files searched with 4 search engines run by SearchGUI. I am not able to load those results in peptide shaker. Below is the Error log I copied out of the Bug Report Window.Do you have any advice how to proceed? Thank you.Thu Nov 10 08:40:53 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95162336.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 49.8/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 95379 and start tag from line 95371 and start tag from line 95267 and start tag from line 95266 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:450)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Fri Nov 11 08:41:18 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95386640.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 47.4/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum29926 scans: 16690 Spectrum31110 scans: 16890 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:856)at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:280)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 716852264java.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum31110 scans: 16890 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs"20160704_12_C_04.mgf_assumptions"_ccs_20160704_12_C_04.mgf_cus_File230304 Spectrum31110 scans: 16890 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:299)at com.compomics.util.experiment.identification.IdentificationDB.addAssumptions(IdentificationDB.java:453)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1302)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1347)at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:700)at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:422)at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:68)at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1473)at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Fri Nov 11 10:21:27 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 94711640.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.1/163.1processors available: 12useCommandThread: falseFri Nov 11 15:40:22 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 99351896.Java version: 1.8.0_102.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47900 scans: 26339 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry Testtest_testtest_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47900 scans: 26339 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:299)at com.compomics.util.experiment.identification.IdentificationDB.addAssumptions(IdentificationDB.java:453)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1302)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1347)at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:700)at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:422)at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:68)at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1473)at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Mon Nov 14 09:50:06 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 163053568.Free memory: 128945600.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol

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DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 51.1/163.1processors available: 12useCommandThread: falsePeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47895 scans: 26334 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry GRAY_MS_GRAY_MS_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47895 scans: 26334 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:856)at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:280)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 1121204296Mon Nov 14 10:23:25 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 99234896.Java version: 1.8.0_102.PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47943 scans: 26386 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry test_test_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47943 scans: 26386 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:299)at com.compomics.util.experiment.identification.IdentificationDB.addProteinMatchParameter(IdentificationDB.java:1256)at com.compomics.util.experiment.identification.Identification.addProteinMatchParameter(Identification.java:654)at eu.isas.peptideshaker.validation.MatchesValidator.fillProteinMap(MatchesValidator.java:1205)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:447)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 840606056Mon Nov 14 10:42:19 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 99894272.Java version: 1.8.0_102.Mon Nov 14 11:54:42 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95303872.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.3/163.1processors available: 12useCommandThread: falsejava.lang.IllegalArgumentException: Object 20160704_03_C_01.mgf_cus_File18780 Spectrum57718 scans: 33903 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_03_C_01.raw] corresponding to entry Test_test_0_id_ccs_"20160704_03_C_01.mgf_assumptions"_ccs_20160704_03_C_01.mgf_cus_File18780 Spectrum57718 scans: 33903 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_03_C_01.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:856)at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:280)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.gui.tablemodels.PsmTableModel.loadDataForRows(PsmTableModel.java:351)at com.compomics.util.gui.tablemodels.SelfUpdatingTableModel$LoadingRunnable.run(SelfUpdatingTableModel.java:486)at java.lang.Thread.run(Unknown Source)Tue Nov 15 13:24:10 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95354632.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle. download jmol. how to use jmol. how to run jmol. how to install jmol. jmol online viewer. jmol download windows 10. jmol for windows. 780 reads; ITI Student Resume Portal.

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ProMolecule ViewersThese are used to view the 3-dimensional structure of a molecule, many are also capable of displaying biological macro,molecules such as proteins.PyMol, VIDA, Chem3D, Chimera, Jmol, JSmol, AstexViewer, CN3D, CylView, DINO, ICM Browser. Molgro Viewer, Qutemol, VMD, Yasara, ICM BrowserChemical SketchersThese are small molecule drawing packages that can be used to create the input for other programs, rendering structures on web pages, and some also provide publication quality output. Traditionally these were heavy duty desktop packages however with the increase in the use of web-based tools there are now a variety of lightweight javascript based sketchers. Many of these new lightweight tools have the advantage in that they can be used on mobile devices like an iPad or smart phone.ChemDraw, Marvin, JME, ChemDoodle, Elemental, JSDraw, PubChem Sketcher, KetcherSMARTSviewer generates a visualisation of a molecular pattern that is given in form of a SMARTS very useful for checking that your search query is what you really want.Chemical Property CalculationsMarvin, Elemental, Stardrop, Vortex, PaDEL (see also Tookits below)3D structure generation, conformersMany drawing packages will generate 1D (SMILES) or 2D (sdf, mol) representations of molecules. However some of the virtual screening tools require 3D structures and often a selection of reasonable conformations.OMEGA, CORINA, ROTATE, CONFLEXDockingSome docking applications will generate a 3D structure and multiple conformations of the proposed ligand, many also include a variety of scoring functions to rank the proposed poses.Autodock, Dock, FlexX, Autodock Vina, Fred, Haddock, Bude, Zdock, GOLD, Glide, FITTED, FlipDock, ADAM, MS-Dock, UCSF Dock, ParDock, FlipDock, PLANTSSimilarity, shape Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.5/163.1processors available: 12useCommandThread: falseWed Nov 16 08:50:29 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95341936.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.3/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3342785 and start tag from line 3342780 and start tag from line 3342712 and start tag from line 3342711 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1862)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:414)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)java.io.EOFException: no more data available - expected end tags to close start tag from line 3825474 and start tag from line 3825473 and start tag from line 3825380 and start tag from line 3825379 and start tag from line 3 and start tag from line 2, parser stopped on END_TAG seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1133)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:347)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.NullPointerExceptionat eu.isas.peptideshaker.parameters.PSPtmScores.changeRepresentativeSite(PSPtmScores.java:227)at eu.isas.peptideshaker.ptm.PtmScorer.peptideInference(PtmScorer.java:1876)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:393)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 463007480

Downloading File /Jmol/Version 14.32/Jmol /Jmol

And that misconduct. The statement follows: of issues as set forth in ST's brief was as 1. Whether "SunTrust Mortgage guidelines" is unambiguous. 2. Whether any ambiguity in "SunTrust guidelines" must be resolved because parol evidence is Mortgage in SunTrust's favor not admissible to resolve a patent ambiguity. 3. Whether any ambiguity in the insurance policy must be resolved against United Guaranty ("UG"), the insurer, under the rule of liberal construction. 4. Whether the district court correctly rejected UG's partial integration doctrine theory. 5. Whether UG waived any right to assert a purported exclusion based on failing to underwrite loans using Desktop Underwriter. 6. Whether UG court's procedure waived its on objections the first regarding material the breach defense by failing to move to re-open evidence or for a new trial or for JMOL. 7. Whether 8. going forward because of its first breach of the policy. Whether policy renewals are void for UG is barred from enforcing consideration when an insurer the policy material no longer lack of has any risk. 9. Whether the district court correctly calculated damages. 10. Whether by the the discovery-related district court was sanction fashioned within its broad discretion. On appeal of the August 2011 Opinion and Order respecting the grant of Counterclaim, summary UG argued judgment that to the ruling on two purported breaches, ST on district Count court IV of "based UG's its both of which were necessary to its conclusion material breach." that United Opening (UG's Guaranty Brief, committed at 46.) a UG first further contended that "the first material breach ruling must be vacated because it depended on the combined effect of the alleged breach of contract and the alleged breach of the duty of good faith and fair dealing." (Id.)(emphasis added). UG also argued: "But even if this Court were to affirm the breach of contract finding,4 the first material breach ruling cannot stand, because (1) the district court erred in concluding that United Guaranty breached the duty of severable, good and faith (3) and fair neither material." (Id. at 46-47.) of dealing, the material ("[W]ith both breaches, only purpose of the the alleged contract breaches is was ST argued in its response brief that UG had breached the policy in two ways, the (2) that both breaches were UG failed to provide coverage - contract") , and that it did not waive its "first material breach defense."5 (ST's

Jmol - Browse /Jmol/Version 16.1/Jmol at SourceForge.net

[S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs_"20160704_12_C_04.mgf_assumptions"ccs_20160704_12_C_04.mgf_cus_File230304 Spectrum29926 scans: 16690 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadAssumptions(IdentificationDB.java:714)at com.compomics.util.experiment.identification.Identification.loadAssumptions(Identification.java:174)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:298)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 531727768java.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum11511 scans: 6471 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs"20160704_12_C_04.mgf_assumptions"_ccs_20160704_12_C_04.mgf_cus_File230304 Spectrum11511 scans: 6471 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadAssumptions(IdentificationDB.java:714)at com.compomics.util.experiment.identification.Identification.loadAssumptions(Identification.java:174)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:298)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 675726576Fri Nov 11 09:00:21 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95229960.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 47.2/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum31110 scans: 16890 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry Gray_HD_Gray_HD_0_id_ccs_"20160704_12_C_04.mgf_assumptions"ccs_20160704_12_C_04.mgf_cus_File230304. download jmol. how to use jmol. how to run jmol. how to install jmol. jmol online viewer. jmol download windows 10. jmol for windows. 780 reads; ITI Student Resume Portal.

Downloading File /Jmol/Version 14.29/Jmol /Jmol