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  1. Jalview
  2. JAL-2135

Cannot view secondary structure annotation for model produced by Phyre2



    • Urgency:


      The attached PDB file was generated by Phyre2 - importing it to Jalview 2.9.0b2 with DSSP/TempFactor annotation preferences enabled results in an alignment containing one sequence, a secondary structure annotation row containing a series of helices and a temperature factor annotation track with no data (all 0.0).

      Loading the same file to the develop version results in only the TempFactor annotation, and an exception:
      Jalview Version: Development Branch Build
      Jalview Installation: webstart git-commit:f7d70c3 [develop]
      Build Date: 29 June 2016
      Java version: 1.8.0_91
      x86_64 Mac OS X 10.10.5
      Operating headless display=null nographicsallowed=true
      (C) 2012 Jmol Development
      Jmol Version: 14.2.14_2015.06.01 2015-06-01 19:39
      java.vendor: Java: Oracle Corporation
      java.version: Java 1.8.0_91
      os.name: Mac OS X
      Access: ALL
      memory: 67.2/90.2
      processors available: 4
      useCommandThread: false
      The Resolver thinks Pdb
      reading 1072 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
      1072 atoms created
      ModelSet: autobonding; use autobond=false to not generate bonds automatically
      Jmol 14.2.14_2015.06.01 2015-06-01 19:39 DSSP analysis for model 1.1 - null

      W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

      We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
      and we thank the CMBI for maintaining it to the extent that it was easy to
      re-engineer for our purposes. At this point in time, we make no guarantee
      that this code gives precisely the same analysis as the code available via license
      from CMBI at http://swift.cmbi.ru.nl/gv/dssp

      All bioshapes have been deleted and must be regenerated.

      Exceptions from Jmol when processing data in pdb file
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at jalview.io.StructureFile.processWithJmolParser(StructureFile.java:279)
      at jalview.io.StructureFile.addSecondaryStructure(StructureFile.java:248)
      at MCview.PDBfile.parse(PDBfile.java:187)
      at jalview.io.AlignFile.doParse(AlignFile.java:170)
      at MCview.PDBfile.<init>(PDBfile.java:54)
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:295)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
      at jalview.io.FileLoader.run(FileLoader.java:327)
      at java.lang.Thread.run(Thread.java:745)
      Caused by: java.lang.NullPointerException
      at MCview.PDBChain.<init>(PDBChain.java:85)
      at jalview.ext.jmol.JmolParser.transformJmolModelToJalview(JmolParser.java:162)
      at jalview.ext.jmol.JmolParser.parse(JmolParser.java:109)
      at jalview.io.AlignFile.doParse(AlignFile.java:170)
      at jalview.io.AlignFile.<init>(AlignFile.java:152)
      at jalview.io.AlignFile.<init>(AlignFile.java:134)
      at jalview.io.StructureFile.<init>(StructureFile.java:57)
      at jalview.ext.jmol.JmolParser.<init>(JmolParser.java:72)
      ... 13 more




            tcnofoegbu Tochukwu Charles N Ofoegbu
            jprocter James Procter
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