Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.10.0
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Component/s: Structures
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Labels:
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Urgency:Urgent
Description
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
java.lang.reflect.InvocationTargetException
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
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
java.lang.reflect.InvocationTargetException
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