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Failed to read incomplete mmCIF just like NRG isssue 157 #3

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Read mmCIF of 1r4e

================================================================================
======================
| Wattos: Programs for Structural Biology & NMR        version 20101011 (r141) 
JFD,GWV,ELU 1999-2010 |
================================================================================
======================
User: jd on: Stella.local (MacOSX/x86_64/2cores/1.6.0_22) at: (37359) Fri Nov 
12 14:17:28 2010

DEBUG: Wattos in interactive mode
DEBUG: Wattos in debugging mode
DEBUG: Executing: InitAll
Doing InitAll
DEBUG: Executing: SetProp
Doing SetProp with arguments: [interactiveSession, false]
Doing SetProp with arguments: [verbosity, 9]
Doing SetProp with arguments: [writeSessionOnExit, false]
Doing SetProp with arguments: [stopOnError, true]
DEBUG: getInputChar read: false
Doing ReadEntryMMCIF with arguments: 
[file:/Users/jd/wattosTestingPlatform/pdb/data/structures/divided/mmCIF/r4/1r4e.
cif.gz, false]
WARNING: Failed to find any atom in first model for entity: 3
WARNING: This was found in for instance entry 1j6t for the PO3 group and was 
reported in NRG issue 157
DEBUG: atomSetNotInFirstModel grew to size: 1
DEBUG: atomSetNotInFirstModel grew to size: 2
...
DEBUG: atomSetNotInFirstModel grew to size: 892
DEBUG: atomSetNotInFirstModel grew to size: 893
DEBUG: atomSetBad size: 893
DEBUG: atomsSetOk size: 8930
DEBUG: atomsSetOk size (after non-Oks zapped): 8037
DEBUG: Disabled syncing over models.
DEBUG: This might lead to inconsistencies in Wattos internal data model.
DEBUG: Needs testing for sure.
DEBUG: The code will definitely not work when reading in restraints on top of 
partily missing atoms.
ERROR: Error invoking reflected command: ReadEntryMMCIF
ERROR: 
java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at Wattos.CloneWars.CommandHub.invoke(CommandHub.java:120)
    at Wattos.CloneWars.UserInterface.doNonGuiMain(UserInterface.java:485)
    at Wattos.CloneWars.UserInterface.main(UserInterface.java:644)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 2147483646
    at Wattos.Soup.Entry.postProcessAfterReading(Entry.java:301)
    at Wattos.Soup.Entry.readmmCIFFormattedFile(Entry.java:620)
    at Wattos.CloneWars.CommandHub.ReadEntryMMCIF(CommandHub.java:617)
    ... 7 more

ERROR: Found throwable error above
WARNING: Command could not be executed: ReadEntryMmCIF
WARNING: Parameter set for stopping on any error: stopOnError

Wattos started at: November 12, 2010 2:17:28 PM CET
Wattos stopped at: November 12, 2010 2:17:30 PM CET
Wattos took (#ms): 2153

Original issue reported on code.google.com by jurge...@gmail.com on 12 Nov 2010 at 1:44

GoogleCodeExporter commented 8 years ago 
Strange, the atoms in the model 5 are are listed as model 0.

HETATM 3571 H H7A    . DDI C 3 .  ? -9.360  -2.232  -0.360  1.00 0.00 ? ? ? ? ? 
? 15 DDI A H7A    4
HETATM 3572 H H7B    . DDI C 3 .  ? -8.729  -2.642  1.250   1.00 0.00 ? ? ? ? ? 
? 15 DDI A H7B    4
ATOM   3573 O "O5'"  . DC  A 1 1  ? 9.625   -9.517  -25.802 1.00 0.00 ? ? ? ? ? 
? 1  DC  A "O5'"  0
ATOM   3574 C "C5'"  . DC  A 1 1  ? 9.621   -9.280  -24.393 1.00 0.00 ? ? ? ? ? 
? 1  DC  A "C5'"  0

So asking PDB for inserting model number for this entry just like the 12 models 
of issue 2.

Original comment by jurge...@gmail.com on 12 Nov 2010 at 2:07

GoogleCodeExporter commented 8 years ago 
RCSB PDB is updating it today for 1r4e.

Original comment by jurge...@gmail.com on 17 Nov 2010 at 10:24