Format converter crash

[GoogleCodeExporter]

It seems to be associated with the non-standard residues, but that shouldn't be 
a problem:

 maxNum = self.numModelsToRead, autoCreateChemComps = True)

I've included the merge log, but here is the traceback anyway:

Doing 2rqo...
Traceback (most recent call last):
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 753, in <module>
    LinkNmrStarData(sys.argv)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 88, in __init__
    self.catchError(raiseError,timeFlag)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 81, in __init__
    self.runSpecific()
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 169, in runSpecific
    self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead, autoCreateChemComps = True)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/NmrStar.py", line 46, in readNmrStarFile
    **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 951, in readProject
    self.getFullProject(fileName,**keywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 566, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1071, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 6035, in checkMolecules
    self.makeChemComp()
  File "/raid/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 14169, in makeChemComp
    chemComp = self.project.newNonStdChemComp(**createDict)     
  File "/raid/docr/workspace/ccpn/python/memops/api/Implementation.py", line 16375, in newNonStdChemComp
    return NonStdChemComp(self, **attrlinks)
  File "/raid/docr/workspace/ccpn/python/ccp/api/molecule/ChemComp.py", line 25608, in __init__
    func(self, value)
  File "/raid/docr/workspace/ccpn/python/ccp/api/molecule/ChemComp.py", line 9847, in setMolType
    + ": %s" % (value,)
memops.general.Implementation.ApiError: 
ccp.molecule.ChemComp.NonStdChemComp.setMolType:
       ccp.molecule.ChemComp.MolType input is not in enumeration ['protein', 'DNA', 'RNA', 'carbohydrate', 'other']: polypeptide(D)

Original issue reported on code.google.com by schulte....@gmail.com on 16 Sep 2010 at 3:09

Attachments:

• 2rqo_merge.log

[GoogleCodeExporter]

Damn non-standard residues. Wim, can you take a look?
I also get a warning when using Analysis to read the --PDB-- file.
Then I get a stack from Analysis but it's unrelated to the above.

##############################################
# FormatConverter: executing readCoordinates #
##############################################

  Warning: adding HET residue MHE in position 0 (index 0) of chain A!
  Warning: adding HET residue I2M in position 2 (index 2) of chain A!
  Warning: adding HET residue TBG in position 4 (index 4) of chain A!
  Warning: adding HET residue TDD in position 5 (index 5) of chain A!
  Warning: adding HET residue TBG in position 6 (index 6) of chain A!
  Warning: adding HET residue DAL in position 7 (index 7) of chain A!
  Warning: adding HET residue TBG in position 8 (index 8) of chain A!
  Warning: adding HET residue TDD in position 9 (index 9) of chain A!
  Warning: adding HET residue TDD in position 13 (index 13) of chain A!
  Warning: adding HET residue MND in position 15 (index 15) of chain A!
  Warning: adding HET residue HVA in position 16 (index 16) of chain A!
  Warning: adding HET residue TBG in position 20 (index 20) of chain A!
  Warning: adding HET residue MND in position 21 (index 21) of chain A!
  Warning: adding HET residue LMQ in position 22 (index 22) of chain A!
  Warning: adding HET residue DHV in position 23 (index 23) of chain A!
  Warning: adding HET residue MND in position 27 (index 27) of chain A!
  Warning: adding HET residue HTN in position 29 (index 29) of chain A!
  Warning: adding HET residue TBG in position 30 (index 30) of chain A!
  Warning: adding HET residue DHV in position 31 (index 31) of chain A!
  Warning: adding HET residue MND in position 33 (index 33) of chain A!
  Warning: adding HET residue MND in position 35 (index 35) of chain A!
  Warning: adding HET residue HTN in position 37 (index 37) of chain A!
  Warning: adding HET residue MND in position 39 (index 39) of chain A!
  Warning: adding HET residue DSN in position 41 (index 41) of chain A!
  Warning: adding HET residue DSG in position 43 (index 43) of chain A!
  Warning: adding HET residue M2S in position 44 (index 44) of chain A!
  Warning: adding HET residue DSG in position 45 (index 45) of chain A!
  Warning: adding HET residue 2TL in position 47 (index 47) of chain A!
  Set covalent bond from 1.N - 0.C1
  Set covalent bond from 0.C1 - 1.N
  Set covalent bond from 1.C - 2.N
  Set covalent bond from 2.N - 1.C
  Set covalent bond from 3.N - 2.C
  Set covalent bond from 2.C - 3.N
  Set covalent bond from 3.C - 4.N
  Set covalent bond from 4.N - 3.C
  Set covalent bond from 4.C - 5.N
  Set covalent bond from 5.N - 4.C
  Set covalent bond from 5.C - 6.N
  Set covalent bond from 6.N - 5.C
  Set covalent bond from 6.C - 7.N
  Set covalent bond from 7.N - 6.C
  Set covalent bond from 7.C - 8.N
  Set covalent bond from 8.N - 7.C
  Set covalent bond from 8.C - 9.N
  Set covalent bond from 9.N - 8.C
  Set covalent bond from 9.C - 10.N
  Set covalent bond from 10.N - 9.C
  Set covalent bond from 12.C - 13.N
  Set covalent bond from 13.N - 12.C
  Set covalent bond from 13.C - 14.N
  Set covalent bond from 14.N - 13.C
  Set covalent bond from 14.C - 15.N
  Set covalent bond from 15.N - 14.C
  Set covalent bond from 15.C - 16.N
  Set covalent bond from 16.N - 15.C
  Set covalent bond from 16.C - 17.N
  Set covalent bond from 17.N - 16.C
  Set covalent bond from 19.C - 20.N
  Set covalent bond from 20.N - 19.C
  Set covalent bond from 20.C - 21.N
  Set covalent bond from 21.N - 20.C
  Set covalent bond from 21.C - 22.N
  Set covalent bond from 22.N - 21.C
  Set covalent bond from 22.C - 23.N
  Set covalent bond from 23.N - 22.C
  Set covalent bond from 23.C - 24.N
  Set covalent bond from 24.N - 23.C
  Set covalent bond from 26.C - 27.N
  Set covalent bond from 27.N - 26.C
  Set covalent bond from 27.C - 28.N
  Set covalent bond from 28.N - 27.C
  Set covalent bond from 28.C - 29.N
  Set covalent bond from 29.N - 28.C
  Set covalent bond from 29.C - 30.N
  Set covalent bond from 30.N - 29.C
  Set covalent bond from 30.C - 31.N
  Set covalent bond from 31.N - 30.C
  Set covalent bond from 31.C - 32.N
  Set covalent bond from 32.N - 31.C
  Set covalent bond from 32.C - 33.N
  Set covalent bond from 33.N - 32.C
  Set covalent bond from 33.C - 34.N
  Set covalent bond from 34.N - 33.C
  Set covalent bond from 34.C - 35.N
  Set covalent bond from 35.N - 34.C
  Set covalent bond from 35.C - 36.N
  Set covalent bond from 36.N - 35.C
  Set covalent bond from 36.C - 37.N
  Set covalent bond from 37.N - 36.C
  Set covalent bond from 37.C - 38.N
  Set covalent bond from 38.N - 37.C
  Set covalent bond from 38.C - 39.N
  Set covalent bond from 39.N - 38.C
  Set covalent bond from 39.C - 40.N
  Set covalent bond from 40.N - 39.C
  Set covalent bond from 40.C - 41.N
  Set covalent bond from 41.N - 40.C
  Set covalent bond from 41.C - 42.N
  Set covalent bond from 42.N - 41.C
  Set covalent bond from 42.C - 43.N
  Set covalent bond from 43.N - 42.C
  Set covalent bond from 43.C - 44.N
  Set covalent bond from 44.N - 43.C
  Set covalent bond from 44.C - 45.N
  Set covalent bond from 45.N - 44.C
  Set covalent bond from 45.C - 46.N
  Set covalent bond from 46.N - 45.C
  Set covalent bond from 46.C - 47.N
  Set covalent bond from 47.N - 46.C
  Set covalent bond from 47.C - 48.N
  Set covalent bond from 48.N - 47.C
Exception in Tkinter callback
Traceback (most recent call last):
  File "/Users/jd/workspace35/ccpnmr/python2.5/lib/python2.5/lib-tk/Tkinter.py", line 1403, in __call__
    return self.func(*args)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 979, in ok
    if (not self.apply()):
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 992, in apply
    returnValue = self.importExportFile(self.component) # If none, will do all components
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 799, in importExportFile
    returnValue = rwFunc(*addArgs,**addKeywds)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 1277, in readCoordinates
    self.getCoordinates()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 4395, in getCoordinatesGeneric
    self.readSequence(**readSeqKeywds)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 1071, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 6060, in checkMolecules
    interaction = self.multiDialog.ChemCompSelection(self.guiParent,self.project, chemCompEntries = ['ChemComp'], origCode = code)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/general/MultiDialog.py", line 1846, in ChemCompSelection
    return self.ChemCompSelectionFunction(guiParent,project,*args,**kw)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/MultiDialog.py", line 353, in ChemCompSelectionFunction
    popup = ChemCompSelectionPopup(guiParent, project, **keywds)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ChemCompSelectionPopup.py", line 82, in __init__
    TemporaryBasePopup.__init__(self, parent=parent, title="Project '%s': " % project.name + "ChemComp selection for code '%s'" % origCode, modal=False, transient=False, width = 200)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/gui/BasePopup.py", line 128, in __init__
    self.initial_focus = self.body(frame)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ChemCompSelectionPopup.py", line 86, in body
    self.frame = ChemCompFrame(master,self.project,**self.keywds)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/gui/ChemCompFrame.py", line 188, in __init__
    selected = [self.showLocalText])
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/gui/CheckButtons.py", line 105, in __init__
    selected=selected[n])
IndexError: list index out of range

Original comment by jurge...@gmail.com on 22 Sep 2010 at 6:51

• Changed state: Started

[GoogleCodeExporter]

Another entry, 2rqz,  crashed FC. The merge log was basically the same as the 
one that we posted originally. I'm upgrading the priority on this one because 
we get it fairly regularly.

I thought "autoCreateChemComps = True" was supposed to fix it but 

Original comment by schulte....@gmail.com on 11 Oct 2010 at 5:48

• Added labels: Priority-High, Entry-2rqz
• Removed labels: Priority-Medium

[GoogleCodeExporter]

This was another issue related to the molecular type. I've now put a fix in, 
2rqo goes through though still has problems... anyway update SF rep:

python/ccpnmr/format/converters/NmrStarFormat.py

and it should work

Original comment by wfvran...@gmail.com on 12 Oct 2010 at 8:34

[GoogleCodeExporter]

Chris, can you check the fix?

Original comment by jurge...@gmail.com on 12 Nov 2010 at 4:50

[GoogleCodeExporter]

These are still crashing.

I updated python/ccpnmr/format/converters/NmrStarFormat.py and there was no 
change. Then I updated all of python/ccpnmr/format/converter/, ran 'python 
makePython.py' and tried again. 

Original comment by schulte....@gmail.com on 17 Nov 2010 at 6:03

[GoogleCodeExporter]

Did you get the latest from the update? 
On my machine it still needs an update.

jd:Stella/ccpn/ cvs -z3 -d:ext:jurgenfd@ccpn.cvs.sourceforge.net:/cvsroot/ccpn 
status python/ccpnmr/format/converters/NmrStarFormat.py
===================================================================
File: NmrStarFormat.py  Status: Needs Patch

   Working revision:    1.70.2.74
   Repository revision: 1.70.2.75   /cvsroot/ccpn/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py,v
   Sticky Tag:      stable (branch: 1.70.2)
   Sticky Date:     (none)
   Sticky Options:  (none)

Same crash report?

If so, I can give it a try here now.

Original comment by jurge...@gmail.com on 17 Nov 2010 at 6:47

[GoogleCodeExporter]

Yes I did get the latest update. FC still crashes.

Original comment by schulte....@gmail.com on 17 Nov 2010 at 7:03

[GoogleCodeExporter]

I had to do:
\rm -rf python/ccp/format
because of a lot of messages like:

cvs update: move away `python/ccp/format/sparky/projectIO.py'; it is in the way

Now I'm stuck at having no development setup working with webserver/mysql 
backend. I'm setting it up....

Original comment by jurge...@gmail.com on 17 Nov 2010 at 7:59

[GoogleCodeExporter]

Ok, mysql is up and ready but I need to stop for the day.

Original comment by jurge...@gmail.com on 17 Nov 2010 at 10:19

[GoogleCodeExporter]

I get further now and FC is only crashing in the export phase, see below. That 
does mean Chris that you must not be at the latest version.

Wim, can you help us with a method by which we can make certain that we are 
looking at the latest version of the ccpn and recoord cvs codes. With svn it is 
very easy by svn info top_dir. It always shows a revision number that all the 
files below must have. Cvs works different but perhaps you can suggest some 
equivalent thing?

I have added this reporting to Wattos the same way we had it in Cing as per 
below.

Aleks, can you take a look at the NMR-STAR exporter code crash report?
Wim, can you still take a look at the below?
Chris, can you try to get this far at least? Or did I miss presets for this 
entry?

jd:Stella/~/ echo Quit | wattos
================================================================================
======================
| Wattos: Programs for Structural Biology & NMR spectroscopy      version r143 
JFD,GWV,ELU 1999-2010 |
================================================================================
======================
User: jd on: Stella.local (MacOSX/x86_64/2cores/1.6.0_22) at:  (3626) Fri Nov 
19 20:09:03 2010

Wattos started at: November 19, 2010 8:09:03 PM CET
Wattos stopped at: November 19, 2010 8:09:05 PM CET
Wattos took (#ms): 2559

jd:Stella/~/ cing --noProject
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r877)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: Stella.local (darwin/64bit/2cores/2.6.6)   at:  (3676) Fri 
Nov 19 20:09:38 2010
CING started at : Fri Nov 19 20:09:21 2010
CING stopped at : Fri Nov 19 20:09:38 2010
CING took       : 16.662 s

Model read finished. Duration 3.93094611168
Model validity check skipped
Read pdbe.adatah.localConstants.py version 4.5.7
Read recoord2.pdbe.localConstants.py version 1.2.3
Read recoord2.pdbe.localConstants.py version 1.2.3
Doing 2rqo...
Traceback (most recent call last):
  File "/Users/jd/workspace35/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 753, in <module>
    LinkNmrStarData(sys.argv)
  File "/Users/jd/workspace35/ccpn/python/pdbe/adatah/Generic.py", line 89, in __init__
    self.catchError(raiseError,timeFlag)
  File "/Users/jd/workspace35/ccpn/python/pdbe/adatah/Generic.py", line 82, in __init__
    self.runSpecific()
  File "/Users/jd/workspace35/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 214, in runSpecific
    self.writeNmrStarProject(outNmrStarFile,self.entry)
  File "/Users/jd/workspace35/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 478, in writeNmrStarProject
    nmrStarExport.createFile(outNmrStarFile,excludeSaveFrames=None)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 201, in createFile
    self.loopSaveFrameData(0)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 292, in loopSaveFrameData
    self.setSaveFrameData(self.nmrStarSfDict['name'])
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 407, in setSaveFrameData
    self.loopStarLevelObjects('saveFrame',saveFrameName,ccpnLoopInfo,self.writeStarSfDict,self.nmrStarSfDict)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 697, in loopStarLevelObjects
    if not self.setTableData(tableName,saveFrame = starElement):
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 442, in setTableData
    self.loopStarLevelObjects('table',tableName,ccpnLoopInfo,self.writeStarTableDict,self.nmrStarTableDict,starElement = table)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 661, in loopStarLevelObjects
    self.setStarTags(starElement,starElementName,tagNames,writeTags,conditionalTags,presetValues,ccpnLoopInfo,parentCcpnLoopInfo,writeStarElementDict,nmrStarElementDict)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1087, in setStarTags
    value = self.getCcpnMapValue(ccpnTagMapping)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 2181, in getCcpnMapValue
    ccpnMapValue = getFunc(self.getCcpnObject(ccpnVarName) )
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/Ccpn_To_NmrStar.py", line 291, in setSerial
    if not self.customSerials.has_key(name):
AttributeError: Ccpn_To_NmrStar instance has no attribute 'customSerials'

Original comment by jurge...@gmail.com on 19 Nov 2010 at 7:13

[GoogleCodeExporter]

Wim, you perhaps need to help Chris with revamping the CCPN setup at BMRB. It 
seems to be out of whack still.

We still haven't got these 2 entries thru NRG although your code is fine.

Original comment by jurge...@gmail.com on 24 Feb 2011 at 2:38

[GoogleCodeExporter]

This is working now. 2rqo and 2rqz have processed on grunt. The changes should 
show up next week.

Original comment by schulte....@gmail.com on 24 Feb 2011 at 6:40

• Changed state: Fixed

[GoogleCodeExporter]

Can I keep this open until I saw the results. Also helps me to check the 
updates for this at NRG-CING. 
I know I could use the Verified status but we don't allows use that.
I'll check Monday.

Original comment by jurge...@gmail.com on 24 Feb 2011 at 7:24

• Changed state: Started

[GoogleCodeExporter]

That's alright with me.

Original comment by schulte....@gmail.com on 24 Feb 2011 at 7:26

[GoogleCodeExporter]

Nice!

Original comment by jurge...@gmail.com on 3 Mar 2011 at 3:36

• Changed state: Fixed