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jakesylvestre / cing

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FC created a CCPN project that fails to read in again. #266

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
 I process in e.g.: http://nmr.cmbi.ru.nl/NRG-CING/prep/C/34/134d/
1. First wattos rewrites the mmCif to NMR-STAR at:
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/34/134d/134d_C_Wattos.str
with log: 134d.log
2. Then FC rewrites that file to dir:
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/34/134d/134d/
which gets packaged to:
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/34/134d/134d.tgz
and copied to:
http://nmr.cmbi.ru.nl/NRG-CING/input/34/134d.tgz
3. Validation then runs in:
http://nmr.cmbi.ru.nl/NRG-CING/data/34/134d/
with logs written to e.g.
http://nmr.cmbi.ru.nl/NRG-CING/data/34/134d/log_validateEntry/134d_2010-11-10_10
-03-47.log

What is the expected output? What do you see instead?
In this last log file the error reads:

================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.9 (r871)        
AW,JFD,GWV 2004-2010 |
================================================================================
======================
User: jd         on: nmr.cmbi.umcn.nl (darwin/32bit/8cores/2.6.5) at: (94210) 
Wed Nov 10 10:03:52 2010
DEBUG: Using:
DEBUG: inputDir:             
file:///Library/WebServer/Documents/NRG-CING/input/34
DEBUG: outputDir:            /Library/WebServer/Documents/NRG-CING/data/34/134d
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          CCPN
DEBUG: modelCount:           None
DEBUG: storeCING2db:         True
Enforcing a redo
copying file: //Library/WebServer/Documents/NRG-CING/input/34/134d.tgz to: 
134d.tgz
==> Importing data from Ccpn project "134d"
Error loading file for:  <ccp.molecule.MolSystem.MolSystem ['134d']>
Reading:  <open file 
'/Volumes/tera4/NRG-CING/data/34/134d/134d/ccp/molecule/MolSystem/134d+134d_user
_2010-11-10-09-52-07-265_00001.xml', mode 'r' at 0x591c8b8>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
CING started at : Wed Nov 10 10:03:48 2010
CING stopped at : Wed Nov 10 10:03:53 2010
CING took       : 4.986 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 348, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 182, in main
    if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 2281, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 317, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 429, in importFromCcpnMolecule
    if not len(ccpnMolSys.structureEnsembles):
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 13467, in getStructureEnsembles
    self.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5069, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5103, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4988, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3933, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['134d', 'A']>

Analysis also fails on it:

jd:Stella/~/Downloads/ analysis 134d
Model read finished. Duration 3.46659207344 
Model validity check skipped
CcpNmr Analysis Version 2.1. Release 3 (Copyright 2003-2009 CCPN)
Distribution created Thu Feb 18 09:41:45 2010

If you use CcpNmr Analysis, please quote the following reference:

Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne 
Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides
and Ernest D. Laue (2005). The CCPN Data Model for NMR Spectroscopy: 
Development of a Software Pipeline. Proteins 59, 687 - 696.

For program documentation the CCPN wiki site is located at:
http://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-software

For help and support visit the mailing list at:
http://www.jiscmail.ac.uk/ccpnmr

For Python API documentation, tutorials and CCPN web applications visit:
http://www.ccpn.ac.uk/

Some files unfindable - has project moved?.
Re-trying, skipping cached TopObjects:
Error loading file for:  <ccp.molecule.MolSystem.MolSystem ['134d']>
Reading:  <open file 
'/Users/jd/Downloads/134d/ccp/molecule/MolSystem/134d+134d_user_2010-11-10-09-52
-07-265_00001.xml', mode 'r' at 0x66d45c0>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
Traceback (most recent call last):
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 231, in <module>
    main(projectDir, max_size, glDirect)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 118, in main
    top.initProject(project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisPopup.py", line 1413, in initProject
    Analysis.initProject(self, project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 310, in initProject
    self.initAtomSetMappings()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 983, in initAtomSetMappings
    for chain in molSystem.chains:
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 13085, in getChains
    self.load()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5066, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5100, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/xml/Implementation.py", line 4881, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 3933, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['134d', 'A']>

Probably entries 135d, 136d, 177d, 1gnc and others are affected too, making 
this a high priority issue for NRG-CING.
134d
135d
136d
177d
1gnc
1msh
2neo
2ofg

Original issue reported on code.google.com by jurge...@gmail.com on 10 Nov 2010 at 1:08

GoogleCodeExporter commented 9 years ago 
One comment already: can't find the 134d joinedCoord file on sunfish, or has 
that changed? Also no joy for 1gnc, 1msh, 2neo, 2ofg, ... didn't try the others

Original comment by wfvran...@gmail.com on 27 Jan 2011 at 2:33

GoogleCodeExporter commented 9 years ago 
These entries have no experimental data in PDB. They're aren't processed at 
BMRB but in Nijmegen at the above locations. Can you look at eg: 
http://nmr.cmbi.ru.nl/NRG-CING/prep/C/34/134d/ ?

I attach in this comment the overall flow for NRG-CING.

Original comment by jurge...@gmail.com on 31 Jan 2011 at 9:07

Attachments:

GoogleCodeExporter commented 9 years ago 
This is still an issue when I redid the preparation and validation steps for 
this entry yesterday.

Original comment by jurge...@gmail.com on 1 Feb 2011 at 10:07

GoogleCodeExporter commented 9 years ago 
Similar problem?

================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r918)       
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: nmr.cmbi.umcn.nl (darwin/32bit/8cores/2.6.5) at:  (9564) 
Mon Jan 31 21:46:39 2011
DEBUG: Using:
DEBUG: inputDir:             
file:///Library/WebServer/Documents/NRG-CING/input/ki
DEBUG: outputDir:            /Library/WebServer/Documents/NRG-CING/data/ki/2kid
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          CCPN
DEBUG: modelCount:           None
DEBUG: storeCING2db:         True
DEBUG: ranges:               cv
Enforcing a redo
copying file: //Library/WebServer/Documents/NRG-CING/input/ki/2kid.tgz to: 
2kid.tgz
Moving CCPN directory from [linkNmrStarData] to [2kid]
==> Importing data from Ccpn project "2kid"
Error loading file for:  <ccp.molecule.ChemComp.NonStdChemComp ['protein', 
'Phq']>
Reading:  <open file 
'/Volumes/tera4/NRG-CING/data/ki/2kid/2kid/ccp/molecule/ChemComp/protein+Phq+2ki
d_user_2010-12-08-13-35-37-016_00001.xml', mode 'r' at 0x7faf498>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
Error loading file for:  <ccp.molecule.MolSystem.MolSystem ['2kid']>
Reading:  <open file 
'/Volumes/tera4/NRG-CING/data/ki/2kid/2kid/ccp/molecule/MolSystem/2kid+2kid_user
_2010-12-08-13-34-39-344_00002.xml', mode 'r' at 0x772bf98>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
Error loading file for:  <ccp.nmr.NmrConstraint.NmrConstraintStore [1]>
Reading:  <open file 
'/Volumes/tera4/NRG-CING/data/ki/2kid/2kid/ccp/nmr/NmrConstraint/1+2kid_user_201
0-12-08-13-34-39-371_00001.xml', mode 'r' at 0x64c1f40>
Last xml tag read:  NMRC.FixedAtomSet.atoms
Parser state was:  reading
Current object was:  <ccp.nmr.NmrConstraint.FixedAtomSet [1, 1]>
CING started at : Mon Jan 31 21:46:34 2011
CING stopped at : Mon Jan 31 21:46:45 2011
CING took       : 11.009 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 355, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 183, in main
    if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 2332, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 317, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 412, in importFromCcpnMolecule
    ccpnConstraintLists.extend(constraintStore.sortedConstraintLists())
  File "/Users/jd/workspace35/ccpn/python/ccp/api/nmr/NmrConstraint.py", line 22236, in sortedConstraintLists
    self.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4912, in loadFromStream
    value = clazz.getByKey(oo,vv[1:-1])
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 1583, in getByKey
    obj1.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4993, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 20447, in checkValid
    ('chemCompVars', (self.linking,  self.descriptor))
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 3974, in getByNavigation
    result.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4993, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/ChemComp.py", line 26753, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: 
ccp.molecule.ChemComp.NonStdChemComp.checkValid:
         constraint protein_DNA_RNA_are_linear_polymers violated: <ccp.molecule.ChemComp.NonStdChemComp ['protein', 'Phq']>

Original comment by jurge...@gmail.com on 1 Feb 2011 at 11:15

GoogleCodeExporter commented 9 years ago 
For the 134d problem, you are sure that this file:

/Volumes/tera4/NRG-CING/data/34/134d/134d/ccp/molecule/MolSystem/134d+134d_user_
2010-11-10-09-52-07-265_00001.xml

exists? It could be CCPN project confusion.

Original comment by wfvran...@gmail.com on 2 Feb 2011 at 3:28

GoogleCodeExporter commented 9 years ago 
I've rerun this entry. Now it's log is at:

http://nmr.cmbi.ru.nl/NRG-CING/data/34/134d/log_validateEntry/134d_2011-02-02_05
-29-06.log

Same problem though, right?

Original comment by jurge...@gmail.com on 2 Feb 2011 at 4:35

GoogleCodeExporter commented 9 years ago 
Indeed, this is a fun one. The sequence is 31 residues long, but not all 
residues have coordinates, and the gaps are flanked by residues with a sequence 
insertion code. Because I set the PDB/author info in CCPN (for NRG reasons), it 
got a bit confused with the sequence insertion code and was not using this for 
the 'missing' residues, so there was duplication of seqCode/insertionCode pairs 
in the sequence (which is not allowed).

Anyway fixed now, again have to check this into SF, not sure when that'll be up 
and running.

Original comment by wfvran...@gmail.com on 3 Feb 2011 at 4:23

GoogleCodeExporter commented 9 years ago 
Great, let me know when you had a chance to commit. The main sf.net site is up 
now.

Original comment by jurge...@gmail.com on 4 Feb 2011 at 8:59

GoogleCodeExporter commented 9 years ago 
But cvs access is still blocked I feel: 
https://sourceforge.net/blog/update-sourceforgenet-attack/#comments

Time to move over to Google Code's svn ? ;-)

Original comment by jurge...@gmail.com on 4 Feb 2011 at 3:15

GoogleCodeExporter commented 9 years ago 
Seriously... I'll keep an eye on it, will do it asap.

Original comment by wfvran...@gmail.com on 4 Feb 2011 at 3:19

GoogleCodeExporter commented 9 years ago 
Is now in SF CVS

Original comment by wfvran...@gmail.com on 22 Feb 2011 at 1:47

GoogleCodeExporter commented 9 years ago 
Analysis got the newly created CCPN project files for entry 134d in fine.
Thanks Wim!

Original comment by jurge...@gmail.com on 23 Feb 2011 at 3:05

GoogleCodeExporter commented 9 years ago 
I'm having to reopen this issue for e.g. entry 1lcc.

Take a look at:
http://nmr.cmbi.ru.nl/NRG-CING/data/lc/1lcc/log_validateEntry/1lcc_2011-03-04_05
-19-17.log
I checked the waters in the input DOCR STAR and they are fine.

Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 357, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/validateEntry.py", line 185, in main
    if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 2334, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 310, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace35/cingStable/python/cing/PluginCode/Ccpn.py", line 422, in importFromCcpnMolecule
    if not len(ccpnMolSys.structureEnsembles):
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 13467, in getStructureEnsembles
    self.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4993, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3933, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['1lcc', 'E']>

I suggest we test read the CCPN project at BMRB so the problem can be caught 
early on.

We've seen this issue at NRG too: 
http://code.google.com/p/nmrrestrntsgrid/issues/detail?id=159

I've checked manually if I'm on the most recent versions of the files and code. 
Indeed so with below output.
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r941)       
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: stella.cmbi.umcn.nl (darwin/64bit/2cores/2.6.6) at: 
(53346) Fri Mar  4 19:36:59 2011
DEBUG: Using program arguments:
DEBUG: inputDir:             
file:///Library/WebServer/Documents/NRG-CING/input/lc
DEBUG: outputDir:            /Library/WebServer/Documents/NRG-CING/data/lc/1lcc
DEBUG: pdbConvention:        .
DEBUG: restraintsConvention: .
DEBUG: archiveType:          BY_CH23
DEBUG: projectType:          CCPN
DEBUG: storeCING2db:         True
DEBUG: ranges:               cv
DEBUG: filterTopViolations:  1
DEBUG: 
DEBUG: Using derived settings:
DEBUG: modelCount:           None
DEBUG: isRemoteOutputDir:    False
copying file: /Library/WebServer/Documents/NRG-CING/input/lc/1lcc.tgz to: 
1lcc.tgz
Moving CCPN directory from [linkNmrStarData] to [1lcc]
==> Importing data from Ccpn project "1lcc"
Error loading file for:  <ccp.molecule.MolSystem.MolSystem ['1lcc']>
Reading:  <open file 
'/Library/WebServer/Documents/NRG-CING/data/lc/1lcc/1lcc/ccp/molecule/MolSystem/
1lcc+1lcc_user_2011-02-25-08-47-48-991_00001.xml', mode 'r' at 0x10853fe40>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
CING started at : Fri Mar  4 19:36:55 2011
CING stopped at : Fri Mar  4 19:37:00 2011
CING took       : 5.088 s

Traceback (most recent call last):
  File "/Users/jd/workspace35/cing/python/cing/Scripts/validateEntry.py", line 393, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace35/cing/python/cing/Scripts/validateEntry.py", line 233, in main
    if not project.initCcpn(ccpnFolder=fileNameTgz, modelCount=modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 2343, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 310, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace35/cing/python/cing/PluginCode/Ccpn.py", line 422, in importFromCcpnMolecule
    if not len(ccpnMolSys.structureEnsembles):
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 13467, in getStructureEnsembles
    self.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4993, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpn/python/ccp/api/molecule/MolSystem.py", line 3933, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['1lcc', 'E']>

Original comment by jurge...@gmail.com on 4 Mar 2011 at 6:39

GoogleCodeExporter commented 9 years ago 
There is a problem in the NMR-STAR file for 1lcc... in the molecule 
description, for chain E, it reads:

       5 5 HOH  1 HOH 1 1 
       5 5 HOH  2 HOH 1 1 
       5 5 HOH  3 HOH 1 1 
       5 5 HOH  4 HOH 1 1 
       5 5 HOH  5 HOH 1 1 
       5 5 HOH  6 HOH 1 1 
       5 5 HOH  7 HOH 1 1 
       5 5 HOH  8 HOH 1 1 
       5 5 HOH  9 HOH 1 1 
       5 5 HOH 10 HOH 1 1 
       5 5 HOH 11 HOH 1 1 
       5 5 HOH 12 HOH 1 1 
       5 5 HOH 13 HOH 1 1 
       5 5 HOH 14 HOH 1 1 
       5 5 HOH 15 HOH 1 1 
       5 5 HOH 16 HOH 1 1 
       5 5 HOH 17 HOH 1 1 
       5 5 HOH 18 HOH 1 1 
       5 5 HOH 19 HOH 1 1 
       5 5 HOH 20 HOH 1 1 
       5 5 HOH 21 HOH 1 1 
       5 5 HOH 22 HOH 1 1 
       5 5 HOH 23 HOH 1 1 
       5 5 HOH 24 HOH 1 1 
       5 5 HOH 25 HOH 1 1 
       5 5 HOH 26 HOH 1 1 
       5 5 HOH 27 HOH 1 1 
       5 5 HOH 28 HOH 1 1 
       5 5 HOH 29 HOH 1 1 
       5 5 HOH 30 HOH 1 1 
       5 5 HOH 31 HOH 1 1 
       5 5 HOH 32 HOH 1 1 
       5 5 HOH 33 HOH 1 1 
       5 5 HOH 34 HOH 1 1 
       5 5 HOH 35 HOH 1 1 
       5 5 HOH 36 HOH 1 1 
       5 5 HOH 37 HOH 1 1 
       5 5 HOH 38 HOH 1 1 
       5 5 HOH 39 HOH 1 1 
       5 5 HOH 40 HOH 1 1 
       5 5 HOH 41 HOH 1 1 
       5 5 HOH 42 HOH 1 1 
       5 5 HOH 43 HOH 1 1 
       5 5 HOH 44 HOH 1 1 
       5 5 HOH 45 HOH 1 1 
       5 5 HOH 46 HOH 1 1 
       5 5 HOH 47 HOH 1 1 
       5 5 HOH 48 HOH 1 1 
       5 5 HOH 49 HOH 1 1 
       5 5 HOH 50 HOH 1 1 
       5 5 HOH 51 HOH 1 1 
       5 5 HOH 52 HOH 1 1 
       5 5 HOH 53 HOH 1 1 

In the coordinates:

       1  991 5 5  1 HOH O    O  21.970 18.650 18.350 1.00 0.0 E A .   52 HOH O    1 1 
       1  992 5 5  1 HOH H1   H  22.400 19.540 18.450 1.00 0.0 E A .   52 HOH H1   1 1 
       1  993 5 5  1 HOH H2   H  22.170 18.090 19.160 1.00 0.0 E A .   52 HOH H2   1 1 
       1  994 5 5  2 HOH O    O   9.910 20.180 29.550 1.00 0.0 E A .   53 HOH O    1 1 
       1  995 5 5  2 HOH H1   H   9.650 20.460 28.620 1.00 0.0 E A .   53 HOH H1   1 1 
       1  996 5 5  2 HOH H2   H   9.310 19.440 29.850 1.00 0.0 E A .   53 HOH H2   1 1 
       1  997 5 5  3 HOH O    O  10.690 19.540 32.470 1.00 0.0 E A .   54 HOH O    1 1 
       1  998 5 5  3 HOH H1   H  10.760 18.700 31.940 1.00 0.0 E A .   54 HOH H1   1 1 
       1  999 5 5  3 HOH H2   H  10.340 19.330 33.390 1.00 0.0 E A .   54 HOH H2   1 1 
       1 1000 5 5  4 HOH O    O  11.960 21.630 33.860 1.00 0.0 E A .   55 HOH O    1 1 
       1 1001 5 5  4 HOH H1   H  11.510 20.830 33.460 1.00 0.0 E A .   55 HOH H1   1 1 
       1 1002 5 5  4 HOH H2   H  11.500 21.880 34.710 1.00 0.0 E A .   55 HOH H2   1 1 
       1 1003 5 5  5 HOH O    O  17.850 27.380 32.270 1.00 0.0 E A .   56 HOH O    1 1 
       1 1004 5 5  5 HOH H1   H  18.730 27.770 32.560 1.00 0.0 E A .   56 HOH H1   1 1 
       1 1005 5 5  5 HOH H2   H  17.230 28.110 32.000 1.00 0.0 E A .   56 HOH H2   1 1 
       1 1006 5 5  6 HOH O    O  15.790 23.850 27.410 1.00 0.0 E A .   57 HOH O    1 1 
       1 1007 5 5  6 HOH H1   H  16.270 24.270 26.650 1.00 0.0 E A .   57 HOH H1   1 1 
       1 1008 5 5  6 HOH H2   H  14.880 23.560 27.110 1.00 0.0 E A .   57 HOH H2   1 1 
       1 1009 5 5  7 HOH O    O  18.180 22.780 17.970 1.00 0.0 E A .   58 HOH O    1 1 
       1 1010 5 5  7 HOH H1   H  18.410 22.090 17.280 1.00 0.0 E A .   58 HOH H1   1 1 
       1 1011 5 5  7 HOH H2   H  18.400 22.430 18.880 1.00 0.0 E A .   58 HOH H2   1 1 
       1 1012 5 5  8 HOH O    O  17.160 34.420 31.500 1.00 0.0 E A .   59 HOH O    1 1 
       1 1013 5 5  8 HOH H1   H  17.730 34.030 32.220 1.00 0.0 E A .   59 HOH H1   1 1 
       1 1014 5 5  8 HOH H2   H  16.880 33.690 30.880 1.00 0.0 E A .   59 HOH H2   1 1 
       1 1015 5 5  9 HOH O    O  18.840 24.980 20.090 1.00 0.0 E A .   60 HOH O    1 1 
       1 1016 5 5  9 HOH H1   H  18.820 24.950 21.090 1.00 0.0 E A .   60 HOH H1   1 1 
       1 1017 5 5  9 HOH H2   H  19.650 25.470 19.790 1.00 0.0 E A .   60 HOH H2   1 1 
       1 1018 5 5 10 HOH O    O  16.080 29.580 31.530 1.00 0.0 E A .   61 HOH O    1 1 
       1 1019 5 5 10 HOH H1   H  15.120 29.300 31.470 1.00 0.0 E A .   61 HOH H1   1 1 
       1 1020 5 5 10 HOH H2   H  16.220 30.090 32.380 1.00 0.0 E A .   61 HOH H2   1 1 
       1 1021 5 5 11 HOH O    O  15.660 34.740 34.520 1.00 0.0 E A .   62 HOH O    1 1 
       1 1022 5 5 11 HOH H1   H  15.430 34.240 33.680 1.00 0.0 E A .   62 HOH H1   1 1 
       1 1023 5 5 11 HOH H2   H  15.980 34.090 35.210 1.00 0.0 E A .   62 HOH H2   1 1 
       1 1024 5 5 12 HOH O    O  11.380 34.520 34.630 1.00 0.0 E A .   63 HOH O    1 1 
       1 1025 5 5 12 HOH H1   H  11.530 35.510 34.590 1.00 0.0 E A .   63 HOH H1   1 1 
       1 1026 5 5 12 HOH H2   H  11.640 34.190 35.540 1.00 0.0 E A .   63 HOH H2   1 1 
       1 1027 5 5 13 HOH O    O  17.190 19.580 18.260 1.00 0.0 E A .   64 HOH O    1 1 
       1 1028 5 5 13 HOH H1   H  16.840 18.840 18.840 1.00 0.0 E A .   64 HOH H1   1 1 
       1 1029 5 5 13 HOH H2   H  16.530 20.340 18.260 1.00 0.0 E A .   64 HOH H2   1 1 
       1 1030 5 5 14 HOH O    O  11.670 25.730 37.590 1.00 0.0 E A .   65 HOH O    1 1 
       1 1031 5 5 14 HOH H1   H  11.900 25.290 38.460 1.00 0.0 E A .   65 HOH H1   1 1 
       1 1032 5 5 14 HOH H2   H  10.990 25.160 37.110 1.00 0.0 E A .   65 HOH H2   1 1 
       1 1033 5 5 15 HOH O    O  32.300 19.840 16.170 1.00 0.0 E A .   66 HOH O    1 1 
       1 1034 5 5 15 HOH H1   H  32.680 19.150 15.550 1.00 0.0 E A .   66 HOH H1   1 1 
       1 1035 5 5 15 HOH H2   H  32.870 19.910 16.990 1.00 0.0 E A .   66 HOH H2   1 1 
       1 1036 5 5 16 HOH O    O  25.210 18.010 15.370 1.00 0.0 E A .   67 HOH O    1 1 
       1 1037 5 5 16 HOH H1   H  25.390 17.060 15.120 1.00 0.0 E A .   67 HOH H1   1 1 
       1 1038 5 5 16 HOH H2   H  24.260 18.090 15.680 1.00 0.0 E A .   67 HOH H2   1 1 
       1 1039 5 5 17 HOH O    O  28.250 18.350 25.940 1.00 0.0 E A .   68 HOH O    1 1 
       1 1040 5 5 17 HOH H1   H  28.900 18.440 25.190 1.00 0.0 E A .   68 HOH H1   1 1 
       1 1041 5 5 17 HOH H2   H  28.200 17.390 26.240 1.00 0.0 E A .   68 HOH H2   1 1 
       1 1042 5 5 18 HOH O    O  25.910 19.390 26.730 1.00 0.0 E A .   69 HOH O    1 1 
       1 1043 5 5 18 HOH H1   H  25.640 20.100 26.070 1.00 0.0 E A .   69 HOH H1   1 1 
       1 1044 5 5 18 HOH H2   H  26.720 18.910 26.390 1.00 0.0 E A .   69 HOH H2   1 1 
       1 1045 5 5 19 HOH O    O  29.690 24.270 21.950 1.00 0.0 E A .   70 HOH O    1 1 
       1 1046 5 5 19 HOH H1   H  29.730 23.490 21.320 1.00 0.0 E A .   70 HOH H1   1 1 
       1 1047 5 5 19 HOH H2   H  29.130 24.990 21.550 1.00 0.0 E A .   70 HOH H2   1 1 
       1 1048 5 5 20 HOH O    O  25.850 19.540 29.360 1.00 0.0 E A .   71 HOH O    1 1 
       1 1049 5 5 20 HOH H1   H  26.170 19.600 28.410 1.00 0.0 E A .   71 HOH H1   1 1 
       1 1050 5 5 20 HOH H2   H  25.730 18.580 29.610 1.00 0.0 E A .   71 HOH H2   1 1 
       1 1051 5 5 21 HOH O    O  14.200 26.840 33.980 1.00 0.0 E A .   72 HOH O    1 1 
       1 1052 5 5 21 HOH H1   H  14.540 27.700 33.610 1.00 0.0 E A .   72 HOH H1   1 1 
       1 1053 5 5 21 HOH H2   H  13.230 26.740 33.780 1.00 0.0 E A .   72 HOH H2   1 1 
       1 1054 5 5 22 HOH O    O  31.320 25.660 18.650 1.00 0.0 E A .   73 HOH O    1 1 
       1 1055 5 5 22 HOH H1   H  30.700 24.870 18.550 1.00 0.0 E A .   73 HOH H1   1 1 
       1 1056 5 5 22 HOH H2   H  30.770 26.480 18.820 1.00 0.0 E A .   73 HOH H2   1 1 
       1 1057 5 5 23 HOH O    O  23.160 19.700 30.160 1.00 0.0 E A .   74 HOH O    1 1 
       1 1058 5 5 23 HOH H1   H  23.560 19.520 31.060 1.00 0.0 E A .   74 HOH H1   1 1 
       1 1059 5 5 23 HOH H2   H  23.880 19.660 29.470 1.00 0.0 E A .   74 HOH H2   1 1 
       1 1060 5 5 24 HOH O    O  24.270 26.570 33.610 1.00 0.0 E A .   75 HOH O    1 1 
       1 1061 5 5 24 HOH H1   H  24.740 26.890 34.430 1.00 0.0 E A .   75 HOH H1   1 1 
       1 1062 5 5 24 HOH H2   H  24.810 25.840 33.190 1.00 0.0 E A .   75 HOH H2   1 1 
       1 1063 5 5 25 HOH O    O  25.990 24.680 32.760 1.00 0.0 E A .   76 HOH O    1 1 
       1 1064 5 5 25 HOH H1   H  25.810 23.710 32.940 1.00 0.0 E A .   76 HOH H1   1 1 
       1 1065 5 5 25 HOH H2   H  26.940 24.800 32.480 1.00 0.0 E A .   76 HOH H2   1 1 
       1 1066 5 5 26 HOH O    O  25.430 20.950 24.590 1.00 0.0 E A .   77 HOH O    1 1 
       1 1067 5 5 26 HOH H1   H  26.140 20.910 23.890 1.00 0.0 E A .   77 HOH H1   1 1 
       1 1068 5 5 26 HOH H2   H  24.550 21.170 24.170 1.00 0.0 E A .   77 HOH H2   1 1 
       1 1069 5 5 27 HOH O    O  13.620 38.770 37.220 1.00 0.0 E A .   78 HOH O    1 1 
       1 1070 5 5 27 HOH H1   H  13.320 38.550 38.150 1.00 0.0 E A .   78 HOH H1   1 1 
       1 1071 5 5 27 HOH H2   H  14.610 38.650 37.170 1.00 0.0 E A .   78 HOH H2   1 1 

So a lot less waters for entity_assembly_ID 5 in the coordinates than in the 
molecule description. Because I reset the water sequence codes (on request!) to 
what's in the coordinates, there is a problem here and some sequence codes end 
up overlapping.

Original comment by wfvran...@gmail.com on 8 Mar 2011 at 9:25

GoogleCodeExporter commented 9 years ago 
I looked some more at this... I introduced a bit of code a while ago to deal 
with water molecules differently on reading the sequence from NMR-STAR, but 
apparently it's changed again now in the joinedCoord files, is that correct? 
Everything seems to work if I comment out that bit. I can check in this change, 
but it is possible it will give problems with other entries (especially if the 
water is handled differently in the coordinate NMR-STAR file of course).

Original comment by wfvran...@gmail.com on 9 Mar 2011 at 10:04

GoogleCodeExporter commented 9 years ago 
This issue is fixed for entries:

134d
135d
136d
177d
1gnc
1msh
2neo
2ofg

I'm tagging this issue for 1lcc where it still does apply today:
http://nmr.cmbi.ru.nl/NRG-CING/data/lc/1lcc/log_validateEntry/1lcc_2011-03-28_20
-08-19.log

Let me look into 1lcc now.

Original comment by jurge...@gmail.com on 30 Mar 2011 at 10:15

GoogleCodeExporter commented 9 years ago 
Note, I'll need to check this fix for all 35 water involved entries:

1ai0 1aiy 1cb9 1crp 1e08 1e0a 1ffj 1gxx 1hum 1lcc 1lcd 1mdi 1oa5 1oa6 1ocd 1ppx 
1pun 1puq 1pus 1r2n 1r84 1rl5 1saf 1tum 1yn2 1z6c 1zrr 2frc 2hji 2hz8 2ke5 2kkh 
2rmk 3usn 6i1b

They can be retrieved from NRG-CING simply by:

sort -n -t, -k3 nrgcing.cingresidue.csv > nrgcing.cingresidue.srt.csv
sort -n -t, -k1 nrgcing.cingentry.csv > nrgcing.cingentry.srt.csv

jd:nmr/~/tmp/ join -t, -2 3 -o 1.2,2.5 nrgcing.cingentry.srt.csv 
nrgcing.cingresidue.srt.csv | grep HOH | sort -u 
1ai0,HOH
1aiy,HOH
1cb9,HOH
1crp,HOH
1e08,HOH
1e0a,HOH
1ffj,HOH
1gxx,HOH
1hum,HOH
1lcc,HOH
1lcd,HOH
1mdi,HOH
1oa5,HOH
1oa6,HOH
1ocd,HOH
1ppx,HOH
1pun,HOH
1puq,HOH
1pus,HOH
1r2n,HOH
1r84,HOH
1rl5,HOH
1saf,HOH
1tum,HOH
1yn2,HOH
1z6c,HOH
1zrr,HOH
2frc,HOH
2hji,HOH
2hz8,HOH
2ke5,HOH
2kkh,HOH
2rmk,HOH
3usn,HOH
6i1b,HOH

Original comment by jurge...@gmail.com on 30 Mar 2011 at 11:03

GoogleCodeExporter commented 9 years ago 
Today after 1lcc was updated by Chris and NRG-CING retried it still fails with:

constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated:

My NRG-CING code can handle absent CCPN projects but not invalid projects. I 
suggest we check the project before accepting it in NRG. Otherwise the 
development cycles take too long and are too complex as well.

Wim, can you fix the actual problem or do you need input from us?

Original comment by jurge...@gmail.com on 8 Apr 2011 at 2:22

GoogleCodeExporter commented 9 years ago 
To be honest. This is an NRG problem more than CING's.

Please see: NRG isssssue 272: Not accept invalid CCPN project anymore at:
http://code.google.com/p/nmrrestrntsgrid/issues/detail?id=272

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:18

GoogleCodeExporter commented 9 years ago 
OK see my comment 15 - on my computer 1lcc works fine because I commented out a 
bit of code that special-cases waters (the problem in 1lcc). That bit of code 
was required before but not any more, I think, because we treat waters 
alltogether differently now anyway... of course it is possible that other 
entries will fail if I do take it out, I cannot guarantee that that won't 
happen.

Let me know what you want me to do with this one.

Original comment by wfvran...@gmail.com on 11 Apr 2011 at 12:25

GoogleCodeExporter commented 9 years ago 
If you have resources to fix, validate and check it, great. If not, let's not 
do this halfway and break other parts. We'll have to accept the fact that FC 
can't provide valid CCPN projects for all NRG entries. I do want NRG to realize 
that though and not put it out in those cases but that's an NRG issue. The 
issue here is closed I should think.

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:39

GoogleCodeExporter commented 9 years ago 
Addressed in r968 but no real fix expected soon.

Original comment by jurge...@gmail.com on 13 Apr 2011 at 10:32

GoogleCodeExporter commented 9 years ago 
Entries that have this problem: 177d 1gnc 1lcc 1lcd 1qch 1sae 1sah 1saj 1sak 
1sal 3sak
They'll not make it into NRG-CING until fixed.

Original comment by jurge...@gmail.com on 10 Oct 2011 at 8:15