Closed GoogleCodeExporter closed 9 years ago
GoogleCodeExporter
commented
9 years ago Not sure about this one, it's a data model issue - can you send the .tgz of the
project to Rasmus with the error message? Better person for this one... .Original comment by wfvran...@gmail.com on 7 Feb 2011 at 10:48
GoogleCodeExporter
commented
9 years ago Rasmus, could you take a look at the attached straight up DOCR CCPN XML.
CING/FC has a problem with it as shown above but also Analysis barfs in the
same way as per below.
Rasmus, do you want to sign up with Google Code?
jd:stella/cingTmp/ analysis linkNmrStarData/
Model read finished. Duration 2.21501994133
Model validity check skipped
CcpNmr Analysis Version 2.1. Release 5 (Copyright 2003-2010 CCPN)
Distribution created Wed Aug 11 17:37:18 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.
A copy of the in-program documentation is located at:
http://www.ccpn.ac.uk/documentation
For how-tos and FAQs visit the CCPN wiki site at:
http://www.ccpn.ac.uk/wiki
To report bugs use the bug tracker at:
http://www.ccpn.ac.uk/bugs
For help and support join the mailing list at:
http://www.ccpn.ac.uk/support
For Python API documentation, tutorials and CCPN web applications visit:
http://www.ccpn.ac.uk/
Error loading file for: <ccp.molecule.ChemComp.NonStdChemComp ['protein',
'Phq']>
Reading: <open file
'/Users/jd/tmp/cingTmp/linkNmrStarData/ccp/molecule/ChemComp/protein+Phq+2kid_us
er_2010-12-08-13-35-37-016_00001.xml', mode 'r' at 0x28525a0>
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
'/Users/jd/tmp/cingTmp/linkNmrStarData/ccp/molecule/MolSystem/2kid+2kid_user_201
0-12-08-13-34-39-344_00002.xml', mode 'r' at 0x28523e8>
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 226, in <module>
main(projectDir, max_size, glDirect)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 111, in main
top.initProject(project)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisPopup.py", line 1516, in initProject
Analysis.initProject(self, project)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 303, in initProject
self.initAtomSetMappings()
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 976, in initAtomSetMappings
for chain in molSystem.chains:
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 13109, in getChains
self.load()
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5030, in load
self.loadFrom(repositories[0])
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5064, 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 4940, in loadFromStream
obj.checkValid()
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 20447, in checkValid
('chemCompVars', (self.linking, self.descriptor))
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 3974, in getByNavigation
result.load()
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5030, in load
self.loadFrom(repositories[0])
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5064, 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 273, in loadFromStream
partialLoad=partialLoad)
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/xml/Implementation.py", line 4940, in loadFromStream
obj.checkValid()
File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/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 7 Feb 2011 at 11:12
Attachments:
GoogleCodeExporter
commented
9 years ago Actually this is a ChemComp issue, once you have done a bit of digging.
The project contains a local ChemComp definition for ChemComp Phq that is
incorrect and breaks the model constraints. The error comes because the
ChemComp is defined as molType='protein'; the code quite rightly notices that
this is inconsistent. There are more problems with the file - for instance it
has no ChemBond records,and so does not define a molecule but only a bag of
atoms. I did not look further than that.
The solution is to use a correct ChemComp. Phq is available from the normal
ChemComp server, you can get it in Analysis by going into M:Molecule:Molecules
{Small Compounds} and selecting Phq under Mol Type: All. Assuming it is the
same molecule (it looks like it) this is benzyl chlorocarbonate.
The most curious thing to my mind is how the incorrect ChemComp got there in
the first place. According to the guid it was created on December 8 2010 at
13:35:37 as part of the 2kid project. Whatever way this ChemComp file was
created should be checked so that 1) we do not create new ChemComps (with
clashing names and distinct globally unique IDs) for ChemComps we already have
on the server, and 2) any ChemComps we do create are correct.
I would be interested to hear more, but I am not the right person to
investigate further. Please let me know.
RasmusOriginal comment by r.h.f...@gmail.com on 8 Feb 2011 at 11:10
GoogleCodeExporter
commented
9 years ago So this is an 'autogenerated' chemComp because the Phq one was not found or
downloaded. I just tried this project on my computer and it works fine, also
reading everything back in. Can you check the original project creation log
file, Jurgen?
It should have gotten the Phq chemComp online (or from the local list of
chemComps if that's being kept up to date). Works for me in any case.Original comment by wfvran...@gmail.com on 8 Feb 2011 at 11:59
GoogleCodeExporter
commented
9 years ago ok, I'll test with my development NRG setup in Nijmegen to recreate and read
back in.
If so, I'll ask Chris at BMRB to do the same.
Thanks guys!Original comment by jurge...@gmail.com on 8 Feb 2011 at 12:43
GoogleCodeExporter
commented
9 years ago My development setup on nmr.cmbi.ru.nl fails in processing the NRG data.
I'll hold off until I can update CCPN or should I modify something in my setup
already Wim?
I did check that I'm using the same presets as Chris S.:
'2kid': {
'authors': ['chris schulte'],
'comment': """
Warning: Did not map CCPN chain codes ['B']
Final mapping: [['A', ' ', 2, 0], ['C', ' ', 1, 148]]
""",
'linkResonances': {
'keywds': {
'forceChainMappings': [['A', ' ', 2, 0], ['B', ' ', 1, 699], ['C', ' ', 1, 701]]
},
},
},
Log:
Model read finished. Duration 1.71581101418
Model validity check skipped
Read pdbe.adatah.localConstants.py version 4.5.6
Read recoord2.pdbe.localConstants.py version 1.2.3
length of presetDict 1387
Read recoord2.pdbe.localConstants.py version 1.2.3
Doing 2kid...
Using preset values...
>
> Warning: Did not map CCPN chain codes ['B']
> Final mapping: [['A', ' ', 2, 0], ['C', ' ', 1, 148]]
>
Traceback (most recent call last):
File "/Users/jd/workspace35/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 707, 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 169, in runSpecific
self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead, autoCreateChemComps = True)
File "/Users/jd/workspace35/ccpn/python/pdbe/adatah/NmrStar.py", line 46, in readNmrStarFile
**localKeywds)
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 951, in readProject
self.getFullProject(fileName,**keywds)
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 566, in getFullProject
chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1071, in readSequence
(createMoleculeDict,molSystemBonds) = self.checkMolecules()
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 6035, in checkMolecules
self.makeChemComp()
File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 14308, in makeChemComp
raise self.FormatConverterError, " Error: no link code %s, %s" % (linkCode,descriptor)
ccpnmr.format.converters.DataFormat.FormatConverterError: ' Error: no link
code next, neutral'
Original comment by jurge...@gmail.com on 10 Feb 2011 at 9:24
GoogleCodeExporter
commented
9 years ago Well it works for me... Chris also has problems with the chemComp part, was
never able to figure out why. You have them in
data/pdbe/chemComp/archive/ChemComp of the CCPN installation? Or are they
checked out elsewhere and do you refer the FC to that directory?Original comment by wfvran...@gmail.com on 10 Feb 2011 at 3:42
GoogleCodeExporter
commented
9 years ago Would you mind looking at my CCPN setup I recall we made an account for you on
nmr but you can get in thru www right?
My one and only setup is in:
jd:nmr/log/ echo $CCPNMR_TOP_DIR/
/Users/jd/workspace35/ccpn/
Original comment by jurge...@gmail.com on 10 Feb 2011 at 5:19
GoogleCodeExporter
commented
9 years ago So the problem is at the BMRB end, because that's where these CCPN projects
originate from, right? If so, I'll see if I can still check over there what's
going on .Original comment by wfvran...@gmail.com on 21 Feb 2011 at 3:38
GoogleCodeExporter
commented
9 years ago Yes.Original comment by jurge...@gmail.com on 21 Feb 2011 at 5:58
GoogleCodeExporter
commented
9 years ago Chris, could you reprocess 2kid please?
Hopefully, the new CCPN code should have improved.Original comment by jurge...@gmail.com on 28 Mar 2011 at 8:21
GoogleCodeExporter
commented
9 years ago It looks like this hadn't crashed the format converter since december. I took a
closer look at the presetDict and CIF file though and realized that I had
chains B and C reversed in the presets. Just to make sure, I updated the
ccpn-chemcomp directory. I'm setting it to fixed - does someone want to varify
it?
Here are the preset settings that get 2866/2867 conversions:
'keywds': {
# 'forceChainMappings': [['A', ' ', 1, 0], ['B', ' ', 1, 699], ['C', ' ',
1, 701]]
'forceChainMappings': [['A', ' ', 1, 0], ['B', ' ', 1, 700], ['C', ' ', 1, 699]],
'useCcpnAtomMatching': True,
'addNameMappings':{
'Gln': [ ["HG","HG*"] ],
'Pro': [ ["HG","HG*"] ],
},
},
Original comment by schulte....@gmail.com on 28 Mar 2011 at 7:52
GoogleCodeExporter
commented
9 years ago Thanks Chris!Original comment by jurge...@gmail.com on 29 Mar 2011 at 9:03
Original issue reported on code.google.com by
jurge...@gmail.comon 7 Feb 2011 at 9:55