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water becoming a different chain for each instead of getting collected in one. #242

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
This is an issue moved from:
http://code.google.com/p/cing/issues/detail?id=199

Original issue reported on code.google.com by jurge...@gmail.com on 8 Feb 2010 at 1:50

GoogleCodeExporter commented 9 years ago 
Wim, can I ask you to take a look at these entries:
I attach the CCPN file for  2i7z here.
CING can't handle entries with more than 60-some chains. There are over 100 in 
this one.

Original comment by jurge...@gmail.com on 20 Sep 2010 at 9:01

Attachments:

GoogleCodeExporter commented 9 years ago 
Important obstacle for NRG-CING as well. Tim might be looking at this on Mon.

Original comment by jurge...@gmail.com on 12 Nov 2010 at 4:53

GoogleCodeExporter commented 9 years ago 
Both Tim and Wim took a look at it.

Wim will change the setup of FC to accomodate waters without giving them each a 
separate chain.

Original comment by jurge...@gmail.com on 17 Nov 2010 at 10:22

GoogleCodeExporter commented 9 years ago 
OK it's changed, can't check into SF at the moment because it's down, but 
remind me! The only difference with the analysis implementation is that it 
keeps the 'water chains' split by original chain code (so if you had a 100 
under 'M', 133 under 'N', then you get two chains in CCPN, one with 100 waters, 
the other with 133).

Original comment by wfvran...@gmail.com on 3 Feb 2011 at 2:55

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Yep this is all checked in, make sure you update python/format/ccp as well...

Original comment by wfvran...@gmail.com on 24 Feb 2011 at 2:06

GoogleCodeExporter commented 9 years ago 
Oops, Chris needs to rerun this at BMRB for the involved entries of course.

Chris can you do that so I can update to NRG-CING? 
First update CCPN again!
It only involves 3 entries: 1lcc 1lcd 2i7z 

I haven't checked the code change on my development machine here yet.

Original comment by jurge...@gmail.com on 24 Feb 2011 at 2:21

GoogleCodeExporter commented 9 years ago 
Doesn't work yet. I updated ccpn and ccpn-chemcomp and still crashed the FC. 
Then I went ahead and updated recoord. No change.

Here is 2i7z's log:

Doing 2i7z...
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 89, in __init__
    self.catchError(raiseError,timeFlag)
  File "/raid/docr/workspace/ccpn/python/pdbe/adatah/Generic.py", line 82, in __init__
    self.runSpecific()
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 214, in runSpecific
    self.writeNmrStarProject(outNmrStarFile,self.entry)
  File "/raid/docr/workspace/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 478, in writeNmrStarProject
    nmrStarExport.createFile(outNmrStarFile,excludeSaveFrames=None)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 180, in createFile
    self.loopSaveFrameData(1)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 292, in loopSaveFrameData
    self.setSaveFrameData(self.nmrStarSfDict['name'])
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 407, in setSaveFrameData
    self.loopStarLevelObjects('saveFrame',saveFrameName,ccpnLoopInfo,self.writeStarSfDict,self.nmrStarSfDict)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 697, in loopStarLevelObjects
    if not self.setTableData(tableName,saveFrame = starElement):
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 425, in setTableData
    ccpnLoopInfo = self.setupCurrentIDs(ccpnMap,self.writeStarTableDict)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 969, in setupCurrentIDs
    self.getCcpnNestedLoopValues(ccpnLoop[:],ccpnMap[:],ccpnLoopInfo,additionalMappings)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1030, in getCcpnNestedLoopValues
    self.getCcpnNestedLoopValues(ccpnLoop[1:],ccpnMap[1:],ccpnLowerLoopInfo,additionalMappings,nmrStarFullKey = nmrStarFullKey[:])
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1030, in getCcpnNestedLoopValues
    self.getCcpnNestedLoopValues(ccpnLoop[1:],ccpnMap[1:],ccpnLowerLoopInfo,additionalMappings,nmrStarFullKey = nmrStarFullKey[:])
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1027, in getCcpnNestedLoopValues
    self.ccpnVar[addCcpnVarKey] = self.getCcpnMapValue(addCcpnMapping)
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 2181, in getCcpnMapValue
    ccpnMapValue = getFunc(self.getCcpnObject(ccpnVarName) )
  File "/raid/docr/workspace/ccpn/python/pdbe/nmrStar/IO/Ccpn_To_NmrStar.py", line 1206, in getActualMolResidue
    waterMolRes = self.chainToWaterMolRes[chain]
AttributeError: Ccpn_To_NmrStar instance has no attribute 'chainToWaterMolRes'

Original comment by schulte....@gmail.com on 24 Feb 2011 at 5:02

Attachments:

GoogleCodeExporter commented 9 years ago 
Ah but exporting this data is another matter - I adapted the code to read it 
into CCPN as one (or several) chains with increasing sequence code, but not the 
re-export to NMR-STAR... . I'll see what I can do, but this could be a problem 
(it's a CCPN to NMR-STAR mapping issue, for which I am not responsible any 
more, but I will try and help out).

Original comment by wfvran...@gmail.com on 24 Feb 2011 at 5:09

GoogleCodeExporter commented 9 years ago 
Thanks guys!

Original comment by jurge...@gmail.com on 24 Feb 2011 at 7:20

GoogleCodeExporter commented 9 years ago 
I've checked in a new version of:

pdbe.nmrStar.Io.Ccpn_To_NmrStar

which at least generates the NMR-STAR file. Whether this is now what it's 
supposed to look like I'm not sure - it's listing a water molecule with many 
residues (reflecting what's stored in CCPN).

Anyway if you give me a description of what it should look like then I'll again 
see what I can do, but no promises on this one.

Original comment by wfvran...@gmail.com on 25 Feb 2011 at 10:44

GoogleCodeExporter commented 9 years ago 
There is an issue with 1lcc

Model read finished. Duration 1.33900213242
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 1lcc...
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 208, in runSpecific
    self.writeNmrStarProject(outNmrStarFile,self.entry)
  File "/Users/jd/workspace35/recoord/python/recoord2/pdbe/linkNmrStarData.py", line 443, in writeNmrStarProject
    nmrStarExport.createFile(outNmrStarFile,excludeSaveFrames=None)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 180, in createFile
    self.loopSaveFrameData(1)
  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 425, in setTableData
    ccpnLoopInfo = self.setupCurrentIDs(ccpnMap,self.writeStarTableDict)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 969, in setupCurrentIDs
    self.getCcpnNestedLoopValues(ccpnLoop[:],ccpnMap[:],ccpnLoopInfo,additionalMappings)
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1030, in getCcpnNestedLoopValues
    self.getCcpnNestedLoopValues(ccpnLoop[1:],ccpnMap[1:],ccpnLowerLoopInfo,additionalMappings,nmrStarFullKey = nmrStarFullKey[:])
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1030, in getCcpnNestedLoopValues
    self.getCcpnNestedLoopValues(ccpnLoop[1:],ccpnMap[1:],ccpnLowerLoopInfo,additionalMappings,nmrStarFullKey = nmrStarFullKey[:])
  File "/Users/jd/workspace35/ccpn/python/pdbe/nmrStar/IO/NmrStarExport.py", line 1027, in getCcpnNestedLoopValues
    self.ccpnVar[addCcpnVarKey] = self.getCcpnMapValue(addCcpnMapping)
  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 1213, in getActualMolResidue
    waterMolRes = self.residueToWaterMolRes[residue]
KeyError: <ccp.molecule.MolSystem.Residue ['1lcc', 'E', 1]>

For entry 2i7z a STAR file was created but Wattos complains about the waters 
having no residue number. Can you simply add a serial starting at 1 for tag:
_Entity_comp_index.ID. That is the only thing different from the water you 
already do in e.g. 1ai0

save_water
    _Entity.Sf_category                      entity
    _Entity.Sf_framecode                     water
    _Entity.Entry_ID                         rr_1ai0
    _Entity.ID                               5
    _Entity.Name                             water
    _Entity.Type                             non-polymer
    _Entity.Ambiguous_conformational_states  no
    _Entity.Ambiguous_chem_comp_sites        no
    _Entity.Nstd_chirality                   yes
    _Entity.Nstd_linkage                     no
    _Entity.Nonpolymer_comp_ID               HOH
    _Entity.Number_of_monomers               1
    _Entity.Paramagnetic                     no
    _Entity.Thiol_state                      "not present"
    _Entity.Parent_entity_ID                 5

    loop_
       _Entity_comp_index.ID
       _Entity_comp_index.Auth_seq_ID
       _Entity_comp_index.Comp_ID
       _Entity_comp_index.Comp_label
       _Entity_comp_index.Entry_ID
       _Entity_comp_index.Entity_ID

       1 . HOH . rr_1ai0 5 
       2 . HOH . rr_1ai0 5 
       3 . HOH . rr_1ai0 5 
       4 . HOH . rr_1ai0 5 
    stop_

save_

Original comment by jurge...@gmail.com on 25 Feb 2011 at 1:23

GoogleCodeExporter commented 9 years ago 
OK check out pdbe.nmrStar.Io.Ccpn_To_NmrStar and try again, think it's working 
now on both 1lcc and 2i7z

Original comment by wfvran...@gmail.com on 25 Feb 2011 at 1:45

GoogleCodeExporter commented 9 years ago 
works for:
http://nmr.cmbi.ru.nl/NRG/MRGridServlet?db_username=wattos1&mrblock_id=1224&pdb_
id=2i7z&request_type=block
and the other 2 entries as well.

Thanks Wim!
Chris can you update and run the conversions again next week?

Original comment by jurge...@gmail.com on 25 Feb 2011 at 2:03

GoogleCodeExporter commented 9 years ago 
It's working here. At first I thought it wasn't because 1lcc and 1lcd threw 
errors in exportCns.py, but when I realized that there were no parsable data 
(program = MR format), some issues would be inevitable. 

Should we call this fixed?

Original comment by schulte....@gmail.com on 25 Feb 2011 at 3:07

GoogleCodeExporter commented 9 years ago 
Let me see it on NRG live first, ok?
Cheers!

Original comment by jurge...@gmail.com on 25 Feb 2011 at 3:35

GoogleCodeExporter commented 9 years ago 
Right. I'm synchronizing now. It should show up tomorrow.

Original comment by schulte....@gmail.com on 25 Feb 2011 at 3:56

GoogleCodeExporter commented 9 years ago 
Excellent!

Original comment by jurge...@gmail.com on 3 Mar 2011 at 3:39