Bad CCPN import for chains

[GoogleCodeExporter]

What is the expected output? What do you see instead?
Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 154, in main
    if not project.initCcpn(ccpnFolder = fileNameTgz):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 2252, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 331, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 447, in importFromCcpnMolecule
    if not self._match2Cing(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 571, in _match2Cing
    chain.ccpn = ccpnChain
AttributeError: 'NoneType' object has no attribute 'ccpn'

Original issue reported on code.google.com by jurge...@gmail.com on 22 Oct 2009 at 10:11

[GoogleCodeExporter]

Still an issue:

Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 154, in main
    if not project.initCcpn(ccpnFolder = fileNameTgz):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 2252, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 331, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 447, in importFromCcpnMolecule
    if not self._match2Cing(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 571, in _match2Cing
    chain.ccpn = ccpnChain
AttributeError: 'NoneType' object has no attribute 'ccpn'

Original comment by jurge...@gmail.com on 28 Oct 2009 at 10:43

[GoogleCodeExporter]

Weird CCPN molecular system because all waters have been fit into a separate 
chain each (see attached pic) whereas in the Wattos generated NMR-STAR file 
there is a simple 5 chain system like in 
the PDB file:
       1  water                                      1 $water                                           0 . no . . . . . . rr_1lcc 1 
       2 "DNA 5 D AP AP TP TP GP TP GP AP GP CP G 3" 3 $DNA__5__D__AP_AP_TP_TP_GP_TP_GP_AP_GP_CP_G__3__ A . no . . . . . . rr_1lcc 1 
       3 "DNA 5 D CP GP CP TP CP AP CP AP AP TP T 3" 2 $DNA__5__D__CP_GP_CP_TP_CP_AP_CP_AP_AP_TP_T__3__ B . no . . . . . . rr_1lcc 1 
       4 "Lac Repressor"                             5 $Lac_Repressor                                   C . no . . . . . . rr_1lcc 1 
       5 "SODIUM ION"                                4 $SODIUM_ION                                      D . no . . . . . . rr_1lcc 1 

Wim, can you figure out why the CCPN molecular system got altered by FC?
http://nmr.cmbi.ru.nl/NRG-CING//data/lc/1lcc/1lcc.tgz was my input from DOCR.

I'll try to work around it anyway so I'm giving it a low priority.

Original comment by jurge...@gmail.com on 28 Oct 2009 at 10:56

• Changed state: Started
• Added labels: Priority-Low
• Removed labels: Priority-Medium

Attachments:

• [Picture 1.png](https://storage.googleapis.com/google-code-attachments/cing/issue-199/comment-2/Picture 1.png)

[GoogleCodeExporter]

Hard to work around since in CING we have a hard limit on the number of chains 
to be limited by the fact that it can only be a single character; one of:
    DEFAULT_ChainNamesByAlphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ^01234567890abcdefghijklmnopqrstuvwxyz'
Currently 64. See issue 130.
This entry has 57; fewer than 64 luckily.

Workaround committed in r655.

Original comment by jurge...@gmail.com on 28 Oct 2009 at 11:25

[GoogleCodeExporter]

Leaving the issue open for Wim.

Original comment by jurge...@gmail.com on 28 Oct 2009 at 11:26

[GoogleCodeExporter]

Wim, can you fix this in FC? If not, I'll move the issue to the NRG project, ok?

Original comment by jurge...@gmail.com on 8 Feb 2010 at 12:54

[GoogleCodeExporter]

Yep move it - if the waters are present then I need a separate chain code for 
each in
CCPN as far as I know. There might be workarounds, but not straightforward.

Original comment by wfvran...@gmail.com on 8 Feb 2010 at 12:58

[GoogleCodeExporter]

Moved to:

http://code.google.com/p/nmrrestrntsgrid/issues/detail?id=242

Original comment by jurge...@gmail.com on 8 Feb 2010 at 1:51

• Changed state: Invalid

[GoogleCodeExporter]

Issue 130 has been merged into this issue.

Original comment by jurge...@gmail.com on 15 Nov 2010 at 10:25