Strange nomenclature breaks linking and assignments

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We might have a non-resolvable mapping issue. If you look at the pdb file, 
there is Gly1, and 
Ser2. Then, instead of Lys3, and Leu4,  you get Lys2A and  Leu2B. The mmCIF 
file is mapped 
normally. It looks like the restraints are mapped to the pathological pdb file.

I tried to work around this, but have been having trouble with the linking and 
assignment steps. 
After looking at this a little closer, I'm not sure if it is a Jurgen or Wim 
issue.

The following seems to fix the mapping in the format coverter, but crashes the 
processing at 
assign (linkNmrStarData.summary looks good, but I think FC is still trying to 
do 
readCoordinates). Changing 'readProject' to 'linkResonances' doesn't crash 
anything, but it 
doesn't fix anything either. This is kind of a rare case. Is it worth putting a 
lot of effort into it?

'2kny': {

 'authors': ['Chris Schulte'],

 'comment': """
 Final mapping: [['A', ' ', 1, 0], ['B', ' ', 1, 80]]
 Automatically setting chain mappings to [['A', ' ', 1, 0], ['B', ' ', 1, 80]]
  -- chain B is the Ca ion.
 """,

 'readProject': {

  'keywds': {

    'forceChainMappings': [
                            ['A', ' ', 1, 0], ['A', ' ', 5, 2],
['B', ' ', 1, 80],
                          ],

     },
   },
 },

ERROR: Error invoking reflected command: ReadEntryNMRSTAR
ERROR:
java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
       at java.lang.reflect.Method.invoke(Method.java:616)
       at Wattos.CloneWars.CommandHub.invoke(CommandHub.java:117)
       at Wattos.CloneWars.UserInterface.doNonGuiMain(UserInterface.java:487)
       at Wattos.CloneWars.UserInterface.main(UserInterface.java:646)
Caused by: java.lang.NullPointerException
       at Wattos.Star.NMRStar.File31.toWattos(File31.java:2031)
       at Wattos.Soup.Entry.readNmrStarFormattedFile(Entry.java:583)
       at Wattos.CloneWars.CommandHub.ReadEntryNMRSTAR(CommandHub.java:585)
       ... 7 more 

Original issue reported on code.google.com by schulte....@gmail.com on 19 Apr 2010 at 1:55

Attachments:

• linkNmrStarData.log

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Wim, is there a problem with Chris trying to renumber starting from 3 so as to 
skip the first couple of residues?
Chris, the error is from Wattos trying to read the NMR-STAR generated by FC? If 
so, can you check if the input to 
Wattos is ok?

Original comment by jurge...@gmail.com on 19 Apr 2010 at 4:42

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Will do.

Original comment by schulte....@gmail.com on 19 Apr 2010 at 5:06

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It looks OK to me, but I'm not sure what to look for.

Original comment by schulte....@gmail.com on 20 Apr 2010 at 1:35

Attachments:

• 2kny_merge.str.gz

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These insertion codes are a nightmare - especially if they occur on the 
restraints
side. Anyway renumbering is perfectly OK!

Original comment by wfvran...@gmail.com on 21 Apr 2010 at 8:45

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Chris want to look at mapping again but close issue if problem can't easily be 
resolved.

Original comment by jurge...@gmail.com on 25 Aug 2010 at 1:42

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This now works! I had to remove the old presetDict settings, and now it 
filtered 2097/2302 restraints. The max violation was 2.466, but that was an 
outlier between an ) and a Ca.

I'm setting this to fixed.

Original comment by schulte....@gmail.com on 25 Aug 2010 at 3:28

• Changed state: Fixed