Incorrect atom numbering for 2jsp

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From Dimitri - I tried to completely redo this, including regenerating 
joinedCoord, which seems to be OK:
(Again, no idea whose software did this)

merged_15373_2jsp.str : row IDs in coordinate table (_Atom_site.ID) go up to 
326 and then change back to 1 in the middle of a residue. that's model 1, in 
other models they reset after 1080 (e.g. model 5).

merged_15137_2jo0.str : same thing in first 6 rows.

In that table ID is part of the primary key, it's supposed to be unique within 
the table.

Dimitri

Original issue reported on code.google.com by schulte....@gmail.com on 22 Dec 2010 at 3:36

Attachments:

• linkNmrStarData.log

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Just for quick reference - joinedCoord matches the mmCIF and PDB numbering:

joinedCoord
        1   314 1 1 21 HIS N    N   4.894  -4.166  12.094 1.00   0.0 A A . 21 HIS N    1 1 
        1   315 1 1 21 HIS CA   C   5.068  -2.868  11.426 1.00   0.0 A A . 21 HIS CA   1 1 
        1   316 1 1 21 HIS C    C   5.604  -3.074  10.003 1.00   0.0 A A . 21 HIS C    1 1 
        1   317 1 1 21 HIS O    O   6.438  -3.944   9.761 1.00   0.0 A A . 21 HIS O    1 1 
        1   318 1 1 21 HIS CB   C   5.927  -1.902  12.260 1.00   0.0 A A . 21 HIS CB   1 1 
        1   319 1 1 21 HIS CG   C   7.338  -2.378  12.627 1.00   0.0 A A . 21 HIS CG   1 1 
        1   320 1 1 21 HIS ND1  N   7.682  -3.010  13.746 1.00   0.0 A A . 21 HIS ND1  1 1 
        1   321 1 1 21 HIS CD2  C   8.461  -1.999  12.028 1.00   0.0 A A . 21 HIS CD2  1 1 
        1   322 1 1 21 HIS CE1  C   9.007  -2.999  13.847 1.00   0.0 A A . 21 HIS CE1  1 1 
        1   323 1 1 21 HIS NE2  N   9.489  -2.376  12.778 1.00   0.0 A A . 21 HIS NE2  1 1 
        1   324 1 1 21 HIS H    H   5.527  -4.878  11.787 1.00 100.0 A A . 21 HIS H    1 1 
        1   325 1 1 21 HIS HA   H   4.114  -2.344  11.369 1.00   0.0 A A . 21 HIS HA   1 1 
        1   326 1 1 21 HIS HB2  H   6.044  -0.983  11.686 1.00   0.0 A A . 21 HIS HB2  1 1 
        1   327 1 1 21 HIS HB3  H   5.402  -1.717  13.197 1.00   0.0 A A . 21 HIS HB3  1 1 
        1   328 1 1 21 HIS HD1  H   7.055  -3.495  14.363 1.00 100.0 A A . 21 HIS HD1  1 1 
        1   329 1 1 21 HIS HD2  H   8.528  -1.467  11.080 1.00   0.0 A A . 21 HIS HD2  1 1 
        1   330 1 1 21 HIS HE1  H   9.593  -3.427  14.660 1.00   0.0 A A . 21 HIS HE1  1 1 

NMR-STAR
       .  1 .  314 . 1 1 21 HIS C    C   5.604  -3.074  10.003 . . . 1.0 . . . . . . . . . . . . A . 21 HIS C    . . . . . . . . . rr_2jsp 1 
       .  1 .  315 . 1 1 21 HIS CA   C   5.068  -2.868  11.426 . . . 1.0 . . . . . . . . . . . . A . 21 HIS CA   . . . . . . . . . rr_2jsp 1 
       .  1 .  316 . 1 1 21 HIS CB   C   5.927  -1.902  12.260 . . . 1.0 . . . . . . . . . . . . A . 21 HIS CB   . . . . . . . . . rr_2jsp 1 
       .  1 .  317 . 1 1 21 HIS CD2  C   8.461  -1.999  12.028 . . . 1.0 . . . . . . . . . . . . A . 21 HIS CD2  . . . . . . . . . rr_2jsp 1 
       .  1 .  318 . 1 1 21 HIS CE1  C   9.007  -2.999  13.847 . . . 1.0 . . . . . . . . . . . . A . 21 HIS CE1  . . . . . . . . . rr_2jsp 1 
       .  1 .  319 . 1 1 21 HIS CG   C   7.338  -2.378  12.627 . . . 1.0 . . . . . . . . . . . . A . 21 HIS CG   . . . . . . . . . rr_2jsp 1 
       .  1 .  320 . 1 1 21 HIS H    H   5.527  -4.878  11.787 . . . 1.0 . . . . . . . . . . . . A . 21 HIS H    . . . . . . . . . rr_2jsp 1 
       .  1 .  321 . 1 1 21 HIS HA   H   4.114  -2.344  11.369 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HA   . . . . . . . . . rr_2jsp 1 
       .  1 .  322 . 1 1 21 HIS HB2  H   6.044  -0.983  11.686 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HB2  . . . . . . . . . rr_2jsp 1 
       .  1 .  323 . 1 1 21 HIS HB3  H   5.402  -1.717  13.197 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HB3  . . . . . . . . . rr_2jsp 1 
       .  1 .  324 . 1 1 21 HIS HD1  H   7.055  -3.495  14.363 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HD1  . . . . . . . . . rr_2jsp 1 
       .  1 .  325 . 1 1 21 HIS HD2  H   8.528  -1.467  11.080 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HD2  . . . . . . . . . rr_2jsp 1 
       .  1 .  326 . 1 1 21 HIS HE1  H   9.593  -3.427  14.660 . . . 1.0 . . . . . . . . . . . . A . 21 HIS HE1  . . . . . . . . . rr_2jsp 1 
       .  1 .    1 . 1 1 21 HIS N    N   4.894  -4.166  12.094 . . . 1.0 . . . . . . . . . . . . A . 21 HIS N    . . . . . . . . . rr_2jsp 1 
       .  1 .    2 . 1 1 21 HIS ND1  N   7.682  -3.010  13.746 . . . 1.0 . . . . . . . . . . . . A . 21 HIS ND1  . . . . . . . . . rr_2jsp 1 
       .  1 .    3 . 1 1 21 HIS NE2  N   9.489  -2.376  12.778 . . . 1.0 . . . . . . . . . . . . A . 21 HIS NE2  . . . . . . . . . rr_2jsp 1 
       .  1 .    4 . 1 1 21 HIS O    O   6.438  -3.944   9.761 . . . 1.0 . . . . . . . . . . . . A . 21 HIS O    . . . . . . . . . rr_2jsp 1 

Original comment by schulte....@gmail.com on 22 Dec 2010 at 3:39

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Original comment by jurge...@gmail.com on 3 Mar 2011 at 3:43

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I just checked this with the updated ccpn. It is still a  problem. It's a weird 
one.

Original comment by schulte....@gmail.com on 3 Mar 2011 at 4:16

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I'll check this on my development setup.

Original comment by jurge...@gmail.com on 4 Mar 2011 at 8:47

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Ok, the problem reproduces here. NB it doesn't break the NRG processing but is 
indeed a problem.

D. does it break something on your side?
W. can you easily fix this?

Original comment by jurge...@gmail.com on 4 Mar 2011 at 9:38

• Added labels: Priority-Low
• Removed labels: Priority-Medium

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It will when (if) we try loading this into RDB.

Dimitri

Original comment by dmitri.m...@gmail.com on 4 Mar 2011 at 3:40

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It looks like we're not able to fix this for now.

Original comment by jurge...@gmail.com on 24 Feb 2012 at 9:57

• Changed state: WontFixForNow

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Fine with me. We will look at these wontfixfornows when we have a chance to 
overhaul the whole shebang.

Original comment by schulte....@gmail.com on 24 Feb 2012 at 4:01