C-terminal atom names not written out correctly

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Eldon reported:

"Just took a look at a remediated restraint file from the BMRB web site and
found that the terminal atoms (both N and C) in the atomic coordinate data
do not match the chem comp atom names. These terminal atoms have the
original IUPAC nomenclature, but not the nomenclature that was later agreed
upon as acceptable in PDB files (OXT, etc.). This will need to be changed
so that the nomenclature matches the PDB chem comp library."

This is now fixed and available, but need to update:

python/msd/nmrStar/IO/Ccpn_To_NmrStar.py

I've tested it on a couple of entries and it seems solid, but obviously let
me know of any problems. Note that the export of the NMR-STAR will be
slightly slower because I need to do extra searches for the remediated PDB
atom names.

Also, I assume you also want to use these atom names for chemical shifts,
restraints, etc.?

Original issue reported on code.google.com by wfvran...@gmail.com on 28 Jul 2009 at 11:15

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I need to check on this.

Yes, please have the atom names consistent through out. Thanks Wim!

Original comment by jurge...@gmail.com on 29 Jul 2009 at 12:54

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OK I doublechecked, should always be using the remediated PDB atom names 
throughout.
Make sure to update the SF repository directory:

python/msd/nmrStar/IO/

Let me know if there's any problems!

Original comment by wfvran...@gmail.com on 29 Jul 2009 at 1:34

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Still not correct when tested with the new code today when testing with new 
entry 2kc6
found first model last residue oxygen to be in star:

        1 .   705 . 1 1 52 CYS O    O   0.841 -13.029  -5.427 . . . 1.0 . . . . . . . . . . . . . . . . . A . . 52 CYS O    . . 
rr_2kc6 1

Not updated the NRG production version with it.

Original comment by jurge...@gmail.com on 4 Aug 2009 at 4:19

• Added labels: Component-FormatConverter, Entry-2k6c

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Can you check whether the sequence in the BMRB file is longer than the PDB one? 
That
might be the issue here... if it was still using IUPAC names the atom would be 
O'.

Original comment by wfvran...@gmail.com on 5 Aug 2009 at 8:26

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The input star file with just one model is attached.
NB it's 2kc6 not 2k6c.

The 52 CYS is the last residue in the PDB seqres too.

Original comment by jurge...@gmail.com on 5 Aug 2009 at 4:26

• Added labels: Entry-2kc6
• Removed labels: Entry-2k6c

Attachments:

• 2kc6_merge.str

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The problem is in the original file: it doesn't have an OXT atom. The NMR-STAR 
output
is fine (right atom names).

Original comment by wfvran...@gmail.com on 6 Aug 2009 at 11:10

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It has a O atom there, see comment 3.
In mmCIF it's the same:
ATOM 700   O O    . CYS A 1 52 ? 0.841   -13.029 -5.427  1.00 0.00 ? ? ? ? ? ? 
52 CYS A O    1

So FC doesn't rename it? That's fine with me, I'm closing the issue.

Original comment by jurge...@gmail.com on 6 Aug 2009 at 3:35

• Changed state: Invalid

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Well you've got two oxygens at the C terminus: O and OXT. I guess in this case 
the
file contains the O and not the OXT - that came from the mmCIF after all... .

Original comment by wfvran...@gmail.com on 6 Aug 2009 at 7:38

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Hi,

These are the files with the broken nomenclature in the remediated restraints 
files:

2kcz_linked.str
2kdd_linked.str
2kfx_linked.str

These file were taken off the BMRB web site from the 
beta_wwPDB_remediated_restraints directory.

Thanks,

Original comment by schulte....@gmail.com on 7 Aug 2009 at 1:24

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I'm changing the status back to started until further notice.

Original comment by schulte....@gmail.com on 7 Aug 2009 at 1:25

• Changed state: Started

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Just going through some old email - can you doublecheck that the problem is not
because the sequence is longer than the coordinate list? Anyway I'm pretty 
certain
this is all working from my perspective.

Original comment by wfvran...@gmail.com on 14 Nov 2009 at 4:51

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I just checked this again. 

2kcz_linked.str
2kdd_linked.str
2kfx_linked.str
 Seem to be ok. I'm going to go ahead and close this.

Original comment by schulte....@gmail.com on 15 Jun 2010 at 6:08

• Changed state: Fixed