BMRB contains empty CS list although non-zero list is mentioned in header.

jakesylvestre / cing

Automatically exported from code.google.com/p/cing

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BMRB contains empty CS list although non-zero list is mentioned in header. #288

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?
1. Import BMRB CS into NRG-CING.

What is the expected output? What do you see instead?
http://nmr.cmbi.ru.nl/NRG-CING/prep/S/k1/2k1b/2k1b_starCS2Ccpn.log
using:
/Users/jd/wattosTestingPlatform/bmrb/rsync/bmr15674/bmr15674_21.str

The empty CS list has no tags which crashes FC.
Chris, can you ask for an update of the BMRB file?

Original issue reported on code.google.com by jurge...@gmail.com on 24 Feb 2011 at 8:32

GoogleCodeExporter commented 9 years ago

I take it, this is what you're accessing. It sure looks empty to me. I'll pass 
it on.

save_assigned_chem_shift_list_1
   _Saveframe_category               assigned_chemical_shifts

   _Details                          .

   loop_
      _Software_label

      $CYANA 

   stop_

   loop_
      _Experiment_label

      '3D HNCO'         
      '3D HBHA(CO)NH'   
      '3D CBCA(CO)NH'   
      '3D HNCA'         
      '3D HCCH-TOCSY'   
      '3D (H)CCH-TOCSY' 
      '3D 1H-13C NOESY' 
      '3D 1H-15N NOESY' 

   stop_

   loop_
      _Sample_label

      $sample_1 

   stop_

   _Sample_conditions_label         $sample_conditions_1
   _Chem_shift_reference_set_label  $chemical_shift_reference_1
   _Text_data_format                 .
   _Text_data                        .

save_

Original comment by schulte....@gmail.com on 24 Feb 2011 at 8:51

GoogleCodeExporter commented 9 years ago

Thanks Chris!

Original comment by jurge...@gmail.com on 24 Feb 2011 at 8:53

GoogleCodeExporter commented 9 years ago

Update from Hongyang:

Hi,

The entry has been corrected, and released again.  The updated version should 
be available in the public domain tomorrow.

I tried to figure out the reason for this problem.  It was deposited and 
processed as 3.1 entry, and released 2008-03-05.  The first back-up file of 2.1 
version (bmr15674_21.str-old-11) contains the data loop.  The entry was updated 
2010-05-18 by Danielle.  The files in ../clean/ are under Dimitri's name.  My 
guess is that this entry was released in one of the batch updates by script (in 
the projects to update system names, natural source, etc.), rather than 
individually and manually.

Anyway, Steve will do a query to find if there might be other similar cases.

Thank you,
Hongyang

Original comment by schulte....@gmail.com on 24 Feb 2011 at 10:02

GoogleCodeExporter commented 9 years ago

Thanks guys, much appreciated.

Original comment by jurge...@gmail.com on 24 Feb 2011 at 10:28

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 31 Mar 2011 at 1:52

GoogleCodeExporter commented 9 years ago

Nicely updated as well in:
http://nmr.cmbi.ru.nl/NRG-CING/data/k1/2k1b/2k1b.cing/2k1b/HTML/Molecule/atoms.h
tml

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:23

Changed state: Fixed