Can't seem to get FC to read CS for 'normal' DNA.

[GoogleCodeExporter]

What steps will reproduce the problem?

1. The DNA residue labels have recently been updated in the NMR-STAR 2.1.1 
files, eg. for 1cjg in 

http://www.bmrb.wisc.edu/ftp/pub/bmrb/entry_directories/bmr4813/bmr4813_21.str

   loop_
      _Revision_date
      _Revision_keyword
      _Revision_author
      _Revision_detail

      2010-07-14 update   BMRB   'update DNA residue label to two-letter code' 

FC fails to read it automatically:
http://nmr.cmbi.ru.nl/devNRG-CING/data/cj/1cjg/log_nrgCing/1cjg_2011-02-04_13-41
-07.log
http://nmr.cmbi.ru.nl/devNRG-CING/prep/S/cj/1cjg/1cjg_starCS2Ccpn.log

Note that I've setup a separate area for development at:
http://nmr.cmbi.ru.nl/devNRG-CING 
that follows the same setup as the production site at:
http://nmr.cmbi.ru.nl/NRG-CING

Original issue reported on code.google.com by jurge...@gmail.com on 4 Feb 2011 at 12:44

[GoogleCodeExporter]

Fixed, update pdbe/adatah/NmrStar.py from SF CVS.

This problem is corrected both on the automatic mapping stage (this example 
will work straight away without mappings) and on the stage where mappings are 
forced from the presetDict.

Note that in this example the mapping is wrong, it should be 3,0 for the 
protein (as listed in the automatic mapping in the comment).

Original comment by wfvran...@gmail.com on 22 Feb 2011 at 3:11

[GoogleCodeExporter]

Nice, now I also understand how I can use the directives to duplicate the 
resonances for a e.g. symmetric dimer. And, indeed, the directives are not 
needed here. Great conversion already at 98%.

jd:Stella/cingTmp/ python -u $CINGROOT/python/cing/NRG/nrgCing.py 1cjg 
prepareEntry 0 1 1
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r934)       
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: Stella.local (darwin/64bit/2cores/2.6.6)   at:  (5237) Wed 
Feb 23 16:17:22 2011

Going to destination: prepareEntry with(out) on entry_code 1cjg with extra 
arguments ['0', '1', '1']
interactive            interactive run is fast use zero for production   False
convertMmCifCoor       Start from mmCIF                                  0
convertMrRestraints    Start from DOCR                                   1
convertStarCS          Adds STAR CS to Ccpn with XXXX                    1
Doing                                                                 1cjg
  DOCR CCPN
  star CS
Testing completeness of FC merge by comparing input STAR with output CING counts
Python nmrStar reader courtesy of Jurgen Doreleijers (BMRB) - with 
modifications added.
Parsing STAR file: 
/Users/jd/wattosTestingPlatform/bmrb/rsync/bmr4813/bmr4813_21.str
Done [87] subs with comment at beginning of line
Done [412] subs with comment not at beginning of line
Parsed: [47] datanodes (top level count only)
BMRB AssignmentCountMap( 13C = 169, 15N = 66, 1H = 513, 31P = 0 )
==> Importing data from Ccpn project "1cjg"
Non-standard (residues and their) atoms added:
DC  : [ 22]
DG  : [ 1]
LEU : [ 62]
==> Calculating rmsd's (ranges: A.1-22,B.1-22,C.1-62,D.1-62, models: 0-10)
==> Ccpn molecule '1cjg' imported
DEBUG: Now in _getShiftAtomNameMapping for ccpnShiftList 
(<ccp.nmr.Nmr.ShiftList ['1cjg', 1]>)
==> CCPN ShiftList 'bmr4813_21.str' imported from CCPN Nmr project '1cjg'
==> Count of (pseudo-)atom with resonances updated 570
==> Count of resonanceSetDone 534 (<= above count)
DEBUG: Now in _getShiftAtomNameMapping for ccpnShiftList 
(<ccp.nmr.Nmr.ShiftList ['1cjg', 2]>)
==> CCPN ShiftList 'bmr4813_21.str' imported from CCPN Nmr project '1cjg'
==> Count of (pseudo-)atom with resonances updated 166
==> Count of resonanceSetDone 165 (<= above count)
==> Ccpn project imported
Found fraction of at least   cutoff 0.05 at 0.98  overall (STAR/CING: 748/730)
Done with 1cjg
CING started at : Wed Feb 23 16:17:17 2011
CING stopped at : Wed Feb 23 16:18:08 2011
CING took       : 50.310 s

Original comment by jurge...@gmail.com on 23 Feb 2011 at 3:20

• Changed state: Fixed