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Older entry fails in FC because compound was not found. #196

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run entry with just a single model will do. Look at output at:

What is the expected output? What do you see instead?

http://nmr.cmbi.ru.nl/~jd/viavia/NRG/ and
http://nmr.cmbi.ru.nl/~jd/viavia/ccpn_tmp/data/

specifically:
http://nmr.cmbi.ru.nl/~jd/viavia/NRG/link/2jn3/2jn3_merge.log
where this issue has been identified before.
and perhaps:
http://nmr.cmbi.ru.nl/~jd/viavia/NRG/Results/perEntry/2jn3.log

Original issue reported on code.google.com by jurge...@gmail.com on 24 Mar 2009 at 8:28

GoogleCodeExporter commented 9 years ago 
Runs through for me - probably because chemComp is available. Still mapping 
issues
with this entry though (not all resonances are linked).

Original comment by wfvran...@gmail.com on 27 Mar 2009 at 9:06

GoogleCodeExporter commented 9 years ago 
I updated the chemComps just now but the results are still the same.
Can you id the xml file you use for this?

Original comment by jurge...@gmail.com on 2 Apr 2009 at 9:21

GoogleCodeExporter commented 9 years ago 
Still fails for me with the following log.

Original comment by jurge...@gmail.com on 4 Aug 2009 at 4:29

Attachments:

GoogleCodeExporter commented 9 years ago 
It definitely finds and loads the jn3 chemComp to create the molecule - the 
problem
here is that the coordinates for the chemComps are not read in and set 
correctly. Not
sure why, will try to find that out today.

Anyway there are also resonance problems for this entry, I suspect there's 
different
sequence numberings in the restraint files?

Original comment by wfvran...@gmail.com on 5 Aug 2009 at 8:35

GoogleCodeExporter commented 9 years ago 
OK I fixed the coordinate problem - update DataFormat.py again!

Original comment by wfvran...@gmail.com on 5 Aug 2009 at 10:14

GoogleCodeExporter commented 9 years ago 
Thanks Wim!

Original comment by jurge...@gmail.com on 5 Aug 2009 at 4:01

GoogleCodeExporter commented 9 years ago 
Chris, can you move this into production? Or is there another reason that 2jn3 
did make it to DOCR?

Original comment by jurge...@gmail.com on 1 Dec 2009 at 2:14

GoogleCodeExporter commented 9 years ago 
This is still a problem. I just tried rerunning it and got this:

ERROR 2jn3 found in merge log file; will now grep for ERROR again.
    >   ERROR: molecule CHENODEOXYCHOLIC ACID does not have any molResidues! Chain creation aborted...

Original comment by schulte....@gmail.com on 18 Mar 2010 at 3:03

GoogleCodeExporter commented 9 years ago 
Just reran this, I get:

  ChemComp file other+Jn3+msd_ccpnRef_2007-12-11-10-17-19_00010.xml copied to /Users/wim/workspace/stable/all/data/recoord/
2jn3/linkNmrStarData/ccp/molecule/ChemComp...
Created molecule CHENODEOXYCHOLIC_ACID (molType other, 1 chemComps)

so working without problems... is this Jn3 file in your chemComp directory?

Original comment by wfvran...@gmail.com on 23 Jul 2010 at 10:09

GoogleCodeExporter commented 9 years ago 
No, Jn3 isn't in the chemcomp directory, which is confusing because I updated 
it this week.

I'll try updating it again. Also, should I update ccpn and recoord? If so, 
should I use the stable option, or are there changes in the latest version that 
I should have?

Original comment by schulte....@gmail.com on 23 Jul 2010 at 1:37

GoogleCodeExporter commented 9 years ago 
Well it's definitely in there... try:

http://ccpforge.cse.rl.ac.uk/plugins/scmcvs/cvsweb.php/~checkout~/ccpn-chemcomp/
data/pdbe/chemComp/archive/ChemComp/other/J/other%2BJn3%2Bmsd_ccpnRef_2007-12-11
-10-17-19_00010.xml?only_with_tag=MAIN;content-type=text%2Fplain;cvsroot=ccpn-ch
emcomp

Original comment by wfvran...@gmail.com on 23 Jul 2010 at 1:48

GoogleCodeExporter commented 9 years ago 
I see it now. When I didn't find it, I was in ChemComp and did an 'ls */*Jn3*'. 
I didn't realize that the 'other' directory had subdirs 0-Z.

I'll try 2jn3 again and see what happens.

Original comment by schulte....@gmail.com on 23 Jul 2010 at 1:59

GoogleCodeExporter commented 9 years ago 
It's working. Thanks all. There was a presetDict entry for it with nothing but 
a comment that seemed to be crashing the processing (I don't understand that), 
but when I commented it out, it worked fine.

Eventually, I had to go with this mapping:

     'forceChainMappings': [['A', 'A', 1, 0], ['A', ' ', 1, 0], ['B', ' ', 1, 129], ['C', ' ', 1, 130]],

You can close this issue if you want. I'm going to take a look at issue 251 
now. I also have a new amber entry, 2kwg, that is giving me some problems.

Original comment by schulte....@gmail.com on 23 Jul 2010 at 2:25

GoogleCodeExporter commented 9 years ago

Original comment by wfvran...@gmail.com on 23 Jul 2010 at 2:28