Non-standard residues crash format converter

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We received an amber entry last week where the authors actually included
the pdb file. Unfortunately, all of the residues were non-standard and
the format converter couldn't handle it.

This might be fixable by updating the chem-comp. I'll try that now.  I'm 
attaching the log file for 
more specifics

Original issue reported on code.google.com by schulte....@gmail.com on 18 May 2010 at 1:34

Attachments:

• 2kvj_merge.log

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I just updated ccpn-chemcomp and tried this again. It didn't work. I noticed 
that the restraints label the residues 
as 
GPM, CPM APM TPM 
but the cif and pdb files label them as 
40A, 40G, 40C, and 40T

Original comment by schulte....@gmail.com on 18 May 2010 at 2:07

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Wim, could you take a look at this when you're in Madison perhaps.

Original comment by jurge...@gmail.com on 20 May 2010 at 1:44

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You should be able to map this using the presetDict... so something like:

     'forceChainMappings': [
                             ['A', '2kvj_amber00', 2, 0],
                             ['B', '2kvj_amber00', 2, 10],
                           ],

The different chemComp name shouldn't make a difference if the chain is mapped 
this way - it should just try and match directly I think.

Original comment by wfvran...@gmail.com on 23 Jul 2010 at 10:35

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Thanks Wim. This is working now. I needed to add these mappings:

        'addNameMappings':{
               '40g': [ ["H1","HN1"], ["H1'","HN1'"], ["H22","H22'"], ["H8'1","H18'"], ["H8'2","H28'"], ["HM1","H2M"], ["HM2","H2MA"], ["HM3","H2MB"] ],
               '40c': [ ["H1'","HN1'"], ["H41","HN4"], ["H42","HN4A"], ["H8'1","H18'"], ["H8'2","H28'"], ["HM1","H2M"], ["HM2","H2MA"], ["HM3","H2MB"] ],
               '40a': [ ["H1'","HN1'"], ["H61","HN6*"], ["H8'1","H18'"], ["H8'2","H28'"], ["HM1","H2M"], ["HM2","H2MA"], ["HM3","H2MB"] ],
               '40t': [ ["H1'","HN1'"], ["H3","HN3"], ["H71","H7"], ["H72","H7A"], ["H73","H7B"], ["H8'1","HXT'"], ["H8'2","H28'"], ["HM1","H2M"], ["HM2","H2MA"], ["HM3","H2MB"] ],
         },

Before closing this, I would like to have a go at 2kwg and see if something 
similar is going on.

Original comment by schulte....@gmail.com on 23 Jul 2010 at 3:47

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I think this is the same problem. At least one chemcomp for 2kwg (Af2) is 
missing from the library, and conversion crashes. Attached is the log file. 

This little bit:
AttributeError: NmrStarFormat instance has no attribute 
'ignoreChemCompsWithNoSysNames'
doesn't seem right.

Original comment by schulte....@gmail.com on 23 Jul 2010 at 5:18

Attachments:

• 2kwg_merge.log

[GoogleCodeExporter]

This is now fixed and checked in, plus fixed another bug that then came up.

Update:

ccpnmr/format/converters/DataFormat.py
ccp/format/general/formatIO.py

and this one should work (does for me!)

Original comment by wfvran...@gmail.com on 5 Aug 2010 at 1:20

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Is this on the stable release, or should I just update?

Original comment by schulte....@gmail.com on 5 Aug 2010 at 1:23

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Yep on stable, just update those files.

Original comment by wfvran...@gmail.com on 5 Aug 2010 at 1:31

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Fantastic! 2kwg now processes completely, and with a few name mappings, gets 
100% conversion. What did you fix? 

I think you can close this if everybody's satisfied.

Original comment by schulte....@gmail.com on 5 Aug 2010 at 2:46

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Yep, glad it's working! It was just a couple of small fixes... just had to find 
the time to look at it and figure out where the niggles occurred.

Original comment by wfvran...@gmail.com on 5 Aug 2010 at 3:12

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Cool, I get the honors to close one more problem. Thanks guys!

Original comment by jurge...@gmail.com on 22 Sep 2010 at 6:38

• Changed state: Fixed