Does FC recognize His HD?

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I was getting conversion errors for 
His HD# and His HE#

At first I tried converting to HD* and HE*, but there were still errors, so I 
checked IUPAC. Both HE 
and HD on a his have a carbon pairing and a nitrogen pairing. Obviously, the 
HND and HNE won't 
be recognized, so I mapped to:
'His': [ ["HD#","HD2"], ["HE#","HE1"] ]

That worked for the HE, but not HD. 

Original issue reported on code.google.com by schulte....@gmail.com on 27 Feb 2009 at 3:39

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There are no HD* or HE* atom sets for histidine - they don't make sense as the 
atoms
are chemically different. It would be like grouping an HN with an HA.

The (nitrogen bound) HE2 and HD1 atoms are present (or not) depending on the
protonation state of the histidine in the CCPN project - I set this based on the
coordinate data. I'm surprised it's not finding the HD2 atom, though - that is 
always
there. Was this done on the new machine or on tang (just to find the .log file).

Original comment by wfvran...@gmail.com on 27 Feb 2009 at 3:49

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I checked the atom's presence in the coordinate list and it's there.
Done on tang.

Original comment by jurge...@gmail.com on 27 Feb 2009 at 3:51

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Wim, can you take a look at this again?

Original comment by jurge...@gmail.com on 31 Mar 2009 at 8:57

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Original comment by jurge...@gmail.com on 31 Mar 2009 at 9:04

• Added labels: Component-FormatConverter

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Issue 204 has been merged into this issue.

Original comment by jurge...@gmail.com on 3 Apr 2009 at 8:25

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When I use these settings (same for 2vy5):

'2vy4': {

  'authors': ['Test'],
  'comment': "",

  'linkResonances': {

   'keywds': {
     'forceChainMappings': [['A', ' ', 1, 50],['B',' ',1, 1087]],
     'addNameMappings': {'His': [['HE#','HE1']]},
      },
    },
  },

It all works for me, except for some HD1 protons for His 64 and 74, but these 
are not
present in the coordinates so the code selects the deprotonated default states 
when
creating the sequence. I could in principle add an option to set the protonation
state in the presetDict if this is a problem.

Original comment by wfvran...@gmail.com on 7 Apr 2009 at 9:18

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How difficult would it be for the software to figure out if it was protonated, 
depending on whether or not the 
protons were there? 

I have similar issues with other small molecules. Databases give one a 
particular atom count, connectivity, 
conformation, and nomenclature for any particular molecule, but nature isn't 
quite like that.

Original comment by schulte....@gmail.com on 7 Apr 2009 at 1:28

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You mean in general? Very difficult - it depends on many circumstances (pH, 
binding,
conformation, ...) in the end whether a particular atom in a molecule is 
protonated
or not. Anyway for our problem I could probably change the protonation state 
while
running linkResonances... although that might turn out to be a nightmare (it's 
code
I'd rather not touch if I can avoid it). I'll have a look.

Original comment by wfvran...@gmail.com on 7 Apr 2009 at 1:40

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It would be easy enough for me to set a flag that says to use a protonated 
molecule - or any other conformation 
for that matter. My main concern is that it makes the process more complicated 
and difficult to teach.

Original comment by schulte....@gmail.com on 7 Apr 2009 at 1:46

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True. Anyway it turned out to be reasonably straightforward, I think, although 
the
changes are in a crucial bit of code so other things could possibly fall over 
because
of this change. Hard to test.

Anyway update the following files in the CCPN SourceForge rep:

python/ccp/general/Util.py
python/ccpnmr/format/process/linkResonances.py

and it automatically resets the protonation state for 2vy4 and 2vy5.

Original comment by wfvran...@gmail.com on 7 Apr 2009 at 2:43

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Can you give this a shot now that I updated on tang today?

Original comment by jurge...@gmail.com on 9 Apr 2009 at 3:05

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We've got complete conversion now. Good job.

Original comment by schulte....@gmail.com on 9 Apr 2009 at 4:18

• Changed state: Fixed