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NMR-STAR file with on author sequence code #214

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I was just working on some projects with ligands, and in 5gcn there are
these lines for the distance constraints (in the joined restr/coord file):

        890   1   2   .   .   .   .   .   .   .   .   .     164   .   HE* 
  parsed_5gcn   2   
        891   1   1   .   .   .   .   .   .   .   .   .     166   .   HA  
  parsed_5gcn   2   
        891   1   2   .   .   .   .   .   .   .   .   .     166   .   HB* 
  parsed_5gcn   2   
        892   1   1   .   .   .   .   .   .   .   .   COA      .   .   H1'
   parsed_5gcn   2   
        892   1   2   .   .   .   .   .   .   .   .   COA      .   .   H2 
   parsed_5gcn   2   
        893   1   1   .   .   .   .   .   .   .   .   COA      .   .   H1'
   parsed_5gcn   2   
        893   1   2   .   .   .   .   .   .   .   .   COA      .   .   H2'
   parsed_5gcn   2   
        894   1   1   .   .   .   .   .   .   .   .   COA      .   .   H1'
   parsed_5gcn   2   

So the COA chain code does not have any sequence code, which makes my code
not work for this ligand. I can 'hack' something so that I set it to 1 (it
will then work), but not sure if this may create problems - I guess my
question is whether this is a valid way to store the data in NMR-STAR or not.

Original issue reported on code.google.com by wfvran...@gmail.com on 15 May 2009 at 2:02

GoogleCodeExporter commented 9 years ago 
The parsed data didn't have it. This is very well possible with xplor e.g.

assi ( resi  32 and name HA   ) ( segid COA and name HP5* ) 0 0 5.0

It is not valid NMR-STAR because the data from author hasn't been linked yet.

Out of curiosity, can FC handle these wild types of atom selections when 
importing xplor to ccpn? I am asking 
because we're trying to integrate cing with xplor-nih at some point. Question 
is to do it thru Wattos or FC or 
rewrite the whole javacc parser thing again inside CING itself.

Original comment by jurge...@gmail.com on 15 May 2009 at 2:17

GoogleCodeExporter commented 9 years ago 
Nope, the FC has a decent CNS/XPLOR parser but not that much provision for 
and/or/xor
type stuff. This could be extended, of course... depends on where you need the 
data
in the end.

Original comment by wfvran...@gmail.com on 15 May 2009 at 2:29

GoogleCodeExporter commented 9 years ago 
I thought so. The one in wattos can do the and/or stuff reasonably well but so 
perhaps we do need to go thru it.

Original comment by jurge...@gmail.com on 15 May 2009 at 2:32