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Chem_comp not being read for non-standard DNA #285

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
The ccpn chem_comp xml files exist for residue 63h and 63g, but Format 
Converter isn't reading them. I get the following message in the log file. Is 
there a setting to check for the path for a nucleic acid chem_comp?:

Error: Cannot find ChemComp XML file other, 63h.
    ######################################
    # Warning: autocreating chemComp 63h #
    ######################################

  Made linkEnd prev
  Made linkEnd next
Created 63h,DNA: neutral,none
Created 63h,DNA: neutral,middle
Created 63h,DNA: neutral,end
Created 63h,DNA: neutral,start
start generating output :  ccp.molecule.ChemComp.NonStdChemComp
  Warning: selected CUSTOM naming system for chemComp DNA,63h because PDB_REMED naming system does not exist.
Created molecule DNA__5__D__CP_GP_TP_AP_CP__63H_P_CP_AP_TP_GP_C__3__ (molType 
DNA, 11 chemComps)
Created molecule DNA__5__D__GP_CP_AP_TP_GP_AP_GP_TP_AP_CP_G__3__ (molType DNA, 
11 chemComps)
Created chain 'A', start seqCode 1, end seqCode 11, molecule 
'DNA__5__D__CP_GP_TP_AP_CP__63H_P_CP_AP_TP_GP_C__3__'...
Created chain 'B', start seqCode 1, end seqCode 11, molecule 
'DNA__5__D__GP_CP_AP_TP_GP_AP_GP_TP_AP_CP_G__3__'...

Original issue reported on code.google.com by schulte....@gmail.com on 12 Jul 2012 at 2:19

GoogleCodeExporter commented 9 years ago 
Hey Chris, sorry it took me a while to look at this. Anyway the problem is that 
the molecular type (molType) of 63h is assumed to be 'other', apparently, from 
the line:

Error: Cannot find ChemComp XML file other, 63h.

so you're saying that 63h exists as XML file but as molecular type DNA, right? 
In that case there's an issue with the molecular type assignment, don't think 
that's customisable (yet).

Also, you're sure the chemCompOverview.py dictionary in ccp/general is updated?

Original comment by wfvran...@gmail.com on 27 Jul 2012 at 12:53