[phenixbb] is phenix trying to polymerize b-octyl glucoside?

Edward A. Berry BerryE at upstate.edu
Thu Aug 8 20:42:43 PDT 2013

I'm refining a model with some molecules of the detergent b-octyl glucoside (BOG).
I got BOG.cif from a recent ccp4 library, so not sure if this is a suggestion for phenix or ccp4, but:
If two BOG molecules are consecutive in the pdb file, phenix stops in setup because it can't find atom HO1 to delete. 
Even if I had H's in my model there would be no HO1 because O1 is in glycosidic linkage with the octyl chain. I'm 
guessing phenix somehow realizes there is a sugar and when two are consecutive it autogenerates a link to make a 
glycosidic bond between them - not appropriate in the case of BOG. easy work around is to intersperse with non-sugar 
molecules, but if there is a better way, I'll take it.

RuntimeError: delete_atom_in_place: unknown atom_id: HO1
apply_mod failure:
   pdbres="BOG R  18 " segid="R   "
   comp id: BOG
   mod id: DEL-O1

   Version: dev
   Release tag: 1420
   Platform: intel-linux-2.6-x86_64 linux

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