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

Pavel Afonine pafonine at lbl.gov
Fri Aug 9 11:33:23 PDT 2013

Hi Ed,

this should work in next nightly build.


On 8/8/13 8:42 PM, Edward A. Berry wrote:
> 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.
> ed
> 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list