On the subject of not (willfully) contaminating the pdb database, any suggestions on the following are appreciated. I am refining the solvent structure of some RNAs. Inspection of difference and anomalous difference maps suggests that some closely-spaced positions are alternately taken by distinct entities with partial occupancy. One pattern suggests partial occupancy by a Ca++ ion with a nearby site partially occupied by water (confirmed by an anomalous peak only for the former). I am refining this with shelxl and expressing this in the ins file is straightforward (and I'd like to express much gratitude for the multi-core version of shelxl!). However it's not clear to me how to say this in PDBese : choosing the HETATM residue name as either HOH or CA and assigning alternate positions with HOH and CA in the atom name field seems to make trouble for pdb reader software, eg mmdb.
thanks,
Alastair Fyfe

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