Dear Alastair, I think that refinement programs usually interpret chain ids A, B, ... the way shelxl uses PART 1, 2, ... and a blank chain ID corresponds to PART 0. You may have to assign different residue numbers to CA and HOH, but I think this is also the case for shelxl.
Does this resolve your problem? Best, Tim On 05/14/2014 07:48 PM, Alastair Fyfe wrote: > 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 > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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