[ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

[Paul Paukstelis]

Greetings,

We have been working on a few DNA crystals in which the asymmetric unit 
contains a stoichiometric (or nearly so) mixture of two similar but 
distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but 
for a few of these there are some hints from the density for two 
different bases at the same position. I'm curious what the best way to 
approach refinement would be in this case. Alternate conformation 
doesn't really work since the residues have different nucleobases. 
Having two complete chains with 0.5 occupancy is overkill since there 
are only 2 (or 4) positions in which the sequence differs. I tried just 
adding a second chain for the varying residues at 0.5 occupancy and 
adding link records to the original chain, however this doesn't seem to 
respect geometry of the phosphodiester for the flanking residues. I 
would appreciate suggestions or any examples in the PDB that might set 
me in the right direction.

--paul