Hi John,
Here are some more details on the refinement situation: it is possible for a piece of duplex DNA to be positioned in two conformations in the crystal, and it appears that both conformations are occupied with roughly the same occupancy. The sequence is not completely palindromic, so at some positions a different base is present depending on the random orientation of the DNA. However, the phosphate and ribose atoms occupy the same positions regardless of the orientation, and I want to enforce this.
I see; this is what Nat was guessing. Could you send me (not the list) the pdb file of this structure?
Yes, that sounds like it would work.
A potential downside is that people have to be careful excluding non-matching sidechain atoms.
Perhaps it could be that there is an override option after an error message.
Sounds like we need two new options, match_conformers=True and match_resid_only=True. Ralf