[phenixbb] Restraining altloc related atoms during refinement

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu May 20 11:42:43 PDT 2010

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


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