[phenixbb] radiation damaged residues occupancy refinement

Nathaniel Echols nechols at lbl.gov
Tue Nov 20 05:27:24 PST 2012

On Tue, Nov 20, 2012 at 3:29 AM, Mikalai Lapkouski <gort105 at gmail.com>wrote:

> I tried to set the occupancy for those atoms 0.8 and refine individually.
> But obviously occupancies for those atoms are individually refined to
> different values which I dont think is the right way. Is there a way of how
> to refine occupancies for those atoms so that they remain identical after
> refinement (say all have 0.6)?

I'm a little surprised that the atoms within a residue aren't already
constrained to be the same occupancy, but that may only apply if they're
labeled as an alternate conformer.  But I think all you need to do this is
to define them as a constrained group, as described here:


(scroll down to Example 4 for the messy details.)  If you're using the GUI,
you can find the relevant controls by selecting "Occupancy" from the menu
labeled "Modify atom selections for" below the strategy choices.

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