Zero occupancy and bad geometry

From: Joel Tyndall
Date: 7 March 2012 01:03

Hi folks,

I have a case where I have changed the occupancy of a lysine residue to 0.00 and after refinement the geometry is wrong, i.e. one of the bonds is extended (no connectivity in Coot and length is 1.76A). I have seen this before with other residues and a previous data set. The break in this case occurs between CG (1.00 occ) and CD (0.00 occ).

Any thoughts on why this is occurring?

Cheers

Joel

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Joel Tyndall, PhD

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From: Eleanor Dodson
Coordinates with occ > 0 are refined and may shift - cds with occ=0 stay where they were.. This may result in bad geometry of course. You can "reglise" the whole residue in coot but that doesnt do nything except make it look tidier.. Eleanor

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Professor Eleanor Dodson