On Fri, Nov 30, 2012 at 6:50 AM, Morten Groftehauge <mortengroftehauge.work@gmail.com> wrote:

Hi guys,

Two quick questions about DEN refinement:
1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind.

A gamma value of 0 corresponds to a non-deformable network, meaning that the model strictly follows the distances derived from the reference. It could be that model should have the same basic conformation as the reference, and that has then given the best result. It's only necessary to try it again if you don't think the overall conformation of your model has converged, or if you wanted to try some different settings. If you haven't tried running with different random seeds, I would suggest trying that first.

2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know.

Correct, this means that the diffraction data that you are refining against drive your model to a conformation that differs from that of the reference model, and that conformation is preferred. I would also suggest trying with different random seeds, just to see if you arrive at the same answer.

Jeff

And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them.

Cheers,
Morten

--
Morten K Grøftehauge, PhD
Pohl Group
Durham University

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