Hi Jan,
Did you run your DEN refinement with optimize=True? If you haven't run the
grid optimization, it's unlikely that you found the optimal gamma/weight
pair for your specific case.
Also, I would recommend not using reference model restraints while running
DEN refinement. This could potentially prevent your model from "deforming",
if you are restraining it to be the same as a reference model.
To use a reference file with DEN, you would use:
den.reference_file="path_to_reference_file"
That will handle the chainID/resID matching automatically, and correctly
use your reference in a DEN context.
Jeff
On Wed, Oct 2, 2013 at 4:43 PM, Jan van Agthoven
Hi everyone, I ran a DEN refinement of my low resolution structure (3.6) to improve my model. I typed in the following command:
phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb reference.params
with reference.params saying:
refinement.reference_model.reference_group { reference = chain A and resseq 1:953 selection = chain A and resseq 1:953 } refinement.reference_model.reference_group { reference = chain B and resseq 1:687 selection = chain B and resseq 1:687 }
because the reference file only contains chain A and chain B.
Unfortunately I obtained much worse R factors then with a regular refinement:
Start R-work = 0.2798, R-free = 0.3176 Final R-work = 0.3733, R-free = 0.4089
Does someone have an idea what could have go wrong?
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