[phenixbb] DEN refinement

[Jan van Agthoven]

Yes, the grid optimization was turned on. Let's see if den.reference_file will help.
Thanks,

Sent from my iPod

On Oct 2, 2013, at 4:56 PM, Jeff Headd <jjheadd at lbl.gov> wrote:

> 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 <janccp4 at gmail.com> wrote:
>> 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?
>> 
>> Thanks,
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> 
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