[phenixbb] Implementation of French & Wilson data correction?

Phil Evans pre at mrc-lmb.cam.ac.uk
Fri Feb 25 09:45:59 PST 2011

Scala outputs negative intensities where appropriate after merging, generally for input into [c]truncate


On 25 Feb 2011, at 17:34, Jeff Headd wrote:

> Hi Joe,
>> Any pointers on implementing the new option in the latest build for French &
>> Wilson correction?
> I'm sorry for the lack of documentation, I'm working on that and it
> should be available soon.
> To run F&W correction from the command line, you can run:
> phenix.french_wilson data.mtz output_file=data_f.mtz
> You can also turn the method on as part of phenix.refine by adding
> this to your parameter file:
> refinement {
>  input {
>    xray_data {
>      french_wilson_scale=True
>    }
>  }
> }
> There is also a GUI for F&W under the 'Reflection tools' header.
>> Does scala output negative intensities so that a proper
>> scaling with this new option can be used?
> I am not experienced with scala, so hopefully someone else can weigh
> in on what it outputs. If you run your data through
> truncate/ctruncate, our F&W wilson scaling is unnecessary and you
> should use the F/SIGF arrays generated by truncate/ctruncate.
>> Also, what column labels should be
>> used particularly for proper treatment of anomalous data? Can one use the
>> labels output by scala?
> Phenix is very tolerant of column labels, so any labels that you have
> used with Phenix before will work fine. In general for anomalous data
> I like I(+), SIGI(+), I(-), SIGI(-), but as far as I know the labels
> coming out of scala should work fine. If you run into an error
> messages I would be interested to know.
> Thanks,
> Jeff
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