[phenixbb] Implementation of French & Wilson data correction?

Jeff Headd jjheadd at lbl.gov
Fri Feb 25 09:34:58 PST 2011

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 {

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.


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