Scala outputs negative intensities where appropriate after merging, generally for input into [c]truncate Phil 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb