[phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default?

Edward A. Berry BerryE at upstate.edu
Sun Dec 3 16:14:04 PST 2017

On 12/02/2017 09:05 PM, Xiao Lei wrote:
> Dear All,
> I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead."  This may force rejecting weak data according to the post.
> The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

You can see the defaults with the command:

erie 233% phenix.refine --show-defaults
. . . .
   xray_data {
       file_name = None
       labels = None
       high_resolution = None
       low_resolution = None
       outliers_rejection = True
       french_wilson_scale = True
       french_wilson {
         max_bins = 60
         min_bin_size = 40

So it seems the default now is to use F&W procedure to preserve
the weak data. Some reflections are rejected as outliers, but
that is a different criterion.

I have seen it argued that there are significant advantages to refining
against I instead of F (after all I is you observed value) and I think
one of the advantages was that you can refine with negative I's whereas
to convert to F's you have to either discard negatives or do F&W.

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