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

Jeffrey, Philip D. pjeffrey at princeton.edu
Mon Dec 4 07:59:48 PST 2017

To put this in context:
I originally wrote that page when phenix.refine used a |F|>0 cutoff in refinement.  Given that I<0 often results in |F|=0 after the conversion the program threw out data for which we knew something (i.e. it was weak) albeit imprecisely.  That was a self-evidently bad idea.  However the defaults in phenix.refine have changed and as Ed Berry observes it does emulate CCP4's TRUNCATE now (in "truncate yes" mode, probably).

I convert my data with CCP4's TRUNCATE or CTRUNCATE programs.  For strong data I don't apply the French and Wilson intensity data remapping.  For weak data I do - but only for refinement purposes, not for SAD/MAD phasing.  My standard ploy is to use CAD to strip out Imean and SigImean from the MTZ file so that phenix.refine cannot attempt to "outsmart" me again.  And by outsmart I really mean "usurp my intentions".  I would suggest that everyone do the same - or at least test the difference.  My known bias is to trust CCP4 programs more.

Phil Jeffrey
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Xiao Lei [xiaoleiusc at gmail.com]
Sent: Saturday, December 02, 2017 9:05 PM
To: PHENIX user mailing list
Subject: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default?

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 ?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20171204/7cb0eb8b/attachment-0001.htm>

More information about the phenixbb mailing list