[phenixbb] structure factor labels in phenix.refine

Ryan Spencer rspencer at uci.edu
Thu Nov 7 15:50:44 PST 2013

Hi Nat,


I have found that phenix.model_vs_data does not deal well with a perfect
twin data set. The refined data is:


                r_work=0.2013 r_free=0.2298 (in PDB file)

                r_work=0.2815 r_free=0.3006 (from phenix.model_vs_data)


There is one merohedral twin operator: -h-k,k,-l (48%) and 6 very small
(<1.0%) pseudo-merohedral twin operators. 


Ryan Spencer


From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Nathaniel Echols
Sent: Thursday, November 07, 2013 2:52 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] structure factor labels in phenix.refine


On Thu, Nov 7, 2013 at 12:57 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

Depending which kind of differences you mean (magnitude). Ideally, R-factors
should be identical. If it's like 0.1856 vs 0.1858, then it's fine, if
larger then some of us here need to investigate what's going on.


Agreed, since the Table 1 program is using phenix.model_vs_data internally,
which was designed to reproduce the R-factors from phenix.refine, any major
discrepancy is cause for concern.  We have seen a handful of cases where
they deviate significantly, but it's been very difficult to isolate the
cause, so data is always helpful.  (Of course this doesn't rule out the
possibility that there's simply a bug in my code somewhere, but I don't
think the program is doing anything fancy.)



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