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: [email protected] [mailto:[email protected]] 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 <[email protected]> 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.)

-Nat