[phenixbb] How to change the FOBS/SIGMA_FOBS value in phenix.refine

[Pavel Afonine]

Hi Engin,

thanks for feedback!

> There is one complication that arises from the report of the 
> MIN(FOBS/SIGMA_FOBS) value in pdb files from phenix.refine. Nearly 
> every PDB entry using phenix.refine reports a F/sig(F) cutoff value of 
> 1.3x, 

As I eluded yesterday, this is not a cutoff but a reported fact about 
your data. No data is removed or otherwise manipulated related to this 
number.

> while Buster and Refmac-generated pdbs have 0 or -/None for that value 
> (just checked again with this week's released PDBs). This is clearly 
> not intended. Again, the value the Protein Data Bank is reporting is a 
> cutoff, based on the minimum value phenix.refine appears to report. 
> Since I use French-Wilson for I to F conversions, I have had to 
> correct this cutoff value by communicating with PDB with every 
> deposition, but it appears that most users rarely go through the trouble.

REMARK 3 records are free format. It's up to program authors to choose 
what to print there.

Nowhere in the record in question produced by phenix.refine is said 
"cutoff":

REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.380

Refmac and Buster print:

REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000

which clearly says "cutoff".

So I guess we are fine as long as there is no wishful thinking involved 
and people carefully read what's written!

> The issue seems to arise from a lack of a cutoff value in the 
> phenix.refine generated .pdb files; Refmac has a DATA CUTOFF 
> (SIGMA(F)) (set to NONE by default), which is picked up during 
> structure deposition. So, either PDB has to be told that phenix.refine 
> min value is just a minumum value and not a cutoff, or phenix.refine 
> might add another REMARK card for DATA CUTOFF (SIGMA(F)) under the 
> DATA USED IN REFINEMENT. section in REMARKS.

Sure, we can add "cutoff"record if you think it is helpful.

In general, there are way more facts to reports about the data than this 
single number. As long as people deposit 1) data actually used in 
refinement (that may be truncated by sigma, resolution, automated 
outlier rejection, Iobs converted to Fobs, anomalous F+/- converted to 
non-anomalous Imean, etc) and 2) original data (not manipulated in any 
way), and as long as PDB actually accepts these data, then all should be 
fine. Note: phenix.refine always outputs MTZ containing the original 
input data and data actually used in refinement.

All the best,
Pavel

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