[phenixbb] Copying mtz file

Tim Gruene tim.gruene at univie.ac.at
Tue Jun 25 00:49:15 PDT 2019

Hi Pavel,

if you would ask that question, you did not read Ian's explanation properly. 
His email reads like a proof, and anyone doubting the validity make claim 
without understanding. On the contrary: what evidence do you provide that 
there was a memory effect?

In case you trust experimental evidence better than mathematical rationale, 
you can repeat the experiments described under "Validation I: How "free" is 
Rcomplete" from  www.pnas.org/cgi/doi/10.1073/pnas.1502136112
with any data set of your choice. Our paper also describes experiments to 
provide evidence that Rcomplete is equivalent to Rfree (or rather better in 
case of small data sets).

I hope that if ever you make such a claim as reviewer, you can provide a 
literature reference with evidence of your claim, because reviewers that make 
claims without references are very time consuming (and often just proove their 


On Tuesday, June 25, 2019 9:22:37 AM CEST Pavel Afonine wrote:
> Hi Mirek,
> based on your description this sounds like a bug or undesired feature at
> least! Could you please send me the files so that I can repeat your
> experience myself and see what's happening?
> As a work-around you can re-generate flags as Tim suggested but chances
> are someone annoying like myself asks to prove no memory left from
> previous set and that is very hard to prove, and if not proven there
> will be a doubt! Although indeed, re-generating and running some
> refinement should be just fine, I agree!
> Good luck!
> Pavel
> On 6/24/19 21:09, Cygler, Miroslaw wrote:
> > Hi Phenixers,
> > I have copied mtz file to a new file with a lower resolution limit
> > using the "Reflection file editor” tool. I copied all arrays to the
> > output file. When I attempted to continue refinement with the new mtz
> > file, a message appears saying that there are no R-free flags in the
> > mtz file. Yet, the new file contains the R-free-flags column but the
> > values are inverted, 1 is changed to 0 and 0 is changed to 1. In the
> > output option dialog the box “Preserve original flag values” was checked.
> > How to fix this?
> > Thanks,
> > Mirek
> > 
> > 
> > 
> > 
> > _______________________________________________
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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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