significant figures in reporting Rfree
Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program? Thank you, Jenn
Hi Jenn,
Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program?
example: 23.11% or 0.2311. I am not aware of this being a function of data quality (resolution or completeness, for example). Pavel. P.S.: In general, programs (should) report values the way you can use them right away without doing any extra work converting them to something else.
On Mon, 2011-07-11 at 14:15 -0400, Jennifer Weinreich wrote:
what is the common practice with respect to how many significant figures should be used for reporting Rfree
If you look up crystallographic papers, you'll find that people routinely report R-values with 3 significant digits, i.e. 23.4% and such. The fourth digit is unreliable - try refining against the same dataset with different test set and you'll find that the Rfree varies within at least 0.1% (depending on resolution, data quality, etc). Most programs report 4 digits, which in my view is needed so that you can properly round it. PDB lists three significant digits as well. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
what is the common practice with respect to how many significant figures should be used for reporting Rfree If you look up crystallographic papers, you'll find that people routinely report R-values with 3 significant digits, i.e. 23.4% and such. The fourth digit is unreliable - try refining against the same dataset with different test set and you'll find that the Rfree varies within at least 0.1% (depending on resolution, data quality, etc).
You don't even need to change the test set to see that even the third one is not reliable too: pages 75-77 here: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p... Pavel.
It should probably have some relation to what you are going to put in REMARK 3 of your pdb file when you deposit it: REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.700 REMARK 3 FREE R VALUE TEST SET COUNT : 4924 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 There was a previous thread on how to calculate this value, I think maybe CNS PDB_DEPOSIT script gives it for you. Jennifer Weinreich wrote:
Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program?
Thank you,
Jenn
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participants (4)
-
Ed Pozharski -
Edward A. Berry -
Jennifer Weinreich -
Pavel Afonine