Re: [ccp4bb] High Rfree in last Shell

Also, values in parentheses (high-res shell) depend on how you (the program you use) do binning. Different programs do it differently and so these values can vary quite substantially. With a little of trial-and-error effort choosing the binning one can make these values farther or closer to

Re: [ccp4bb] High Rfree in last Shell

Hi, No-one else seems to have said this, but just from the data in that table, if I were a referee I would almost certainly be asking why you seem to have discarded useful data at higher resolution than 3.1A! Best wishes, Randy Read > On 16 Apr 2019, at 20:59, Jan van Agthoven wrote: > >

Re: [ccp4bb] High Rfree in last Shell

Send your manuscripts to any of the IUCr journals! Might still get the occasional referee like that, but the editors should ignore those comments. plus you'd be supporting a scientific society [sorry for the advert...] Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de

Re: [ccp4bb] High Rfree in last Shell

Ah, even though it seems a long time ago, approximately one out of every two referee comments that I receive complain about our modern methods for processing, scaling and reporting our data collection/processing/refinement statistics. I’m afraid it’s an ongoing effort at education. Diana

Re: [ccp4bb] High Rfree in last Shell

Jan, tell your reviewer to join us all in the 21st century. Diederichs and Karplus, Science, about 2 decades ago.  (Technically, 2012 , but it really is a long long time ago now.) On 16/04/2019

Re: [ccp4bb] High Rfree in last Shell

Dear all, The last resolution shell is 3.1-3.2 Å. I corrected high resolution Rmerge and Rmeas which seemed truncated, and added cc1/2. Rsym is Rpim which was a typo. Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)

Re: [ccp4bb] High Rfree in last Shell

Sorry, I meant to write Why are the values for R(free) in parentheses LOWER than R(factor) in parentheses? Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

Re: [ccp4bb] High Rfree in last Shell

Why are the the values for R(free) in parentheses higher than R(factor) in parentheses? I would not expect that to happen, if the same resolution limits for the last shell are used for both values. And I echo the previous commentator, please provide the resolution limits for the values in

Re: [ccp4bb] High Rfree in last Shell

Dear all, on top of other peoples remarks and out of interest: (1) What is the supposed difference between Rmerge and Rsym in your table and what software/tool computed those? Are you sure Rsym is not supposed to be Rpim? There is a slight historical difference between the

Re: [ccp4bb] High Rfree in last Shell

> I’ve been told that the Rfree factor in the last shell are too high. > that's rubbish. You can not judge the absolute value without looking at the data and the model. If you have a certain amount of disorder, smearing, freezing effects, ice rings, and/or diffuse scatter, your Rfree will be

Re: [ccp4bb] High Rfree in last Shell

Dear Jan, You statistics look quite solid. R-factors are not good criteria to judge the resolution cut-off. The weighting schemes in refinement programs have much improved since the late 1990s. A good starting point to learn more is Rupp's "Against Method: Table 1 -Cui Bono?",

[ccp4bb] High Rfree in last Shell

Hi everyone, I’m trying to publish two structures at 3.1Å resolution with the following refinement statistics: Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)24.0 (32.4)