[phenixbb] Picking Rfree in thin resolution shells using command line

Felix Frolow mbfrolow at post.tau.ac.il
Tue Jan 31 10:07:07 PST 2012

I have a question of  general significance: in what resolution NCS restrains and Rfree become IRRELEVANT?
Axel Brunger invented Rfree to save our necks from refining garbage into the structure distantly looking like protein.
Since than Rfree was idolized. However, there is a big difference between structures at  4.1 Angstrom and 1.4 Angstrom. 
In small molecule crystallography we can easily achieve 10 or 20 observations per refined parameter (depends on presence or absence of inversion center), therefore, no one care about Rfree in the small molecules community.
In the well ordered protein structures, the bulk water region is working against us lowering diffraction strength contributing to 1/Volume, but it is also on our side minimizing a volume occupied 
by protein molecules (less atoms, fewer parameters). I have a structure (not yet published) where for 18000 protein atoms and about 9000 other atoms  (water molecules, sulfate ions, sugars from cryo-protection etc)
there are  750,000 independent observations. It makes about 28 observations per atom and together with the chemical observations such as bonds and angles which rarely differs from their classical values defined by small structures, if we keep anomalous data properly scaled and separated (there will be differences in good data sets that depends on S atoms and some other ions in solute, or even oxygen atoms) -
we have quite good ratio of observations per refined parameter.
So my question is: Do WE and WHAT FOR need to mess with Rfree in structures of relatively/very high resolutions? 

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jan 31, 2012, at 17:35 , Pavel Afonine wrote:

> Hi Simon,
> the difference is well illustrated in
> F. Fabiola, A. Korostelev and M. S. Chapman
> Acta Cryst. (2006). D62, 227-238
> Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry
> The question is whether we can reproduce it in the exact same set of test structures.
> Pavel
> On 1/31/12 1:46 AM, Simon Kolstoe wrote:
>> Thanks for the interesting comments.
>> I was just wondering what sort of "difference" we are expecting to see? Is it just a case of preventing an artificially lowered Rfree or is there an expectation to see a difference in the quality of the electron density?
>> Simon
>> ---------------------------------------------------------------
>> Dr Simon Kolstoe
>> Laboratory for Protein Crystallography
>> Wolfson Drug Discovery Unit
>> University College London
>> Rowland Hill Street, London NW3 2PF
>> Tel: 020 7433 2765
>> http://www.ucl.ac.uk/~rmhasek
>> ---------------------------------------------------------------
>> On 31 Jan 2012, at 08:47, A Leslie wrote:
>>> Hi Randy,
>>>                   I can't remember if I ever mentioned this to you, but when I was working on the HepB capsid structure (30 fold ncs if i remember correctly) I tried using a "thin shell within a thick shell" method of selecting Rfree, to avoid the issue that within a thin shell there are still relationships between those reflections within the shell and those just outside it. I forget the details, but I think I used a thin shell of 1-2 rlps wide for the reflections to be used for Rfree, but I also excluded from the refinement reflections within a thick shell 4-5 rlps wide (the thin shell was in the middle of the thick shell). Because this excluded so many reflections I could only have 3 thick/thin shells altogether, so I chose them at low, middle and highish resolution.
>>> The upshot of all this was that it was no help at all. Almost regardless of, say, the relative weight I put on the Xray terms, or anything else I did, I could never get the Rfree to go up ! The strict NCS restraints were so strong that the refinement essentially always "behaved".
>>> This for me destroyed all my faith in this thin shell idea !
>>> So this is definitely NOT an example where it worked.
>>> I have not sent this to the bulletin board because my memory of exactly what I did is a bit hazy, but the message was clear enough.
>>> Cheers
>>> Andrew
>>> On 30 Jan 2012, at 17:06, Randy Read wrote:
>>>> I'd be meaning to contribute to this debate, and now that I see my name mentioned...
>>>> I used to be a very strong believer in selecting the cross-validation data in thin shells, when you have NCS.  I even had a recollection (a case of false memory syndrome, it seems) that we did this for our own case of 20-fold NCS, i.e. four copies of the Shiga-like toxin B-subunit pentamer cocrystallized with the Gb3 trisaccharide (Ling et al, 1998).
>>>> As a believer in thin shells, I was trying to convince Pavel to put an option for this in Phenix (like the one in sftools).  He said that he'd never seen any evidence that it was necessary or made any difference.  So I went back to the Shiga-like toxin structure and started parallel refinements from the MR solution, either choosing the cross-validation data randomly or in thin shells.  And, guess what, I couldn't see any significant difference in how well the refinement went, even though I was pretty certain before doing that experiment that it would make a big difference.  In fact, both refinements went pretty well.
>>>> So if thin shells aren't necessary even in an extreme case of NCS, then I suspect that they're not that useful in the more usual case of lower-order NCS.
>>>> In any case, there is a problem even with the thin shells (which Bart Hazes pointed out even as he implemented it in sftools).  The theory suggests that reflections within some distance in reciprocal space of some reflection or a point related to it by an NCS rotation should be correlated to the original reflection.  All the points related by rotation will fall into the same resolution shell but, since the reciprocal-space distance is related to the inverse of the diameter of the molecule, the shell would have to have some thickness, and the reflections at the edge of the shell would still be correlated to reflections not in the shell.  So even thin-shell cross-validation doesn't get around all the theoretical problems.
>>>> I'd be interested if someone has an example where it really does make a difference, but in the meantime it's hard to argue with Pavel's point of view!
>>>> Regards,
>>>> Randy
>>>> On 30 Jan 2012, at 15:26, Nathaniel Echols wrote:
>>>>> On Mon, Jan 30, 2012 at 3:43 AM, Simon Kolstoe<s.kolstoe at ucl.ac.uk>  wrote:
>>>>>> I see from a quick google that it is possible to pick my Rfree's using thin resolution shells (coz I've got 20 fold NCS), however as I am someone who tries to avoid the GUI where at all possible,
>>>>> Why?  Some things are simply easier to do in the GUI, or at least more
>>>>> obvious - otherwise we wouldn't bother writing one.
>>>>>> could someone let me know what the command line way of doing this is?
>>>>> In phenix.refine, you probably want something like this (some
>>>>> parameters optional, but the defaults are probably not what most
>>>>> people expect):
>>>>> xray_data.r_free_flags.generate=True
>>>>> xray_data.r_free_flags.fraction=0.05
>>>>> xray_data.r_free_flags.max_free=None
>>>>> xray_data.r_free_flags.use_dataman_shells=True
>>>>> xray_data.r_free_flags.n_shells=20
>>>>> Randy and Paul claim that this doesn't help very much with the NCS
>>>>> issue, however.
>>>>> -Nat
>>>>> _______________________________________________
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>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> ------
>>>> Randy J. Read
>>>> Department of Haematology, University of Cambridge
>>>> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
>>>> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
>>>> Hills Road                                    E-mail: rjr27 at cam.ac.uk
>>>> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
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