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

Randy Read rjr27 at cam.ac.uk
Mon Jan 30 09:06:19 PST 2012

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!



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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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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