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

A Leslie andrew at mrc-lmb.cam.ac.uk
Tue Jan 31 00:47:08 PST 2012

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  

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.



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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> ------
> 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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