[phenixbb] Picking Rfree in thin resolution shells using command line
andrew at mrc-lmb.cam.ac.uk
Tue Jan 31 00:47:08 PST 2012
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!
> 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
>> obvious - otherwise we wouldn't bother writing one.
>>> could someone let me know what the command line way of doing this
>> In phenix.refine, you probably want something like this (some
>> parameters optional, but the defaults are probably not what most
>> people expect):
>> Randy and Paul claim that this doesn't help very much with the NCS
>> issue, however.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> 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-
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