Because refining in the (right) higher symmetry space group leads to a
better model.
On Thu, 2010-10-21 at 11:34 -0500, Jacob Keller wrote:
>
> I have heard many times that it is a black eye to refine in a
> lower-symmetry spacegroup, but I could never really understand why.
> The higher symmetry could be considered merely a helpful theoretical
> lens to improve signal-to-noise, and therefore imposing higher
> symmetry on the data could be seen as a sort of *leniency* of
> scientific (or at least empiric) rigor. I think similarly about using
> discrete spot intensities rather than the whole image--we assume Bragg
> conditions and neglect certain things about the image between the
> spots, which is usually valid, but not always. I wonder why it is
> considered maladroit to refine in a lower spacegroup, then--don't
> higher spacegroup impose more assumptions than p1?
>
> Jacob Keller
>
> ----- Original Message -----
> From: James Holton
> To: [log in to unmask]
> Sent: Thursday, October 21, 2010 10:55 AM
> Subject: Re: [ccp4bb] Regarding space group P1, P21
>
>
>
> You pick the Rfree flags in the high-symmetry space group, and
> then use "CAD" with "OUTLIM SPACE P1" to symmetry-expand them
> to P1 (or whatever you like).
>
> Things get trickier, however, when your NCS is close to, (bot
> not exactly) crystallographic (NECS?). Or if you are simply
> not sure. The best way I can think of to deal with this
> situation is to "road test" your Rfree:
> 1) do something that you know is "wrong", like delete a helix,
> or put some side chains in the wrong place
> 2) refine with NCS turned on
> 3) check that Rfree actually goes up
> 4) un-do the "wrong" things
> 5) refine again
> 6) check that Rfree actually goes down
> 7) try again with NCS turned off
>
> Remembering these timeless words of wisdom: "Control, Control,
> you must learn CONTROL!" -Yoda (Jedi Master)
>
> -James Holton
> MAD Scientist
>
> On 10/21/2010 8:46 AM, Christina Bourne wrote:
> > Dear all,
> > How would one properly select reflections for R-free in
> > these situations? Presumably if the selection is done in P1
> > then it mimics twinning or high NCS, such that reflections
> > in both the work and free set will be (potentially?) related
> > by symmetry.
> > -Christina
> >
> >
> >
> > ____________________________________________________________
> > From: Mohinder Pal <[log in to unmask]>
> > To: [log in to unmask]
> > Sent: Thu, October 21, 2010 7:05:42 AM
> > Subject: [ccp4bb] Regarding space group P1, P21
> >
> > Dear CCP4BB members,
> >
> > I have solved a protein-drug complex structure in P21212
> > space group. In this structure, the drug molecule is
> > falling on the two-fold symmetry axis having averaged
> > electron density with 0.5 occupancy. We tried a lot to
> > crystallize this protein-drug complex in different space
> > group but no success so far. I have tried to solve the same
> > data in space group P1 (statistics are fine as I have
> > collected data for 360 degree). The map looks even better
> > with one conformation for a drug. Interestingly, then I
> > reprocessed the same data using imosflm in P21 space group
> > which have penalty 1 compared to 4 for P21212. The
> > structure in P21 is also refining well (with one
> > conformation of the drug compound without symmetry axis at
> > the ligand position). The question is , is it a good
> > practice to solve this structure in P1 and P21 even if the
> > data has higher symmetry?
> >
> > Secondly, I have been advised that I have to be careful to
> > refine structure in P1 as there will be problem regarding
> > observation/parameter ratio if I add too many water
> > molecules. What will be the case if the electron density
> > present for water molecules?
> >
> > I can put restrains to protein structure but I am just
> > curious to know one restrain equals how many observations.
> >
> > I look forward to hear your suggestions.
> >
> > Kind regards,
> >
> > Mohinder Pal
> >
> >
>
>
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: [log in to unmask]
> *******************************************
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
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