On Thursday, October 21, 2010 09:34:58 am 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.
The "black eye" comes not from the treatment of the observations, but from the
treatment of the model. If you want to refine the same model against lower
symmetry and/or unmerged data - go right ahead. I think the result will not
usually be an improvement, but in some cases this may work around systematic
artefacts in the data. What you should _not_ do is replicate the model to
produce multiple copies which are then refined as if they were independent.
That amounts to doubling/tripling/whatever the number of model parameters.
Ethan
> 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: CCP4BB@JISCMAIL.AC.UK
> 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 <m...@soton.ac.uk>
> To: CCP4BB@JISCMAIL.AC.UK
> 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: j-kell...@northwestern.edu
> *******************************************
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
