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: 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 > ******************************************* > -- 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 /
