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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: [log in to unmask] href="mailto:[log in to unmask]">James Holton
To: [log in to unmask] href="mailto:[log in to unmask]">[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:
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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



 
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
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email: [log in to unmask]
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