Dear Herman,
so I should correct myself to say "if you think you know where the screw axis is and where not" instead of "if you know where the screw axis is and where not".
As we know, there is no certainty about the space group until you have solved and satisfactorily refined the structure (and even then someone may prove you wrong, but it's rare). So, during structure solution, there is a (hopefully growing) belief in (or likelihood of) a space group:
a) if you see systematic absences, you form a hypothesis about the screw axes
b) molecular replacement and/or expel phasing may disprove the hypothesis, or enlarge your belief in it
c) refinement might once again give extra evidence for or against it
So the question remains, how to express what your belief is? This question is clearly relevant for xia2, which deals with the first stage of hypothesis formation. And my answer is simply: run pointless (within xia2) with "SETTING SYMMETRY-BASED", as explained in the Pointless article of XDSwiki.
best,
Kay
On Fri, 29 Jan 2016 15:29:34 +0000, [log in to unmask] wrote:
> Dear Kai,
> you are right, but the original question was posed in the context of
> xia2. At that stage I think only diffraction data are available to
> decide about screw axes.
> Best,
> Herman
>
> -----Ursprüngliche Nachricht-----
> Von: Kay Diederichs [mailto:[log in to unmask]]
> Gesendet: Freitag, 29. Januar 2016 16:16
> An: Schreuder, Herman R&D/DE; [log in to unmask]
> Betreff: Re: AW: [ccp4bb] Spacegroups, screw axes and ordering
>
> Dear Herman,
>
> I did not write anything about the question of assigning a spacegroup
> based on screw axes absences. _Of course_ this is unreliable, but this
> was not the question (to me, at least). And of course I agree that one
> should try molecular replacement with all possible space groups, unless
> the assignment is clear.
>
> The question, as I understand it, was whether _if you know where the
> screw axis is and where not_ if you then want
> a) to order the axes such that a < b < c , and call the space group e.g.
> P 21 2 21 (because in that axis ordering, it is the b axis that does not
> have a screw),
> or,
> b) if you want to have the "unique" axis last, giving P 2 2 21 or P 21
> 21 2 , respectively, and accept the fact that this may result in a > b
> or b > c .
>
> And my preference is choice b) for reasons I tried to explain.
>
> best,
>
> Kay
>
|