[phenixbb] HLs not recognised

Randy Read rjr27 at cam.ac.uk
Tue May 13 06:59:10 PDT 2014


Just to be a bit more precise about that — the part of the phase information that comes from the two hands of the Friedel pair is missing for centric reflections in SAD phasing, but the part of the phase information that comes from knowing even a small part of the structure (i.e. the real scattering of the anomalous substructure) is still present.  So, in general, the HL coefficients should not all be zero for the centric reflections in Phaser SAD phasing output, but they will generally be smaller (and the figures of merit will also be smaller) than for the acentric reflections.  The same goes for singletons (our term for the acentric reflections where only F+ or F- but not both have been measured).


On 12 May 2014, at 17:25, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Mon, May 12, 2014 at 8:54 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:
> I don't know the formula for HL by heart and I don't see the
> Miller-Indices, but couldn't centric reflections have all four HLs = 0
> if the two-fold ambiguity is resolved and those reflections have
> phi=0? I thought phi=0 corresponds to A=B=C=D=0.
> Based on my reading of the ccp4 wiki, this appears to be incorrect:
> http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Hendrickson_Lattman_coefficients
> C=D=0 would be consistent with the phase ambiguity being resolved, but if A=B=0 that would imply that the figure of merit is also zero.  However, it turns out that the tutorial output I was looking at does have all centric HL coefficients equal to zero - but my understanding (possibly incorrect) was that the centric reflections can't be phased using SAD (which explains why the figure of merit for centrics is always really poor in the Phaser output).  In any case, if the MTZ file contains only centric reflections that by itself is worrying, although I found some lovely examples of this in the PDB yesterday.
> -Nat
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Randy J. Read
Department of Haematology, University of Cambridge
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