Hi Almudena,
in case you should have tiny spots (which would surprise me in this resolution shell), you could play
with the MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT parameter in the XDS.INP file. Of course, this
also depends on the detector you used; however, it sometimes makes sense to decrease it to allow
the program to find more spots and to change the criteria for a strong spot (STRONG_PIXEL=3.0).
The same can be done with DIALS; in the spotfinding step; you can change the spotsize:
dials.find_spots datablock.json min_spot_size=2
or the criterium for a strong spot
dials.find_spots datablock.json sigma_background=6 sigma_strong=3
Good luck,
Selina
From: CCP4 bulletin board <[log in to unmask]> on behalf of Almudena Ponce Salvatierra <[log in to unmask]>
Reply-To: Almudena Ponce Salvatierra <[log in to unmask]>
Date: Friday, 19 April 2019 at 19:12
To: ccp4bb <[log in to unmask]>
Subject: [ccp4bb] pointless warning - space group ambiguity
Dear all,
I'm processing my data with XDS and with DIALS and at first sight it would seem reasonable to assume that the Laue group is
either orthorrombic or monoclinic. Autoprocessing brings me always to P212121, but I have tried also to solve the
structure in space groups 1, 3, 4, 16, 17 and 18, without success.
Pointless gives the following warning:
WARNING: The data were integrated on a primitive lattice, but show some apparent features of a centered
lattice of type I, Mean(E^2) for lattice absences = 1.15
However, it might be pseudo-centered, due to translational non-crystallographic symmetry
Mn(I/sigI) for potentially absent reflections in the first 7 resolution bins = 4.76 is significantly above 0.0
Rough estimated probability of true centering = 0.714
NB: I lattice was chosen for further analysis rather than lattice type I
Best Solution: space group P 21 21 21
Reindex operator: [h,k,l]
Laue group probability: 0.762
Systematic absence probability: 0.682
Total probability: 0.520
Space group confidence: 0.478
Laue group confidence 0.702
However XDS doesn't give me option to choose any other lattices if not those in which I have already failed to
solve the structure, those marked with starts that are consistent with the observed locations of the diffraction spots.
So, I don't know what to do, I'm guessing it could be that it is C222, C2221 or C2 as well... but when I try space groups 5, 20 or 21 XDS
gets stalled and DIALS can not proceed with the step of refinement.
I'll be very thankful for any suggestions on how to continue on this venture...
Have a nice weekend and a happy Easter!
Best,
Almudena
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