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 <[email protected]> on behalf of Almudena Ponce Salvatierra <[email protected]> Reply-To: Almudena Ponce Salvatierra <[email protected]> Date: Friday, 19 April 2019 at 19:12 To: ccp4bb <[email protected]> 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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
