Dear Almudena, Am 20.04.19 um 14:52 schrieb Almudena Ponce Salvatierra: > Dear Kay, > > Thank you very much for your reply. It prints an error message, a couple of > them, return code = ier 0, or that there was an insufficient number of > reflections for indexing/ refinement did not converge. > > Is it possible that due to the pseudocentering, the indexing is proceeding in > such a way that the found unit cell is actually smaller than the real one? > Using the same unit cell parameters that I obtain for space group 21, doesn't > work when I try to process in space groups 23 or 24.
I understood your posting in the following way: 1) you (auto-)process in oP 2) pointless tells you that there is I centering What I meant in my suggestion is: 1) explicitly specify the cell from the oP indexing 2) and use that for indexing in oI Of course, indexing in oI will only index half the reflections of oP if the cell is the same. But pointless says these are weak ... I don't think that using the oC cell for indexing in oI will get you anywhere. If you make your (raw) data available to me, I'll take a look. best, Kay > > Best, > > Almudena > > El vie., 19 abr. 2019 a las 22:33, Kay Diederichs > (<kay.diederi...@uni-konstanz.de <mailto:kay.diederi...@uni-konstanz.de>>) > escribió: > > Dear Almudena, > > what do you mean with "XDS get stalled"? Does it print an error message, > and if so, which? > > Your description makes me think that you may want to try space group 23 > (I222) or 24 (I212121) since Pointless says it may be I-centered. In XDS.INP, > you just enter > SPACE_GROUP_NUMBER=23 ! or 24 but for indexing that does not make a > difference > UNIT_CELL_CONSTANTS=<the same a b c that you get in P212121, and angles > all 90> > > hope this helps, > Kay > > On Fri, 19 Apr 2019 20:11:18 +0200, Almudena Ponce Salvatierra > <maps.fa...@gmail.com <mailto:maps.fa...@gmail.com>> wrote: > > >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 > > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
smime.p7s
Description: S/MIME Cryptographic Signature
