Dear Iris, just to add to Fred's posting: since XDS Version June 2, 2008 re-indexing is no longer necessary if REFERENCE_DATA_SET is used - XDS then does the re-indexing automatically in the CORRECT step. This makes it very easy to avoid the problem of alternative indexing in space groups like P3x, P4x , P6x and others. You should also inspect the top of XSCALE.LP. In case you forgot to use REFERENCE_DATA_SET and the wrong setting was picked by chance, you probably see some very small correlation coefficients (they should be >0.9, say). There may also be a warning message to that effect.
HTH, Kay On Fri, 19 Oct 2012 13:45:48 +0200, vellieux <[email protected]> wrote: >Well, the first thing I note is that P6(3) is a polar space group. > >Hence what I would do myself is the following: > >take your crystal 'number 1' (as a reference); > >take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it; > >try to see which of the original XDS_ASCII or the reindexed XDS_ASCII >file gives you the lowest R-sym values, the one with the lowest Rsym's >has consistent indexing with your 'reference' crystal 1 - normally >somewhere in the XDS output (forgot where) there is a reindexing card >mentioned > >repeat with crystal 3; > >Then you know what is consistent w.r.t. crystal 1. So you take the 3 >files that are appropriate and repeat the XSCALE scaling. > >It may very well be that you do not have any twinning but that you have >not consistently indexed the 3 data sets. Unless you have already taken >care of consistent indexing but didn't say (write) it. > >HTH, > >Fred. > >On 19/10/12 13:17, Iris Gawarzewski wrote: >> Hello everybody, >> >> I collected datasets with a resolution to 2.8A from 3 crystal grown >> in the same condition. The space group seems to be P63. Statistic of >> XSCALE.LP >> >> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF >> RESOLUTION >> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR >> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano >> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed >> expected Corr >> >> 10.00 1023 173 204 84.8% 7.4% >> 14.1% 1023 10.86 8.1% 99.5* -28 0.422 156 >> 6.00 4199 704 709 99.3% 11.1% >> 15.1% 4199 10.43 12.1% 99.1* -25 0.515 640 >> 4.00 12401 2131 2137 99.7% 15.5% >> 15.5% 12400 9.91 17.0% 97.7* -18 0.684 1893 >> 3.50 8429 1486 1486 100.0% 18.3% >> 18.0% 8426 8.10 20.1% 96.4* -8 0.788 1259 >> 3.30 4630 842 842 100.0% 23.0% >> 22.3% 4627 6.59 25.5% 94.5* -13 0.768 686 >> 3.10 6057 1121 1121 100.0% 28.3% >> 26.3% 6053 5.50 31.4% 93.6* -3 0.829 882 >> 3.00 3527 664 664 100.0% 33.7% >> 34.2% 3524 4.56 37.5% 86.8* 6 0.827 502 >> 2.90 3961 756 756 100.0% 48.4% >> 49.5% 3956 3.24 53.8% 82.7* 2 0.784 549 >> 2.80 2140 699 862 81.1% 31.6% >> 37.4% 2057 2.51 37.7% 87.0* 2 0.789 178 >> total 46367 8576 8781 97.7% 17.2% >> 18.1% 46265 7.15 19.0% 98.2* -9 0.730 6745 >> >> >> I tried Xtriage and got the following: >> >> merohedral twin operator >> twin law: h,-h-k,-l >> Britton plot: 0.423 >> H-test: 0.439 >> Maximum Likelihood Method: 0.457 >> >> I have a model with the sequence of my protein and did Phaser_MR >> (Z-score around 4... I know that this is quiet bad...). This solution >> I refined with phenix.refinement using the twin law from Xtriage. >> Rfree is around 0.44 best but the model looks weird... >> >> >> Greetings, >> >> Iris >> >> ___________________________________ >> Iris Gawarzewski >> PhD student >> Arbeitskreis Schmitt >> Institut f�r Biochemie >> Geb. 26.32.03.21 >> Heinrich-Heine-Universit�t D�sseldorf >> Universit�tsstr. 1 >> 40225 D�sseldorf >> -Germany- >> Tel: 0049-211-81-13577 >> >> >> > > >-- >Fred. Vellieux (B.Sc., Ph.D., hdr) >IBS / ELMA >41 rue Jules Horowitz >F-38027 Grenoble Cedex 01 >Tel: +33 438789605 >Fax: +33 438785494 > >
