Dear Sabine,
indeed, the differences between the last XDS versions are in the area of indexing, with BUILT=20180409 being the most robust (and recommended) one. This gives the desired results in all my tests, and GlobalPhasing has successfully tested it with ~60 difficult cases. But there is no rule without exception, which means that it could nevertheless give the wrong answer in your case.
According to CCP4 othercell, the two cells that you cite are related by the [h-2l,-h,k] reindexing operator. However the cell volumes differ by slightly more than a factor of 2 , namely 232274 / 110672 = 2.1 which I find astonishing because typically such different indexing results result in a pseudo-centering situation, where the indexing results differ in that one tries to explain the weak and strong reflections, whereas the other only explains the strong reflections. What exactly happens in your case I don't know; I'd have to see the data and the detailed output of XDS. It could also be a case of two lattices (from two crystals) superimposed.
You can probably get the small cell with BUILT=20180409 if you either
a) specify it in XDS.INP (together with SPACE_GROUP_NUMBER=1)
b) or remove the weak reflections from SPOT.XDS
c) or by adjusting some parameters in XDS.INP
To really understand what is going on in your case, you could
a) run the checkcentering program (from ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin ) which will analyze your data w.r.t. pseudo-centering (similar to what pointless does)
b) look, in a representation of reciprocal space, at the spots that are used for indexing and that are indexed, or not. For this, you need the spot2pdb program (same download directory). Run it
grep -s allow-duplicate-sequence-numbers ~/.coot || echo "(allow-duplicate-sequence-numbers)" >>~/.coot
spot2pdb
coot SPOT-*.pdb
as suggested in https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#tools
BTW it is normal that R factors with tNCS are higher ("stuck") than without; this is due to the wider distribution of reflection intensities in the case of tNCS (many weak ones, and many strong ones; less with intermediate intensity). Most people would say that the space group and cell where the refinement proceeds best must be the correct one; however if that does not explain all the reflections of the lattice then this is not quite satisfactory.
best wishes,
Kay
On Mon, 6 Aug 2018 16:50:56 +0200, Sabine Schneider <[log in to unmask]> wrote:
>Dear all,
>
>We are encountering a differences in indexing using different XDS
>versions, which results in either 2 or 4 mols/asu (SG P1; structure
>determination via MR (30% seq ID model)) and either successful
>refinement or stuck R/Rfree
>
>- the data were collected at ESRF ID30A3 (Aiger detector) and extend to
>about 2.3A resolution (CC1/2 ~50%)
>
>The XDS version build 20180126 (and or autoprocessing at the ESRF via
>autoproc, dials, xdsapp or grenade -> here also xds version from
>20180126 used) gives us:
>
>P1 38.65 50.76 61.11 110.057 99.945 90.197
>XDS complains and I need to use "DEFPIX INTEGRATE CORRECT"
>-> 2mols/asu, structure refines to R/Rfree of 22/25
>
>In contrast the actual XDS-Version BUILT=20180409 results in:
>P1 39.2 51.3 116.8 86.3 82.3 89.8
>but XDS runs smoothly.
>-> 4mols/asu, tNCS, R/Rfree stuck at 28/32
>If I feed XDS with the smaller cell above, it fails.
>
>(The smaller cell is also found by Xia2/dials via the CCP4i2 interface.)
>
>Thus I am wondering, what are the differences between the two
>XDS-versions? (I remember vaguely that there was a tread about different
>XDS-versions, but couldn't find it..)
>
>Cheers Sabine
>
>
>--
>------------------------------------------
>Dr. Sabine Schneider
>Research Group Leader
>Technical University of Munich
>Department of Chemistry
>Chair of Biochemistry
>Lichtenbergstr. 4
>85748 Garching
>Germany
>Tel.: +49 (0) 89 289 13759
>Fax: +49 (0) 89 289 13363
>http://www.biochemie.ch.tum.de/index.php?id=919
>
>--
>------------------------------------------
>Dr. Sabine Schneider
>Research Group Leader
>Technical University of Munich
>Department of Chemistry
>Chair of Biochemistry
>Lichtenbergstr. 4
>85748 Garching
>Germany
>Tel.: +49 (0) 89 289 13759
>Fax: +49 (0) 89 289 13363
>http://www.biochemie.ch.tum.de/index.php?id=919
>
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