Jacob,
could it be that your several runs were merged without referring to a reference? That would result in close-to-perfect twinning.
I don't know which program you mean with "proprietary algorithm in one of the popular indexing programs". Anyway, if you want to give XDS/XSCALE a try I could offer to help - but I need your raw data (I'd be treating them confidentially of course).
best,
Kay
On Tue, 14 Jul 2015 15:17:01 +0000, Keller, Jacob <[log in to unmask]> wrote:
>Dear Crystallographers,
>
>I am concerned that possibly my data need to be reindexed--here are the facts:
>
>--From refined structure, data is highly twinned ~45%, p3212 spacegroup, taken on home source
>
>--three 180-degree sweeps at 0.1 deg/image were taken, one starting at phi = 0, two taken starting at phi = 180, with one of those having chi = 10 deg.
>
>--when scaled together, there is no appreciable anomalous signal in scaling, even though the data are really high-quality to 1.7 (corner of detector). I realize twinning may be playing a role here, but since data are so good, I would think I would see something. When I use the model against a single dataset, I can see even small anomalous peaks from Cl and S.
>
>If left to its own devices, Pointless puts it in 622, but that's wrong because of the twinning. When told to do p3212, it gives the info below. I am curious--is it possible that the 0 and 180 datasets were indexed such that the Bijvoet differences are cancelling? Is that theoretically possible? Could it happen in mosflm? Autoindexing has always been a black box to me, partially because of the proprietary algorithm in one of the popular indexing programs.
>
>All the best,
>
>Jacob Keller
>
>=======================================================================
>
>
>
>Choosing specified space group P 32 1 2 with reindex operator [h,k,l]
>
>
>Alternative indexing scores relative to reference
> Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation
> [-h,-k,l] 0.129 0.830 0.164 495755 0.06
> [k,h,-l] 0.127 0.828 0.165 445580 0.06
> [k,-h-k,l] 0.088 0.791 0.188 428484 0.06
> [h,-h-k,-l] 0.084 0.786 0.189 425693 0.06
> [h+k,-h,l] 0.084 0.785 0.193 424023 0.08
> [-h,h+k,-l] 0.083 0.784 0.191 431379 0.08
> [h+k,-k,-l] 0.080 0.779 0.191 435826 0.06
> [-h-k,h,l] 0.075 0.773 0.194 434008 0.06
> [-h-k,k,-l] 0.070 0.764 0.200 444985 0.08
> [-k,h+k,l] 0.068 0.761 0.198 437727 0.08
> [h,k,l] 0.057 0.737 0.212 454077 0.08
> [-k,-h,-l] 0.056 0.735 0.210 466665 0.07
>
>
>Alternative indexing scores relative to reference
> Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation
> [-h,-k,l] 0.166 0.890 0.126 568040 0.07
> [k,h,-l] 0.100 0.848 0.135 525759 0.07
> [h,-h-k,-l] 0.092 0.839 0.155 513814 0.07
> [-h,h+k,-l] 0.091 0.839 0.156 510382 0.08
> [h+k,-k,-l] 0.077 0.823 0.159 527763 0.06
> [h+k,-h,l] 0.074 0.819 0.158 508182 0.08
> [-h-k,k,-l] 0.071 0.815 0.161 527394 0.08
> [-k,h+k,l] 0.071 0.815 0.162 519381 0.07
> [-h-k,h,l] 0.071 0.814 0.158 507974 0.07
> [h,k,l] 0.069 0.812 0.169 540345 0.08
> [k,-h-k,l] 0.063 0.802 0.163 516689 0.06
> [-k,-h,-l] 0.056 0.789 0.171 538172 0.07
>
>
>Alternative indexing relative to first file(s):
>
> Reindex operator CC Lklhd Confidence File name
> 2 [-h,-k,l] 0.830 0.129 0.016 DataSetAinv_p1.mtz
> 3 [-h,-k,l] 0.890 0.166 0.104 DataSetAchi10_p1.mtz
>
>Chosen Solution: space group P 32 1 2
>
> Reindex operator: [h,k,l]
> Laue group probability: 0.004
> Systematic absence probability: 0.996
> Total probability: 0.004
> Space group confidence: 1.000
> Laue group confidence 1.000
>
> Unit cell: 98.89 98.91 128.55 90.00 89.98 119.98
>
> 23.08 to 1.73 - Resolution range used for Laue group search
>
> 23.08 to 1.70 - Resolution range in file, used for systematic absence check
>
>
>
>
>*******************************************
>Jacob Pearson Keller, PhD
>Looger Lab/HHMI Janelia Research Campus
>19700 Helix Dr, Ashburn, VA 20147
>email:�[log in to unmask]
>*******************************************
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