Hi,

There are some odd things that I would want to sort out.

First, xtriage thinks that your data merge in much higher symmetry, i.e. point group P622 rather than P3.  Using the ccp4i cell content analysis option under Molecular Replacement -> Analysis, 2 copies of your DNA in P622 should give 50% solvent.  That would fit with the apparent translational NCS.  However, I would want to keep in mind the possibility that, if your DNA adopts some helical arrangement, that would also generate large Patterson peaks.  So you could test the result of telling Phaser not to apply the tNCS correction.

Second, it's not clear whether there is any twinning.  After correcting for tNCS, Phaser says the second intensity moment is very nearly 2, which would imply no twinning.  The L-test in xtriage might, however, imply at least partial twinning.  If the crystal is twinned, then you would indeed have to consider that the true point group might be lower than the apparent P622.

Third, I would worry about the presence of a lot of outliers.  There appears to be a large number of reflections with significant net negative intensities, which implies that something might have gone wrong in the integration step. Maybe these come from the weak direction of diffraction, because the diffraction is strongly anisotropic.

You've told Phaser that the model is 100% identical, from which it is inferring a rather small RMS.  However, it sounds like you have greater uncertainty about the quality of your model, so you might be better off describing model quality in terms of expected RMS error.

By the way, we've only just realised that Phaser wasn't dealing properly with cell content analysis for nucleic acids.  The development version now takes into account the different partial specific volumes of protein and nucleic acids, but the distributed version doesn't give the right results for the solvent content. 

Good luck!

Randy Read

On 21 Apr 2016, at 14:39, Qixu Cai <[log in to unmask]> wrote:

Dear all,

I have a twinning dataset with translational NCS. And I cannot get molecular replacement solution while lots of solutions with high TFZ (>10) are rejected because of packing.

The log files of xtriage and phaser are attached.

Could you please give me any suggestion?

Best wishes,

Qixu Cai
Email: [log in to unmask]

<xtriage_4.log><3_phaser_MR.log>

------

Randy J. Read

Department of Haematology, University of Cambridge

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