For unmerged data input using both the merged data and unmerged data protocols the output mmCIF file from the merging step (no diffraction cut-off) is concatenated (using Unix 'cat'), after insertion of a suitable software loop, to the final output mmCIF file from the corresponding protocol pipeline.
For merged data input the input file in mmCIF format is concatenated to the output mmCIF file from the server.
The deposition advice has been updated accordingly.
In the case of unmerged data input the values of the half-dataset mean intensities are added automatically to the input data and the random-selection method is used.  The weighted 'σ-τ' method is used for merged input data unless the user includes columns labelled 'IHALF1' and 'IHALF2' as the half-dataset mean intensities, in which case the first method is used.  The advantage of using wCC½ over the mean I /σ(I) as the cut-off criterion becomes apparent when the estimates of σ(I) are inaccurate, as appears to be the case for serial data.  Note that the 'σ-τ' method also relies on the σ(I) values being accurate so should not be used if those values are questionable.  The inverse-variance weighting also uses the σ(I) values but since the weighting is relative they need not be on the same scale as the values of Imean.
A fourth type of interactive colour-coded reciprocal-lattice display has been added when the input data are given as an unmerged XDS_ASCII.HKL file (not MTZ format).  The left-most scene then shows the value of the CORR statistic produced by XDS (item 11 in the file), i.e. for each reflection, the correlation coefficient between the observed reflection profile and the predicted profile that was used to integrate it.
The profile correlation plot gives a primary diagnostic of problems at the integration stage, as a mismatch of profiles could result from shortcomings in the sample (e.g. a cracked crystal) or in the profile estimation method (e.g. too coarse a partitioning of the detector surface).  As the profile correlation is given on a per-reflection basis, it is a more sensitive indication of such problems than the loss in <I /σ(I)> that it causes, since the latter quantity is a local average.
This development is in line with our philosophy of making as few prior assumptions as possible about the data (motto: \"Let the data speak!\").
Implicit assumptions made (incorrectly) by some software - namely that the anisotropic diffraction-limit surface is ellipsoidal with principal axes either parallel to the crystal axes or to the principal axes of the anisotropy tensor ellipsoid - were already relaxed in the previous version of the server, through a complete separation of the rôles of the anisotropic diffraction limit and of the anisotropy tensor.
With this new development of a protocol for anisotropy correction at the unmerged data stage, we go further.  By applying the anisotropic diffraction cut-off at an earlier stage in processing to the unmerged data, we try to ensure that weak measurements that can impact the quality of the final data by biasing the image scales and the error model can be eliminated early on in the process.
You are strongly advised to disable any Java plug-ins that were installed solely for the purpose of using previous versions of this server but are now no longer needed.