Tips and Tricks
P1 data collection / Pilatus
According to the classical paper (Z. Dauter (1999), Acta Cryst D55, 1703), the required rotation range for native data in space group P1 is 180°, and for anomalous data is 180° + 2 theta_max (theta is the diffraction angle). In the case of the standard geometry (direct beam vertical to, and central upon, the detector), this leads to 2-fold redundancy.
However, experience shows that collection of more than that is a good idea, as the scaling will be more stable, and there is some leeway to discard radiation-damaged frames at the end of the data set. So we regularly collect 360° for native data unless we have specific reasons to deviate from that rule.
The Pilatus and Eiger detectors are composed of many panels, and have horizontal and vertical dead areas. This generally lowers completeness, and the effect is particularly noticeable in low-symmetry spacegroups. Make sure (if necessary, by moving the detector) that the direct beam is not at a crossing between horizontal and vertical dead areas, nor at the middle of a panel, because this prevents symmetry-equivalent reflections from all being unmeasured.
SAD/MAD data reduction
With FRIEDEL'S_LAW=FALSE, run CORRECT twice, with STRICT_ABSORPTION_CORRECTION=TRUE and STRICT_ABSORPTION_CORRECTION=FALSE, and compare the results. I find that the (apparent) anomalous signal in SeMet-SAD/MAD is significantly enhanced (but see below for a caveat!) in the "Anomal Corr" and the "SigAno" disciplines with STRICT_ABSORPTION_CORRECTION=TRUE (which used to be the default in older versions but is not the default since Version May 8, 2007).
Example: 269 frames, 0.5°/frame, F222; SeMet; high remote; STRICT_ABSORPTION_CORRECTION=TRUE:
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 Rmrgd-F Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
9.24 14085 4860 5073 95.8% 2.9% 3.5% 13978 26.78 3.7% 2.8% 66% 1.623 2115
6.59 24901 8560 8869 96.5% 4.6% 4.6% 24757 19.46 5.7% 5.5% 46% 1.356 3880
5.40 32411 11152 11422 97.6% 6.8% 6.6% 32194 14.14 8.4% 9.2% 28% 1.085 5121
4.68 37640 13022 13499 96.5% 6.7% 6.4% 37340 13.99 8.4% 10.0% 21% 1.017 5924
4.19 42764 14793 15307 96.6% 7.7% 7.2% 42425 12.59 9.5% 11.9% 19% 1.021 6746
3.83 48129 16600 16938 98.0% 11.4% 11.2% 47750 8.99 14.1% 18.6% 13% 0.914 7648
3.55 52640 18097 18333 98.7% 15.8% 16.1% 52229 6.61 19.5% 26.9% 10% 0.840 8384
3.32 56093 19557 19723 99.2% 24.3% 25.5% 55490 4.41 30.0% 42.9% 8% 0.781 8941
3.13 37869 18334 21008 87.3% 33.9% 36.3% 32035 2.33 43.6% 69.9% 6% 0.741 5214
total 346532 124975 130172 96.0% 9.5% 9.6% 338198 9.77 11.8% 18.8% 21% 0.964 53973
same data, STRICT_ABSORPTION_CORRECTION=FALSE (default):
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 Rmrgd-F Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
9.24 14082 4858 5073 95.8% 3.0% 3.6% 13975 26.06 3.7% 2.9% 63% 1.530 2115
6.59 24893 8554 8869 96.4% 4.7% 4.7% 24749 19.08 5.8% 5.6% 42% 1.287 3876
5.40 32407 11147 11422 97.6% 6.8% 6.7% 32190 13.93 8.4% 9.2% 25% 1.035 5118
4.68 37631 13016 13499 96.4% 6.8% 6.5% 37331 13.76 8.5% 10.1% 16% 0.946 5915
4.19 42726 14775 15307 96.5% 7.8% 7.3% 42387 12.40 9.7% 12.1% 9% 0.889 6733
3.83 48125 16600 16938 98.0% 11.4% 11.2% 47746 8.89 14.2% 18.5% 3% 0.813 7646
3.55 52642 18095 18333 98.7% 15.8% 16.1% 52231 6.55 19.5% 26.7% 4% 0.773 8383
3.32 56102 19563 19723 99.2% 24.3% 25.6% 55499 4.39 30.1% 42.9% 3% 0.743 8943
3.13 37830 18318 21008 87.2% 34.9% 37.0% 31996 2.32 45.0% 70.5% 2% 0.709 5206
total 346438 124926 130172 96.0% 9.6% 9.7% 338104 9.62 11.9% 18.8% 15% 0.892 53935
However: please note that this is just an internal indicator of data quality. Improved values of internal indicators are not necessarily meaningful, and the true improvement has to be verified by calculating external indicators. In this case it was found that when calculating the correlations of the anomalous signals between wavelengths (using SHELXC), the correlations are higher when STRICT_ABSORPTION_CORRECTION=TRUE is used. See also Quality Control.
A good indicator that STRICT_ABSORPTION_CORRECTION=TRUE should be used is the following: if, when the default STRICT_ABSORPTION_CORRECTION=FALSE is used, the three values of CHI^2-VALUE OF FIT OF CORRECTION FACTORS given near the beginning of CORRECT.LP are significantly higher than 1 (e.g. if they are 2 or more), then you should switch to TRUE and make sure that this reduces those values to about 1.
Transfer the anomalous signal to the .mtz file even if it is not expected to exist
The last step of data reduction is usually the conversion of XDS_ASCII.HKL to a MTZ file, using XDSCONV.
I suggest that XDSCONV.INP always should include a line "FRIEDEL'S_LAW=FALSE" - even if the crystal is not supposed to have anomalous scatterers (like most native crystals). Having this line results in three additional columns (DANO, SIGDANO, ISYM if FILE_TYPE=CCP4) in the MTZ file, and has no downsides that I know of (in particular, it does not require XDS.INP to have this line, but if the anom signal is substantial then XDS.INP should have it because otherwise strong anomalous differences will be treated as outliers (misfits).
The advantage of doing this is that one may easily calculate an anomalous difference Fourier map (this can e.g. be performed in [coot]) to identify ions in the structure. For example, a Mn ion (f"=1.35 at 1 Å) may easily be distinguished from a Mg ion (f"=0.076 at 1 Å). Calibration of the anomalous peak height can be done using the sulfur atoms (f"=0.24 at 1 Å), and the tables of anomalous scattering coefficients at http://skuld.bmsc.washington.edu/scatter/AS_periodic.html.
Index and integrate multiple-crystal diffraction
It can happen that you have two different mono-crystals in your loop, and that both are in the X-ray beam. If their relative orientation is sufficiently distinct, it is easy with XDS to index and integrate both crystal diffraction from the same data-set. You end-up with two distinct reflection files and can try to scale them using XSCALE to complete or increase the redundancy of your measurement.
After indexing and integration of a first lattice, you can extract the un-indexed reflections to create a new SPOT.XDS file (don't forget to copy the result of the first processing!) and re-run XDS from the IDXREF stage :
mkdir xtal1 cp *.* xtal1 cp SPOT.XDS SPOT.XDS.1 grep " 0 0 0" SPOT.XDS.1 > SPOT.XDS echo " JOB= IDXREF INTEGRATE CORRECT" >> XDS.INP xds_par
pick the h+k+l=2n reflections from a primitive dataset
grep \! XDS_ASCII.HKL | grep -v "END_OF_DATA" > x
grep -v \! XDS_ASCII.HKL | awk '{if ( ($1+$2+$3)%2==0 ) print $0}' >>x
echo \!END_OF_DATA >> x
and now use e.g.
phenix.xtriage x
to analyze x in terms of body-centered statistics.