Tips and Tricks: Difference between revisions

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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 A°) may easily be distinguished from a Mg ion (f"=0.076 at 1 A°). Calibration of the anomalous peak height can be done using the sulfur atoms (f"=0.24 at 1 A°), 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 trajectory. 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 indexation and integration of a first lattice, you can remove 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

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 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 A°) may easily be distinguished from a Mg ion (f"=0.076 at 1 A°). Calibration of the anomalous peak height can be done using the sulfur atoms (f"=0.24 at 1 A°), 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 trajectory. 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 indexation and integration of a first lattice, you can remove 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