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Tips and Tricks: Difference between revisions
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→P1 data collection / Pilatus: update & make more general
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== P1 data collection / Pilatus == | == P1 data collection / Pilatus == | ||
According to the classical paper ([http://dx.doi.org/10.1107/S0907444999008367 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. <br /> However, experience shows that collection of | According to the classical paper ([http://dx.doi.org/10.1107/S0907444999008367 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. <br />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. <br />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. | ||
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The last step of data reduction is usually the conversion of XDS_ASCII.HKL to a MTZ file, using [[XDSCONV]]. | 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 | 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 | 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 == | == Index and integrate multiple-crystal diffraction == | ||
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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. | 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 | 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 | mkdir xtal1 | ||
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echo " JOB= IDXREF INTEGRATE CORRECT" >> XDS.INP | echo " JOB= IDXREF INTEGRATE CORRECT" >> XDS.INP | ||
xds_par | 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. | |||