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Tips and Tricks: Difference between revisions
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→Transfer the anomalous signal to the .mtz file even if it is not expected to exist
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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 '' | 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 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. | 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. | ||