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Tips and Tricks: Difference between revisions
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→pick the h+k+l=2n reflections from a primitive dataset: fix echo command
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(→pick the h+k+l=2n reflections from a primitive dataset: fix echo command) |
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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]]. | 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 == | == 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 ''not'' require [[XDS.INP]] to have this line). | 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 == | ||
It can happen that you have two different mono-crystals in your loop, and that both are in the X-ray | 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. | |||