Tips and Tricks: Difference between revisions

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== 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 ~~a few degrees~~ more than that is a good idea, as the scaling will be more stable. So we regularly collect ~~200°~~ for native data. <br /> The Pilatus ~~6M detector at the SLS is~~ composed of many panels, and ~~therefore has~~ horizontal and vertical dead areas. This generally lowers completeness, and the effect is particularly noticeable in P1. ~~Untested idea: it may be good to make~~ sure (if necessary, by moving the ~~Pilatus~~) that the direct beam is not at a crossing between horizontal and vertical dead areas, nor at the middle of a panel (because this ~~avoids that~~ equivalent reflections ~~suffer the same fate)~~.

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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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.

@@ Line 1: / Line 1: @@
 == 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 a few degrees more than that is a good idea, as the scaling will be more stable. So we regularly collect 200° for native data. <br /> The Pilatus 6M detector at the SLS is composed of many panels, and therefore has horizontal and vertical dead areas. This generally lowers completeness, and the effect is particularly noticeable in P1. Untested idea: it may be good to make sure (if necessary, by moving the Pilatus) that the direct beam is not at a crossing between horizontal and vertical dead areas, nor at the middle of a panel (because this avoids that equivalent reflections suffer the same fate).
+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.
@@ Line 65: / Line 65: @@
   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.