Cheat sheet: Difference between revisions

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|'''9.''' '''Spacegroup and resolution cutoff.''' If the spacegroup that CORRECT determined differs from the one that pointless determined: in <code>XDS.INP</code>, fix SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS, change the JOB=... line to JOB=CORRECT, and <code>Run XDS</code>. If the spacegroup is correct, decide about the high-resolution cutoff: go to the section after STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL" and inspect the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 . A useful estimate of the high-resolution limit is the last resolution range that still gets a star "*" in the CC1/2 column; you may also consider the <nowiki><I/sigma> column. </nowiki>Put the upper resolution value into the INCLUDE_RESOLUTION_RANGE line in <code>XDS.INP</code>, and set JOB=CORRECT. Go to step 6.

|Use FRIEDEL'_LAW=FALSE if the anomalous signal is so strong that you want to see the proper statistics (completeness ...). Use FRIEDEL'S_LAW= TRUE if scaling and merging should not take the anomalous signal into account. Low resolution anomalous correlation above 60% is what I consider strong. Modify <code>XDS.INP</code> accordingly.

|Use FRIEDEL'_LAW=FALSE if the anomalous signal is so strong that you want to see the proper statistics (completeness ...). Use FRIEDEL'S_LAW= TRUE if scaling and merging statistics should not take the anomalous signal into account. Low resolution anomalous correlation above 60% is what I consider strong. Modify <code>XDS.INP</code> accordingly.

|-

|'''10.''' '''Optimize by iterative comparison.''' Second and further runs of XDS typically refine the upper resolution limit and optimize the geometric parameters. It is useful to compare, after each modification, the resulting CORRECT.LP with the best one previously available. This is achieved by items in <code>tools / Saving and comparing good results</code> and <code>tools / Optimizing data quality</code>

|Thus, re-run INTEGRATE CORRECT or just CORRECT as needed (step 6). See [[Optimisation]], [[XDSGUI#How to use XDSGUI]]

|-

|'''11. Statistics tab.''' The XDSCC12 and XDSSTAT programs give you additional statistics for the frames of the DATA_RANGE.

|Look out for radiation damage. Bad frames have negative delta-CC1/2.

|-

|12. '''Creating MTZ file.''' XDSCONV tab. Un-comment GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 if you intend to use the MTZ file for refinement.

|FRIEDEL'S_LAW=FALSE is good even if little anomalous signal (FRIEDEL'S_LAW= TRUE in <code>XDS.INP</code>) since you may see metals or sulphur atoms in anomalous map.

|}

The XDSGUI paper (Brehm, Triviño, Krahn, Usón and Diederichs (2023) XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J. Appl. Cryst. 56) is open access at <nowiki>https://doi.org/10.1107/S1600576723007057</nowiki> .

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 |<small>'''9.''' '''Spacegroup and resolution cutoff.''' If the spacegroup that CORRECT determined differs from the one that pointless determined: in <code>XDS.INP</code>, fix SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS, change the JOB=... line to JOB=CORRECT, and <code>Run XDS</code>. If the spacegroup is correct, decide about the high-resolution cutoff: go to the section after STATISTICS OF SAVED DATA SET "XDS_ASCII.HKL" and inspect the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 . A useful estimate of the high-resolution limit is the last resolution range that still gets a star "*" in the CC<sub>1/2</sub> column; you may also consider the <nowiki><I/sigma> column. </nowiki>Put the upper resolution value into the INCLUDE_RESOLUTION_RANGE line in <code>XDS.INP</code>, and set JOB=CORRECT. Go to step 6.</small>
-|Use FRIEDEL'_LAW=FALSE if the anomalous signal is so strong that you want to see the proper statistics (completeness ...). Use FRIEDEL'S_LAW= TRUE if scaling and merging should not take the anomalous signal into account. Low resolution anomalous correlation above 60% is what I consider strong. Modify <code>XDS.INP</code> accordingly.
+|Use FRIEDEL'_LAW=FALSE if the anomalous signal is so strong that you want to see the proper statistics (completeness ...). Use FRIEDEL'S_LAW= TRUE if scaling and merging statistics should not take the anomalous signal into account. Low resolution anomalous correlation above 60% is what I consider strong. Modify <code>XDS.INP</code> accordingly.
 |-
 |<small>'''10.''' '''Optimize by iterative comparison.''' Second and further runs of XDS typically refine the upper resolution limit and optimize the geometric parameters. It is useful to compare, after each modification, the resulting CORRECT.LP with the best one previously available. This is achieved by items in <code>tools /  Saving and comparing good results</code> and <code>tools /  Optimizing data quality</code></small>
 |Thus, re-run INTEGRATE CORRECT or just CORRECT as needed (step 6). See [[Optimisation]], [[XDSGUI#How to use XDSGUI]]
+|-
+|<small>'''11. Statistics tab.''' The XDSCC12 and XDSSTAT programs give you additional statistics for the frames of the DATA_RANGE.</small>
+|<small>Look out for radiation damage. Bad frames have negative delta-CC<sub>1/2</sub>.</small>
+|-
+|<small>12. '''Creating MTZ file.''' XDSCONV tab. Un-comment GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 if you intend to use the MTZ file for refinement.</small>
+|<small>FRIEDEL'S_LAW=FALSE is good even if little anomalous signal (FRIEDEL'S_LAW= TRUE in <code>XDS.INP</code>) since you may see metals or sulphur atoms in anomalous map.</small>
 |}
 The XDSGUI paper (Brehm, Triviño, Krahn, Usón and Diederichs (2023) XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J. Appl. Cryst. 56) is open access at <nowiki>https://doi.org/10.1107/S1600576723007057</nowiki> .