Cheat sheet: Difference between revisions

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<small>INTEGRATE tab: are the curves smooth (good) or are there jumps (bad)? Try to think of reasons for jumps/spikes! Could it be the beamline flux or the crystal changing? Are their straight red and green lines all along the "Beam divergence" and "Mosaicity" plots? If not, too few strong reflections were found (inspect the "THREE-DIMENSIONAL PROFILE" output in the text part) and you should add DELPHI=20 in <code>XDS.INP</code>, or increase the parameter if the keyword already exists.</small>

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|8. Inspect the CORRECT tab: Numerical values and plots are only meaningful if the spacegroup is correct (screw axes don't matter for the statistics, though). If the spacegroup is unknown, the text part reports the spacegroup that XDS determines automatically. To benefit from a more advanced (but not infallible) algorithm, in <code>tools / Further analyses</code> use <code>determine spacegroups with pointless</code>. Output is in the terminal window! Modify the SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS in <code>XDS.INP</code> accordingly (unless you know better, of course). Often there are two [[Space group determination#Space group selected by XDS: ambiguous with respect to enantiomorph and screw axes|enantiomorphic spacegroups]] possible (~~also see~~ [[Space group determination#Table of space groups by Laue class and Bravais type|~~this~~]]), or a [[Space group determination#Subgroup and supergroup relations of these space groups|subgroup]] is correct; keep that in mind for the structure solution - the correct spacegroup is only confirmed when the structure is solved and well refined.

|8. Inspect the CORRECT tab: Numerical values and plots are only meaningful if the spacegroup is correct (screw axes don't matter for the statistics, though). If the spacegroup is unknown, the text part reports the spacegroup that XDS determines automatically. To benefit from a more advanced (but not infallible) algorithm, in <code>tools / Further analyses</code> use <code>determine spacegroups with pointless</code>. Output is in the terminal window! Modify the SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS in <code>XDS.INP</code> accordingly (unless you know better, of course). Often there are two [[Space group determination#Space group selected by XDS: ambiguous with respect to enantiomorph and screw axes|enantiomorphic spacegroups]] possible ([[Space group determination#Table of space groups by Laue class and Bravais type|table]]), or a [[Space group determination#Subgroup and supergroup relations of these space groups|subgroup]] is correct; keep that in mind for the structure solution - the correct spacegroup is only confirmed when the structure is solved and well refined.

|The first look should go to the the first plot (I/sigma unmerged data). The red horizontal line is ISa - what is its value? The exact numerical value is in the text part, but the plot is enough for a good estimate. If the value is less than 5, something (likely indexing or spacegroup) is severely wrong. Good values are 20 and higher~~. See [[ISa]]~~.

|The first look should go to the the first plot (I/sigma unmerged data). The red horizontal line is [[ISa]] - what is its value? The exact numerical value is in the text part, but the plot is enough for a good estimate. If the value is less than 5, something (likely indexing or spacegroup) is severely wrong. Good values are 20 and higher.

The blue line should be well below the red line, otherwise this is a sign of overexposure - the systematic error limits the quality of the data, not the random error.

The blue line should be well below the red line, otherwise this is a sign of overexposure - in that case, the systematic error limits the quality of the data, not the random error.

|-

|9. If the spacegroup that CORRECT determined differs from the one that pointless determined, CORRECT should be re-run: change the JOB=... line to JOB=CORRECT, and go to step 6.

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 <small>INTEGRATE tab: are the curves smooth (good) or are there jumps (bad)? Try to think of reasons for jumps/spikes! Could it be the beamline flux or the crystal changing? Are their straight red and green lines all along the "Beam divergence" and "Mosaicity" plots? If not, too few strong reflections were found (inspect the "THREE-DIMENSIONAL PROFILE" output in the text part) and you should add DELPHI=20 in <code>XDS.INP</code>, or increase the parameter if the keyword already exists.</small>
 |-
-|8. Inspect the CORRECT tab: Numerical values and plots are only meaningful if the spacegroup is correct (screw axes don't matter for the statistics, though). If the spacegroup is unknown, the text part reports the spacegroup that XDS determines automatically. To benefit from a more advanced  (but not infallible) algorithm, in <code>tools / Further analyses</code> use <code>determine spacegroups with pointless</code>. Output is in the terminal window! Modify the SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS in <code>XDS.INP</code> accordingly (unless you know better, of course). Often there are two [[Space group determination#Space group selected by XDS: ambiguous with respect to enantiomorph and screw axes|enantiomorphic spacegroups]] possible (also see [[Space group determination#Table of space groups by Laue class and Bravais type|this]]), or a [[Space group determination#Subgroup and supergroup relations of these space groups|subgroup]] is correct; keep that in mind for the structure solution - the correct spacegroup is only confirmed when the structure is solved and well refined.
+|8. Inspect the CORRECT tab: Numerical values and plots are only meaningful if the spacegroup is correct (screw axes don't matter for the statistics, though). If the spacegroup is unknown, the text part reports the spacegroup that XDS determines automatically. To benefit from a more advanced  (but not infallible) algorithm, in <code>tools / Further analyses</code> use <code>determine spacegroups with pointless</code>. Output is in the terminal window! Modify the SPACE_GROUP_NUMBER and UNIT_CELL_CONSTANTS in <code>XDS.INP</code> accordingly (unless you know better, of course). Often there are two [[Space group determination#Space group selected by XDS: ambiguous with respect to enantiomorph and screw axes|enantiomorphic spacegroups]] possible ([[Space group determination#Table of space groups by Laue class and Bravais type|table]]), or a [[Space group determination#Subgroup and supergroup relations of these space groups|subgroup]] is correct; keep that in mind for the structure solution - the correct spacegroup is only confirmed when the structure is solved and well refined.
-|The first look should go to the the first plot (I/sigma unmerged data). The red horizontal line is ISa - what is its value? The exact numerical value is in the text part, but the plot is enough for a good estimate. If the value is less than 5, something (likely indexing or spacegroup) is severely wrong. Good values are 20 and higher. See [[ISa]].
+|The first look should go to the the first plot (I/sigma unmerged data). The red horizontal line is [[ISa]] - what is its value? The exact numerical value is in the text part, but the plot is enough for a good estimate. If the value is less than 5, something (likely indexing or spacegroup) is severely wrong. Good values are 20 and higher.
-The blue line should be well below the red line, otherwise this is a sign of overexposure - the systematic error limits the quality of the data, not the random error.
+The blue line should be well below the red line, otherwise this is a sign of overexposure - in that case, the systematic error limits the quality of the data, not the random error.
 |-
 |9. If the spacegroup that CORRECT determined differs from the one that pointless determined, CORRECT should be re-run: change the JOB=... line to JOB=CORRECT, and go to step 6.