Cheat sheet: Difference between revisions

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|'''7. First run of XDS: inspect and analyse diffraction.''' COLSPOT tab: is the "number of spots" evenly distributed among the frames? If not, it may be a sign of radiation damage or anisotropy, or plate-shaped crystal. Maybe see [https://wiki.uni-konstanz.de/xds/index.php?search=COLSPOT&title=Special%3ASearch&fulltext=1 COLSPOT] . IDXREF tab: does the plot of spots appear elliptical - that would indicate anisotropy? Inspect the <code>predictions</code> in <code>Frame</code> . Do they match the observed reflections? ''Visualize reflections in reciprocal space'' : in <code>tools</code> go to <code>Further analyses</code> and click the second button from the top. This will load the indexed reflections (yellow) and non-indexed ones (pink) as pseudo-PDB files into <code>Coot</code>. Inspect the lattices: is the "yellow lattice" convincing, and/or do the pink reflections form their own lattice(s), or are they just random?

|IDXREF tab: are the "CLUSTER INDICES" of the difference vectors integer numbers, or close to integers? Are the cell parameters reasonable? Is the first POPULATION of the first SUBTREE close to 3000? Ice rings? See [[IDXREF.LP]] and [[IDXREF]] .~~~~

|IDXREF tab: are the "CLUSTER INDICES" of the difference vectors integer numbers, or close to integers? Are the cell parameters reasonable? Is the first POPULATION of the first SUBTREE close to 3000? Ice rings? See [[IDXREF.LP]] and [[IDXREF]]. 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.

~~~~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.

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|'''8.''' '''Inspect scaling & statistics.''' In 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.

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 |<small>'''7.  First run of XDS: inspect and analyse diffraction.'''</small> <small>COLSPOT tab: is the "number of spots" evenly distributed among the frames? If not, it may be a sign of radiation damage or anisotropy, or plate-shaped crystal. Maybe see [https://wiki.uni-konstanz.de/xds/index.php?search=COLSPOT&title=Special%3ASearch&fulltext=1 COLSPOT]</small> . <small>IDXREF tab: does the plot of spots appear elliptical - that would indicate anisotropy? Inspect the <code>predictions</code> in <code>Frame</code> . Do they match the observed reflections? ''Visualize reflections in reciprocal space'' : in <code>tools</code> go to <code>Further analyses</code> and click the second button from the top. This will load the indexed reflections (yellow) and non-indexed ones (pink) as pseudo-PDB files into <code>Coot</code>. Inspect the lattices: is the "yellow lattice" convincing, and/or do the pink reflections form their own lattice(s), or are they just random?</small>
-|<small>IDXREF tab: are the "CLUSTER INDICES" of the difference vectors integer numbers, or close to integers? Are the cell parameters reasonable? Is the first POPULATION of the first SUBTREE close to 3000? Ice rings? See [[IDXREF.LP]] and [[IDXREF]] .</small>
+|<small>IDXREF tab: are the "CLUSTER INDICES" of the difference vectors integer numbers, or close to integers? Are the cell parameters reasonable? Is the first POPULATION of the first SUBTREE close to 3000? Ice rings? See [[IDXREF.LP]] and [[IDXREF]]. 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>
-<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>
 |-
 |<small>'''8.''' '''Inspect scaling & statistics.''' In 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.</small>