Cheat sheet: Difference between revisions

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|If XDS stops after the IDXREF step (with ERROR in IDXREF.LP), this most often happens because it could index less than 50% of the spots only. This may be due to ice rings that obviously cannot be indexed, or due to additional lattices. In most cases, this should at least prompt you to think about the possible reasons. To continue, set JOB=DEFPIX INTEGRATE CORRECT in the XDS.INP tab, <code>Save</code> and <code>Run XDS</code>.

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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]~~Once~~ IDXREF ~~has run, 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?

|'''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]] .

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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 |<small>If XDS stops after the IDXREF step (with ERROR in IDXREF.LP), this most often happens because it could index less than 50% of the spots only. This may be due to ice rings that obviously cannot be indexed, or due to additional lattices. In most cases, this should at least prompt you to think about the possible reasons. To continue, set JOB=DEFPIX INTEGRATE CORRECT in the XDS.INP tab, <code>Save</code> and <code>Run XDS</code>.</small>
 |-
-|<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>Once IDXREF has run, 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>'''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>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>