Cheat sheet: Difference between revisions
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!why? what to look out for? what else to know? | !why? what to look out for? what else to know? | ||
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|<small>'''1.''' '''Set up environment.''' Open a terminal and position it on the left side of your screen. Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI, or the <code>pointless</code> output. | |<small>'''1.''' '''Set up environment.''' Open a terminal and position it on the left side of your screen. Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI, or the <code>pointless</code> output. Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.</small> <small>Optional: before typing <code>xdsgui</code> ,<code>cd</code> to an existing XDS processing directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>; <code>mkdir <xds-directory>; cd <xds-directory></code></small> | ||
|<small>If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. (For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code> instead). The path must match YOUR computer; the given one is just an example. The path must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code>.</small> | |<small>If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. (For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code> instead). The path must match YOUR computer; the given one is just an example. The path must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code>.</small> | ||
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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> | |<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 statistics should not take the anomalous signal into account | |Use FRIEDEL'_LAW=FALSE only if the anomalous signal is so strong that you want to see the proper statistics (completeness ...). Low resolution anomalous correlation above 60% is what I consider strong. Use FRIEDEL'S_LAW= TRUE if scaling and merging statistics should not take the anomalous signal into account (typically for your "Table 1"). Modify <code>XDS.INP</code> accordingly. | ||
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|<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> | |<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> | ||