Cheat sheet: Difference between revisions

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|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. The path to the HDF5 library 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> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>;<code>mkdir <xds-directory>; cd <xds-directory></code>

|-

|2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory

|2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory

|If XDS files exist in the XDS directory, they appear in the XDSGUI tabs. Note that the XDS directory name appears in the title bar of the XDSGUI window!

|-

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|Watch the green crosshair at ORGX ORGY, the green circle around it (lower INCLUDE_RESOLUTION_RANGE), the red UNTRUSTED_RECTANGLEs at the module borders, and the blue TRUSTED_REGION appear. The corresponding keyword=parameter lines in <code>XDS.INP</code> have the same colour code.

|-

|4. Mask the shaded regions of the detector: at least the beamstop and its holder. There is a button <code>Untrusted areas (...)</code> towards the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL

|4. Mask the shaded regions of the detector: at least the beamstop and its holder. There is a button <code>Untrusted areas (...)</code> towards the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL

|This step is important, do not forget it! Reason is in the XDSGUI paper (reference at the end). More explanation of the tools is at [[XDSGUI#Frame]] . Wrongly placed UNTRUSTED areas can be removed by deleting their lines in <code>XDS.INP</code> .

|-

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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.

|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.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.

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 ...). 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.

|-

@@ Line 18: / Line 18: @@
 |<small>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. The path to the HDF5 library 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> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>;<code>mkdir <xds-directory>; cd <xds-directory></code></small>
 |-
-|2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory
+|<small>2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory</small>
 |<small>If XDS files exist in the XDS directory, they appear in the XDSGUI tabs. Note that the XDS directory name appears in the title bar of the XDSGUI window!</small>
 |-
@@ Line 24: / Line 24: @@
 |<small>Watch the green crosshair at ORGX ORGY, the green circle around it (lower INCLUDE_RESOLUTION_RANGE), the red UNTRUSTED_RECTANGLEs at the module borders, and the blue TRUSTED_REGION appear. The corresponding keyword=parameter lines in <code>XDS.INP</code> have the same colour code.</small>
 |-
-|4. Mask the shaded regions of the detector: at least the beamstop and its holder. There is a button <code>Untrusted areas (...)</code> towards the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL
+|<small>4. Mask the shaded regions of the detector: at least the beamstop and its holder. There is a button <code>Untrusted areas (...)</code> towards the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL</small>
 |<small>This step is important, do not forget it! Reason is in the XDSGUI paper (reference at the end). More explanation of the tools is at [[XDSGUI#Frame]] . Wrongly placed UNTRUSTED areas can be removed by deleting their lines in <code>XDS.INP</code> .</small>
 |-
@@ Line 45: / Line 45: @@
 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.
 |-
-|<small>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.</small>
+|<small>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.</small><small>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>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 ...). 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.
 |-