Cheat sheet: Difference between revisions

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In the following, I describe the steps that I typically do ~~for~~ processing ~~a dataset~~. The links given in the form [[XDSGUI#Frame]] refer to the webpage wiki.uni-konstanz.de/xds/index.php/ , in this example wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame .

In the following, I describe the steps that I typically do in my processing workflow. The links given in the form [[XDSGUI#Frame]] refer to the webpage https://wiki.uni-konstanz.de/xds/index.php/ (in this example https://wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame ). I assume that the programs have been properly installed - see . Troubleshooting hints are at [[Problems]].

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1. open terminal and move the window to the left side of the screen. ~~Optional (since this can be done in XDSGUI):~~ <code>cd</code> ~~to an existing XDS directory, or create~~ a ~~new (empty) directory (<code>mkdir <name></code>~~). Type '<code>xdsgui</code>' and move its window so that you still see the left half of the terminal window.

1. open a terminal and move the window to the left side of the screen. If you work with HDF5 data, type <code>export NEGGIA_PATH=/usr/local/lib64/dectris-neggia.so</code> (the path must match YOUR computer; the path given is just a typical one) in the terminal.

|Keeping the terminal window ~~in sight~~ makes it possible to see some output of XDSGUI, e.g. error messages, or the pointless output.

Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.

|Keeping the terminal window to the left of the XDSGUI window makes it possible to see some screen output of XDSGUI, e.g. error messages, or the <code>pointless</code> output. For HDF5 data from DIAMOND, use <code>export DURIN_PATH=/usr/local/lib64/durin-plugin.so</code>instead (of course with the correct path).

Optionally, 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>).

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|2. click the 'Projects' tab and either choose an existing entry (if there is a list of previous projects) or browse to an existing XDS directory, or create a new (empty) directory

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

|Note that the directory name appears in the title bar of the XDSGUI window!

|If XDS's files already exist in the XDS directory, their content is shown in the tabs of XDSGUI. Note that the XDS directory name appears in the title bar of the XDSGUI window!

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|-

|3. click the 'Frame' tab and load a frame of your dataset. Click 'generate XDS.INP' - this reads the header of that frame, and counts the frames of the dataset. Use Zoom, Contrast and Brightness and move around the frame to evaluate the shape and separation of the reflections: are they smeared or sharp, tiny or broad, regular of broken, symmetric or asymmetric? Look at other frames as well!

|3. click the <code>Frame</code> tab and load a frame of your dataset (for HDF5, load <code>xxx_master.h5</code>). Click <code>generate XDS.INP</code> - this reads the header of that frame, and counts the frames of the dataset. Use <code>Zoom</code>, <code>Contrast</code> and <code>Brightness</code> and move around the frame to evaluate the shape and separation of the reflections: are they smeared or sharp, tiny or broad, regular or broken, symmetric or asymmetric? Look at other frames as well!

|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.

|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.

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|4. mask the shaded regions of the detector: ~~most likely~~ the beamstop shadow, and the beamstop holder. There is a button on the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL

|4. mask the shaded regions of the detector: at least the beamstop shadow, and the beamstop holder. There is a button on the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL

|This step is important, do not skip it! Reason is in the XDSGUI paper (reference at the end). More technical explanation of the tools at [[XDSGUI#Frame]]

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

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|-

|5. click the 'XDS.INP' tab and inspect its contents. For HDF5 data, make sure that the LIB= line points to the "Generic frame library" that appears in XDSGUI under 'Preferences' (macOS) or 'settings' (Linux). For a first XDS run, typically you would leave everything else at its defaults, except with broad reflections covering many pixels, set MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT to 6 instead of 3.

|5. click the <code>XDS.INP</code> tab and inspect its contents. For HDF5 data, make sure that the LIB= line points to the "Generic frame library" that appears in XDSGUI under 'Preferences' (macOS) or 'settings' (Linux). For a first XDS run, typically you would leave everything else at its defaults, except with broad reflections covering many pixels, set MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT to 6 instead of 3.

|Depending on where you measured the HDF5 data, export the environment variable NEGGIA_PATH=/usr/local/lib64/dectris-neggia.so or DURIN_PATH=/usr/local/lib64/durin-plugin.so (the path must match YOUR computer; the paths given are just reasonable defaults). That should work for both XDSGUI ''and'' XDS.

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-In the following, I describe the steps that I typically do for processing a dataset. The links given in the form [[XDSGUI#Frame]] refer to the webpage wiki.uni-konstanz.de/xds/index.php/ , in this example wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame .
+In the following, I describe the steps that I typically do in my processing workflow. The links given in the form [[XDSGUI#Frame]] refer to the webpage https://wiki.uni-konstanz.de/xds/index.php/ (in this example https://wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame ). I assume that the programs have been properly installed - see . Troubleshooting hints are at [[Problems]].
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-. open terminal and move the window to the left side of the screen. Optional (since this can be done in XDSGUI): <code>cd</code> to an existing XDS directory, or create a new (empty) directory (<code>mkdir <name></code>). Type '<code>xdsgui</code>' and move its window so that you still see the left half of the terminal window.
+. open a terminal and move the window to the left side of the screen. If you work with HDF5 data, type <code>export NEGGIA_PATH=/usr/local/lib64/dectris-neggia.so</code> (the path must match YOUR computer; the path given is just a typical one) in the terminal.
-|Keeping the terminal window in sight makes it possible to see some output of XDSGUI, e.g. error messages, or the pointless output.
+Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.
+|Keeping the terminal window to the left of the XDSGUI window makes it possible to see some screen output of XDSGUI, e.g. error messages, or the <code>pointless</code> output. For HDF5 data from DIAMOND, use <code>export DURIN_PATH=/usr/local/lib64/durin-plugin.so</code>instead (of course with the correct path).
+Optionally, 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. click the 'Projects' tab and either choose an existing entry (if there is a list of previous projects) or browse to an existing XDS directory, or create a new (empty) directory
+|2. click the <code>Projects</code> tab and either choose an existing entry (if there is a list of previous projects) or browse to an existing XDS directory, or create a new (empty) directory
-|Note that the directory name appears in the title bar of the XDSGUI window!
+|If XDS's files already exist in the XDS directory, their content is shown in the tabs of XDSGUI. Note that the XDS directory name appears in the title bar of the XDSGUI window!
 |
 |
 |-
-|3. click the 'Frame' tab and load a frame of your dataset. Click 'generate XDS.INP' - this reads the header of that frame, and counts the frames of the dataset. Use Zoom, Contrast and Brightness and move around the frame to evaluate the shape and separation of the reflections: are they smeared or sharp, tiny or broad, regular of broken, symmetric or asymmetric? Look at other frames as well!
+|3. click the <code>Frame</code> tab and load a frame of your dataset (for HDF5, load <code>xxx_master.h5</code>). Click <code>generate XDS.INP</code> - this reads the header of that frame, and counts the frames of the dataset. Use <code>Zoom</code>, <code>Contrast</code> and <code>Brightness</code> and move around the frame to evaluate the shape and separation of the reflections: are they smeared or sharp, tiny or broad, regular or broken, symmetric or asymmetric? Look at other frames as well!
-|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.
+|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: most likely the beamstop shadow, and the beamstop holder. There is a button on the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL
+|4. mask the shaded regions of the detector: at least the beamstop shadow, and the beamstop holder. There is a button on the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL
-|This step is important, do not skip it! Reason is in the XDSGUI paper (reference at the end). More technical explanation of the tools at [[XDSGUI#Frame]]
+|This step is important, do not skip it! Reason is in the XDSGUI paper (reference at the end). More technical explanation of the tools at [[XDSGUI#Frame]] . Wrongly positioned UNTRUSTED areas can be removed by deleting their lines in <code>XDS.INP</code> .
 |
 |
 |-
-|5. click the 'XDS.INP' tab and inspect its contents. For HDF5 data, make sure that the LIB= line points to the "Generic frame library" that appears in XDSGUI under 'Preferences' (macOS) or 'settings' (Linux). For a first XDS run, typically you would leave everything else at its defaults, except with broad reflections covering many pixels, set MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT to 6 instead of 3.
+|5. click the <code>XDS.INP</code> tab and inspect its contents. For HDF5 data, make sure that the LIB= line points to the "Generic frame library" that appears in XDSGUI under 'Preferences' (macOS) or 'settings' (Linux). For a first XDS run, typically you would leave everything else at its defaults, except with broad reflections covering many pixels, set MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT to 6 instead of 3.
-|Depending on where you measured the HDF5 data, export the environment variable NEGGIA_PATH=/usr/local/lib64/dectris-neggia.so or DURIN_PATH=/usr/local/lib64/durin-plugin.so  (the path must match YOUR computer; the paths given are just reasonable defaults). That should work for both XDSGUI ''and'' XDS.
+|
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 |