Previous: collect: Data collection strategy and data collection
Next: Cell determination using Denzo

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Data collection

For a datacollection experiment, two buttons appear in the experiment window:

• Make Scan-set
• Collect data

There is one advantage of doing it in 2 steps: it makes it possible to "Save" the experiment using the "File" menu before the actual data collection is started. Doing so will make it easier to recover from a power failure or a system crash.

In this example we will start from a directory where we have already performed a successful cell determination. As you will see later, it is possible to perform a data collection without first determining the unit cell orientation matrix. However, some questions might give other defaults and/or be asked at different moments.

We start by pressing the "Make Scan-set" button. A dialog box is shown asking you for information about the data to be collected.

Maximum diffraction angle theta

For a Mo-K-alpha dataset, a normal dataset is complete to 27.5 degrees theta, equivalent to a full sphere for Cu-K-alpha (~0.79 Angstrom resolution). If a higher resolution dataset is required (e.g. for electron density deformation studies), this value can be raised. If the crystal diffracts very badly, this value can be lowered. Results from the findresolution program will be used to fill in the default value; if that program has not been run, it is filled in from a configuration parameter.

Minimum diffraction angle theta

Due to the beamstop, some very-low resolution reflections can sometimes be occluded. That is why this value defaults to 1.5 degrees and not 0.0. It can be increased if an efficient datacollection is desired to collect a shell around a previous Ewald sphere (e.g. you already have a data collection up to 27.5 degrees, and now want to collect the rest upto very high resolution).

Reduce cell axes to not lower than

For large unit cells, a large data set will result. Simulating all these reflections will take a lot of memory and calculation time. Using this parameter, collect will reduce the cell dimensions by integer factors (hence leaving out intermediate reflections) for large cells such that the data set size is reduced, and strategy calculations become faster. 10 Angstrom is normally sufficiently small on one side, and sufficiently accurate on the other (For radiations other than Mo, appropriate scaling will be performed on the default).

Once you have confirmed the settings using "OK", another dialog will pop up asking you where to get the unit cell parameters.

Two paths can now be followed:

1. You know the unit cell and orientation, and want to use it for the strategy.
2. You simply want to measure a half sphere or a full sphere.

If you want to make use of the symmetry and orientation of the unit cell, you will need:

• EITHER: a ".x" file from DENZO, plus the corresponding ".kcd" file. (Note to experienced users: If you are a regular user of the Denzo-SMN or HKL2000 GUI, you might store your '.x' files in a different directory from the '.kcd' files. Please see the cellaskkcdfilename configuration manual).
• OR: a ".rmat" file from DIRAX.

Under "More options", you will find two more parameters:

Point group of data set

If this is set to "Default", the lowest laue group for the crystal system will be chosen as the symmetry of the data set. If you know that the symmetry is higher than the minimum, or if you want to collect as many Friedel pairs as possible, you can change the point group here.

When lowering the symmetry using this parameter, please remember that some (many?) Friedel pairs will always be measured, but unless the pointgroup is acentric, that will not be one of the goals of the data collection strategy. Please note that switching to an acentric pointgroup will make the data collection strategy go a long way to make sure that all Friedel pairs are measured. This might result in a much less efficient strategy (collecting the full sphere is much more than 2 times more difficult than collecting a half sphere). Remember that the absolute configuration of the structure is probably apparent from a few low-resolution reflections, and hence one does not need a complete set of Friedel pairs to determine the absolute configuration. For borderline cases (very weak anomalous scattering), please also see the description of the Friedel strategy (below).

Coinciding axes criterion

This is a value used by Y.Le Page's algorithm to determine the symmetry of the lattice. If you have an inaccurate cell, this value might need to be raised above the default of 0.2 degrees, in case of pseudo-symmetry it might need to be lowered.

Should unit cell be normalized

If this is switched to "No", the Buerger cell reduction and Le Page lattice symmetry algorithms will not be used. The crystal system will be guessed from the given unit cell parameters using the "Coinciding axes criterion".

Note: If a ".rmat" file includes a transformation matrix, that transformation is used to determine the conventional cell instead of using the Y.Le Page algorithm (See the rmat format specifications)

Press the "OK" button to continue. Yet another dialog box will pop up, requesting the host name of the Windows PC that controls the goniometer.

CCD Controller host name

If you have only one goniometer, this name should be correct, and all that is required is to press the button labelled "OK" to make the connection.

If your generator is remote-accessible, and the settings are lower than "collect" thinks they should be (to configure what collect thinks is too low, please see configuration of generator settings), you will now get a one-time warning.

If your generator is in "REMOTE" mode, you can change the generator setting later when making the "scan set" if desired.

At this point the main experiment window will show the current status: the hardware connection, the unit cell, and the calculated dataset.

For the hardware connection, the following buttons may be present:

• A button starting with "Connection", containing the name of the CCD PC. Click on this button to rebuild the connection or to select a different CCD controller.
• Possibly a red button with the text "Acquire mastership". Mastership is required to perform positionings and scans on the goniometer. Press this button to attempt to acquire mastership over the goniometer.
• A Button "Communication log", enabling you to follow the commands that are sent to the goniometer, and to interact with the goniometer directly via a command-line interface (Using the command line interface in collect is not advisable, as it might confuse "collect". See nkcd for a better possibility).

For the data set, a line will be shown summarizing the hkl limits and the internal symmetry. Press the button to change the parameters.

At this point, an empty scanset will appear in a separate window, plus a number of buttons that enable you to change the scanset.

The most important button is the one labeled "Strategy". If the strategy button is pressed, a dialog box containing the parameters of the strategy will be shown:

Those are:

Detector to crystal distance

A strategy is normally carried out at a single detector to crystal distance. The default value will be calculated from earlier results (if available), if nothing is known yet, it is set to the value of a configuration parameter. The distance needs to be large enough to be able to separate the individual diffraction spots (For Mo K-alpha radiation this can normally be accomplished if the detector to crystal distance in mm is larger than the the longest axis of the unit cell in Angstrom). Obviously, if this value is set to unnecessarily large values, the measurement will take longer than needed.

Datacollection strategy

Choose the type of strategy here. Normally, a phi scan is made that captures as many reflections as possible, followed by omega scans to complete the dataset. Alternative strategies can be selected using the arrow at the right of the entry. There are a number of specialized strategies for special cases (described below). If you prefer one of the alternative strategies as a default, this can be set using a configuration variable

Enable low-temperature kappa limitations

For low-temperature measurements, |kappa| should be restricted to values between 15 and 120 degrees. At |kappa| lower than 15 degrees excessive cooling of the phi motor could occur, and at |kappa| higher than 120 degrees icing of the crystal could result. Enable this option to enforce these kappa limitations.

Prevent overlap by the longest axis

If the longest axis in the reduced cell is very long, normally very fine slices must be taken to prevent overlap of neighbouring reflections. Switching this flag to "on" tries to avoid this type of overlap by avoiding to point the long vector in the direction of the detector, allowing for bigger slices. This is especially useful if the longest axis of the reduced cell is much larger than the other two.

Enable strict efficiency theta limitations

Normally one does not allow the detector swing angle to be higher than strictly necessary for the outside edge to reach the highest reflections that should be collected. However, when collecting the full sphere of data, collection of some high-resolution reflections might require a larger detector-swing. In such cases this limitation can be removed. Note, however, that the integration of high-swing scans might be problematic, and that datacollection efficiency will suffer. Please remember that there are normally better ways of obtaining a redundant data set than to enforce a full sphere. The determination of absolute configuration is performed best by accurately collecting redundant low-resolution data (e.g. using a Friedel strategy) and not by measuring as many Friedel pairs as possible.

Desired completeness

The strategy calculation will stop when the data collection is sufficiently complete. The default completeness, 0.995, should normally be fine.

Desired redundancy of the dataset

If this is set to a value larger than 1.0, the strategy will try to collect most reflections (normally 90%) at least that number of times. This can be useful if absorption correction is required or if extremely accurate data are needed for e.g. electron density studies.

Make phi scans + omega scans to fill asymmetric unit

Standard catch-all strategy. Choose this one unless you have very good reasons to choose another.

Make optimized phi scans at kappa=0

Skips the omega scans, only makes phi scans. This is not guaranteed to give a complete data set.

Make omega scans to fill asymmetric unit

Skips the phi scans, only makes omega scans.

Make omega scans with even order axes vertical + other omega scans

Tries to measure as much as possible using 2 fold axes in the lattice vertical. The rest of the data collection is done using other omega scans. This is also known as the "Friedel" strategy, since for all lattice axes that are also axes in the structure, Friedel pairs will be measured in the same frame minimizing errors in the Bijvoet differences and optimizing the discriminating power between the enantiomeric structures.

Make a phi scan + 2 standard omega scans

This strategy (at dx=35 mm) can collect a half sphere. It has relatively low redundancy, but is very quick to calculate, and makes "the same" measurements regardless of the crystal.

Make 360 degree phi scans at kappa=0

For when you want that. This is not guaranteed to give a complete data set.

Make 180 degree phi scans at kappa=0

For when you want that. This is not guaranteed to give a complete data set.

Make omega scans at chi=55 degrees

A quick and easy strategy using only scans at chi=+/-55 degrees, at 120 degree intervals of phi. Not guaranteed to give a complete data set.

After selecting the right strategy, press "OK" to proceed. All necessary information has now been supplied, and the strategy will be calculated.

Depending on the complexity of the question this can take anywhere between a few seconds and several minutes to complete. During this time, "collect" talks to your goniometer controller to ask it about hardware limitations.

The calculated strategy will be displayed in the strategy editor. At the right side in a yellow background the number of "new" reflections measured by each scan is shown.

You can (temporarily) remove scans from the strategy using the checkboxes at the beginning of each line. A permanent removal can be achieved by pressing the "X" button to the right of each scan, or by leaving the scan set editor using "OK" while scans are deselected.

The "Overflow scans" button in the scan set editor achieves the same as the strategy for a subset of low-resolution reflections. It will add the necessary scans to the end of the strategy, and will make sure that they are measured at a much higher speed.

Scans can be edited by clicking on the line itself using the left mouse button:

Some expert options are hiding under the "More options" button:

The extra two lines allow the user to require that a specific scan uses a different data collection time or a different frame angle than all other scans. This can be specified by "overwriting" the normal values or by "multiplying" the normal values by a factor. These extra parameters can be useful to make a quick data collection to capture overloaded reflections at low resolutions.

Click "Ok" to continue (and to confirm any changes you may have made).

Back in the scan set window, the button "Remove deselected" removes from the display those scans that have their checkboxes disabled. The "Unique Data" button can be used to calculate the effect of the changes on the completeness of the measured data set.

Pressing the "Redundancy" button will start an alternative procedure that will calculate the redundancy of the dataset after each scan, and the number of reflections with the lowest redundancy:

In this example, a total of 3525 reflections will be measured. 90% of all data will be measured 1.0 times or more, and 104 reflections were measured only once (and no reflections were missed).

A more complete overview of the redundancy of the final dataset is shown in another window that will pop up:

Click "Ok" to dismiss this window and continue building the scan set.

Using the "Add operation" button, you can manually add scans, generator settings, cryostat commands, and dark images to the data collection. The defaults for the generator settings, cryostat control and view position can be set in the collect configuration files.

This will be mainly used to change the generator settings before and/or after the measurement:

We have already seen that the individual operations in the scan set can be modified by clicking the left mouse button on the green area. Other manipulations (moving the operations around or duplicating them) is possible by clicking the right mouse button over the operation description. A small menu will pop up from which the desired operation can be selected.

Press "OK" to complete the generation of the scan set. You will notice that the "Make scan-set" button has now turned green, indicating that a valid (non-empty) scan set has been constructed.

Now a Dialog window pops up asking for the scan parameters.

• The default "Scan angle per frame" is calculated from earlier results. A normal value is 1.0 degrees. In case of very large unit cells, or problematic mosaicity, it might be lower. For very small unit cells, this will be increased up to 2.0 to speed up measurement. Larger values than 2.0 degrees will not be proposed to prevent inaccuracies due to background radiation.

  Integration procedures from denzo and evalccd both can handle fine-slicing as well as wide-slicing. Hence, the best value for the scan angle per fram is only dependent on the sample. Wider slices will reduce readout noise, and reduce the size of the data set. Integration of widely-sliced data will therefore be speedier than finely-sliced data. Images should not be made too wide to prevent buildup of background radiation noise (e.g. from the crystal mount) or reflection overlap.

• The default "Integration time" will be calculated from earlier results as well. It should be chosen such that reflections with the highest desired resolution are still above the noise, but ideally also so low that no overflows occur. Reasonable values are between 5 and 600 seconds, depending on the quality of the crystal. If both of these restrictions can not be met at the same time (which can happen for a badly diffracting crystal or when very accurate and very high resolution data is required), it is advisable to perform a slow datacollection first, and a second faster datacollection later with much lower theta limits to fill in the overflows.

• The "filename pattern", which should contain two sets of "#" characters (at least 2 # characters in the first set, and 3 in the second). The first set of # will contain the scan number from the scan set, the second set will contain the frame number. The default value of "s##f###.kcd" will normally be OK. If "s01f001.kcd" already exists, the default will start with a "t" instead. The rest of the default pattern can be changed using a configuration variable. Advanced users: You can add ".Z" or ".gz" or ".bz2" to use the programs "compress", "gzip" or "bzip2", respectively, to reduce the size of the images during data collection. YOU MUST HAVE the appropriate compression program installed on your system, or the datacollection will fail.
• "Number of iterations" (number of times the same image is measured). Normally this value is 2, for so-called de-zingering of images. If the exposure time is very short (around 10 seconds), you might want to change this to 1 iteration per frame since zinger pixels will be very rare. If the exposure time is very long (more than an hour), a triple image might be needed to get rid of all zinger pixels completely (but please note that triple images can not be used in denzo).
• "Number of the first scan" (usually 1), can be changed to start collecting e.g. at s05f001.kcd instead of always starting at s01f001.kcd.

Click "OK".

At this point it is desirable to save the experiment. Select "Save experiment" from the "File" menu, and give the experiment a name (If the experiment is not saved, "collect" will attempt to auto-save the experiment as "autosave.non").

For advanced users: it is possible to change the unit cell (e.g. make it triclinic, or lowering the symmetry) and the data set (e.g. to measure to higher resolution) using the buttons in the main experiment window, and re-enter "Edit scan set". You can then complete the new data set by calculating another strategy. The target dataset for the additional strategy is the dataset listed in the status row at the bottom of the scan set window.

An example:

Measuring Friedel pairs Bijvoet differences are most notable in low-resolution reflections. It may be inefficient to measure all Friedel pairs out to high diffraction angles. Instead: First make a dataset upto 27.5 degrees theta, and use it to make a base-strategy. Press OK on the scan-set window to return to the main window of collect. Click on the unit cell line, and change to a non-centric point group. Chances are that there are multiple possibilities. Choose the right one. Now click on the dataset line, and change "theta max" to a lower angle, like 15 degrees. OK. Re-enter "edit scan set", Use "Strategy" to find an efficient way of measuring the additional data. If you expect very small Bijvoet differences, you can use the Friedel strategy.

If you press "Collect Data" in the main window, the measurement will be started. If possible, the disk-space available on the current disk is checked just before.

or even:

Obviously, this warning will not appear if you have enough diskspace when the measurement starts, but subsequently fill up your disk while doing other projects. If the disk fills up, data collection will be stopped.

If, for some reason, the measurement would stop or be stopped in the middle, simply press the "Collect data" button again to continue. All images that have been collected so far will automatically be skipped. Do not remove e.g. scan 1 from the scan set before clicking "Collect data" again, because this will effectively renumber all scans, and what was earlier meant to be scan 2 will now be collected as "s01f###.kcd"!

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Previous: collect: Data collection strategy and data collection
Next: Cell determination using Denzo

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(C) 1997-2008, Bruker AXS BV, R.W.W. Hooft