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Npeakref: cell refinement gui

The "npeakref" program is a GUI frontend to the peakref program from the evalccd program suite.

Usage:

  npeakref [.pk and .pk3 file names] [.rmat file names]

When the program starts, it will read in the ".rmat" and ".pk" or ".pk3" files specified on the command line (if any), and start a GUI that shows all parameters that can be refined with their current values.

In the top panel the "rmat" files and the "pk" files are displayed that are used for the refinement.

"pk" files are files that describe the locations of peaks in diffraction images. These can consist of x,y 2D coordinates in mm (.pk file extension) or x,y,rotation 3D coordinates in mm and degrees of rotation (.pk3 file extension). They are automatically produced by the "phichi" procedure for the images used for cell determination. To create a ".pk" file for a whole data collection, run:

  any final_noshift.y
  any> sigma 5
  any> forbid all-good
  any> pk
  any> exit

(This procedure is automatically performed by the "postrefine" button in supergui, so you might already have the ".pk" file if you used that procedure before) Any ".y" file that was produced by evalccd without the "fixfinal" argument can be used as input for this procedure, "final_noshift.y" is the default name of a suitable file if the integration is run from supergui. "rmat" files describe a unit cell that should explain the diffraction peaks. These files are produced by all indexing programs based on dirax. It is possible to convert a ".x" file to a ".rmat" file using the xmatrix program.

It is possible to refine on multiple sets of "pk" files, and to refine multiple (up to 4) unit cells simultaneously. In such cases, the file names should be given in the user interface separated by spaces. Adding a single file to one of the two boxes can be done using the file selection dialog available under the "Select" button.

If "Return" is typed in the "pk" box, the new "pk" files will be used from then on in the refinement. Typing "Return" in the "rmat" box, results in a complete restart of the refinement.

At the bottom left, two buttons allow you to access the 2 most frequently used actions in the npeakref program: "Go once!" will start a refinement, and show you the results. "Go 3 times!" will repeat the refinement three times with increasingly tighter step sizes.

Above these two buttons there are up to three numbers expressing the goodness of the fit. "resmm" is the average distance on the detector between the predicted and observed position of all peaks in the refinement, expressed in mm. "resrot" is the average distance in the rotation angle between the predicted and observed position of all peaks in the refinement, expressed in degrees. "res" is the weighed sum of resrot and resmm; this is the value that is the target of the minimization.

In the big window at the bottom right, the output of the of the last command is shown. This normally shows the current statistics about all variables and some summary values for all reflections. There are three buttons above this window that allow for pagination. All previous output (including output from underlying peakref commands issued by the npeakref program) can be displayed by paging back and forth with these buttons.

Options menu

The "Options" menu contains the following options:

"Edit variables": This will pop up a dialog offering you to change the value of all non-fixed variables. For each of the variables it also contains a check box to enable refinement of that variable (but see the Fix/Free menus described below for a better way to do this in general). See above for a screenshot.
"Redetermine pointgroup": This will make a judgement about the pointgroup, and make appropriate changes to the restrictions placed on the unit cell refinement. Please note that the algorithm in the peakref program is not capable of doing a cell transformation to increase the symmetry of the lattice.
"Reject outliers": Selecting this option will reject all peaks that are more than 5 times further away from their predicted position than the average.

Fix and Free menus

Using the "Fix" and "Free" menus you can add or remove groups of variables from the refinement process.

List menu

The list menu can be used to show listings of reflections rejected for any reason, reflections rejected because they are too far off in the rotation direction and reflections that are rejected because they are too far off in their position on the detector.

The list menu also contains an item to go back to the default refinement status view.

Storing the results

The detector displacement and missetting can be stored using the option "Save detector alignment" under the file menu. All (up to four) refined unit cells can be stored using the "Save rmat" options in the same menu. All of these options offer you to specify an alternative name for the output file.

Expert mode

The "npeakref" program shows an extra "command line" in case the peakrefexpert configuration parameter has been set. Use this with care.

Some background

The peakref program that forms the engine behind the "npeakref" user interface is using a so-called simplex optimization algorithm to find the best fit. A big advantage of this optimization procedure is that it does not make any assumptions about the form of the function that is optimized, nor about the parameters and their interrelations. The disadvantage is that there is no way to extract standard deviations in the parameters, and that it needs a bit of baby-sitting for the best results.

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