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Ndirax: find lattice using dirax

Usage:

ndirax [drx-file]

Pull-down menus

Load .drx

Loads reflection or peaks from a ".drx" file, replacing all reflections that were already loaded.

Merge .drx

Loads reflection or peaks from a ".drx" file, adding them to the reflections that were already loaded.

Load .rmat

Load the unit cell from a ".rmat" file and reindex all reflections based on this lattice.

Quit

Quit the "ndirax" program

The "Option menu" contains 6 commands:

Balloon help

Toggles the status of the balloon help in the program.

Modify dirax settings...

Changes some of the parameters used by the "dirax" program to find the unit cell.

List reflections

Pops up a window listing all reflections with their assigned h/k/l's.

Show kept cells

Pop's up a window showing all cells that were saved in this and previous sessions of "ndirax" in the same project directory.

Modify cellcompare settings

Allows you to edit the cell-comparison criteria used by "ndirax"'s kept cells window.

Remove fitting reflections

This option only works with recent (2000/08/16 or newer) versions of dirax. It provides a new approach for finding twin lattices. The standard approach tries to find a unit cell fitting the remaining reflections, but it will use all reflections to make the final least squares refinement of the unit cell found. Using this new option, one can remove all fitting reflections from the set in dirax, and continue using only the non-fitting reflections.

This option will ask you whether you want to go on to find a cell using the remaining reflections. This is normally what you'd want.

Level fit criterion

This number expresses how tightly a reflection must fit a specific lattice direction before it is taken as contributor. The default value of 1000 (reflections must fit the lattice to 1 in 1000) normally works for good KappaCCD data of a well calibrated detector. Problematic data might need increase (more accurate) or decrease (less accurate) of this parameter to find the cell.

Index fit leniency

Expresses how much worse than the "Level fit" a reflection can fit the final lattice to be still assigned a "H" status and be used in unit cell refinement. E.g. a reflection with an error of 1/300 will not be considered fitting at level fit 1000, index fit 2 (1000/2=500 is more tight than 1 in 300). If there are strange effects in the data that make it difficult to get accurate peak positions, this value might need to be raised above the default value of 2. But be careful, because increasing it too much might result in fractioned crystals being described by one average lattice. This may not be what you want (see below).

Longest cell axis

The longest axis considered. This number should be set to approximately 2 times the longest axis expected in the unit cell. Lowering this number to the appropriate value increases the efficiency of the algorithm (speed and accuracy). Even though this limit exists, unit cells with longer axes might appear in the result list.

Number of triangles to use

The "dirax" algorithm uses triangles of 3 reflection positions to calculate direct vectors. The number of triangles used in the calculation is selected by this parameter. The default (2600 = 26*25*24/6) is to use all triangles for up to 25 reflections. If you have many more reflections, you can increase this number to increase the chance to find the unit cell, at approximately linear cost in CPU time.

Axis equal criterion

To transform a cell to standard setting, axis lengths are considered identical if their difference is smaller than this number.

Angle equal criterion

To transform a cell to standard setting, unit cell angles are considered identical if their difference is smaller than this number.

Length criterion

Two axes are considered identical by the comparison algorithm if their relative difference is less than this number.

Angle criterion

Two axes are considered identical by the comparison algorithm if their relative difference is less than this number.

Matrix criterion

Two cells are considered to have the same volume by the comparison algorithm if the relative difference of the two volumes is less than this number.

The main window

• Use all reflections read from the file. This is the normal start.
• Use all currently fitting reflections. This can be used to "refine" the unit cell found at an earlier stage.
• Use all non-fitting reflections. This can be done to find a twin lattice.

Once you are happy with the unit cell, it can be written to an rmat file using the "Save as .rmat" button at the bottom. The "Keep for later" button adds the cell to the bottom of the "Kept cells" window.

Kept Cells

The "Kept cells" window shows a list of all unit cells that were "kept" using ndirax.

This can be used to compare unit cells found by "ndirax" using the comparecell algorithms. Just select any 2 cells from the list using the checkboxes, and press the "compare" button. If only 1 cell is selected, the cell is compared with itself (useful to detect possible twinning relationships).

When ndirax terminates, the kept cells are automatically saved in a file named "keptcells.dat"; this file is automatically reloaded when ndirax is restarted.

If you have any ideas on how to improve the functionality of the Kept Cells, please send mail to collect@bruker-axs.nl.

Twins

As a group, all samples containing more than a single lattice are commonly referred to as "twins". Actually, there are at least four different common cases of multiple-lattice samples.

Fragmented crystals

A "single crystal" that is broken into two or more fragments. Every reflection is thus split into multiple different spots on the detector. If such a sample is run through dirax, a unit cell is found that fits only part of the reflections. Relaxing the "levelfit" and "indexfit" conditions will result in more reflections fitting the lattice, but the lattice itself does not change very much. At very relaxed values, you will get a sort of "average" lattice, whereas strict parameters will home in to a single fragment crystal. Using strict values, a second fragment lattice might be found using the twinning options in dirax; a comparison of the two lattices will show a small rotation of 0.2--2.0 degrees. This rotation is very small, so the rotation axis is not very well defined. Since the partially overlapping diffraction spots come from the same h,k,l it is possible to integrate the data set by adding everything together as if it were a single spot. If the fragmenting pattern is a "bundle of misaligned needles" or a "stack of misaligned disks", the Anisotropic Mosaicity can be used when integrating in EvalCCD. If the rotation angle between the fragments is a bit larger, the two lattices may be better integrated as separate entities.

Plane rotations

If one of the layers in the crystal is "almost centrosymmetrical", sometimes a mistake can be made in the buildup of the crystal. If e.g. in the a,c direction such a plane exists, the next layer may be mis-built as -a,-c. The b axis for the two parts of the crystal will then point in two different directions, whereas the a and c directions coincide. In reciprocal space, the h0l planes of the two different crystals coincide, and the other planes will have more or less overlap depending on the k index. The reflections that are close together do not have the same h,k,l index in the two lattices, so it is essential that they are separated as much as possible. Reflections that are too close to be separated will need to be de-twinned at a later stage.

The same misfitting process can happen once (the two crystals might even be visible separately under the microscope) or multiple times, depending how close to centro-symmetric the a,c plane is.

False fits

If one of the diagonals of the unit cells has a length comparable to one of the unit cell axes, twinning can sometimes occur where this diagonal is used instead of the cell axes in the buildup of the unit cell. This will result in a similar situation as for the "plane rotations", but with a different pattern of overlapping and non-overlapping reflections.

Merohedrical twins

These are the easiest. The diffraction pattern from a merohedrical twin looks like a single crystal in every aspect. Cell determination and integration can proceed following single crystal procedures. However, unless the twin law is known, there is no way to solve/refine the structure.

Twins in dirax

• Only part of the reflections (half?) fit the lattice. In such a case, it might be worth to relax the fit-conditions a bit (raise indexfit). If that causes more reflections to fit, you are either dealing with a fragmented crystal, or with a badly aligned system. A fragmented crystal might reveal itself further from the diffraction images, especially split peaks in a phi/chi image are a very good indication of crystal fragmentation. If the fragmentation is into 2 well-separated crystals, you can find the second component by using the "start using non-fitting reflections" button in ndirax. If this doesn't work, you should try to tighten the "levelfit" a bit on the first cell before looking for the twin lattice.
• Approximately half of the reflections fit the lattice, and the other half fits another, comparable lattice in the cell listing. Congratulations, you have found the two components of your twin crystal.
• All of the reflections fit a much-too-large lattice. In such a case, look through the list for smaller unit cells that fit a reasonable amount of reflections. If necessary, lower "indexfit" or raise "levelfit" and re-try to find the lattice. Once you have found a good lattice, see if the remaining reflections fit a twin lattice using the "start using non-fitting reflections" button

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