dtprocess on-line help

Refine crystal, detector and source properties

1. Select a header from the top list. Usually this is dtindex.head, dtrefine.head or dtintegrate.head.
2. Select a reflection list from the bottom list. Usually this is dtfind.ref or dtintegrate.ref.
3. Set the menu options described below.
4. Select Run refine
5. View the dtrefine log file.

Refine menu options

Reflns

Reflections can come from either a reflnlist file or from images themselves. The option menu allows two choices:

Reflnlist

Select a reflnlist from the Reflnlist scrolled list.

Image sequence

Select one or more images from the Images scrolled list. Reflections will be predicted for each of the selected images and the centroids of the predicted reflections will be determined and stored in a reflnlist for use in refinement.

Prompt to save

If set, then you will be asked if you wish to write a new results header at the conclusion of the refinement. You may answer yes (y) or no (n). If not set, then a new header is automatically written with the dtrefine results. The prompt option has no effect in dtintegrate and the Integrate menu.

Macros

Use this option menu to select Interactive dialog or a macro. Macros are read from the input header file. They may be edited and saved to the header with File / Save As.... You may change the name of a macro by using -name as the last option in the macro followed by the desired name, then click on the macro option menu to update the name in the option menu. A final -go is always appended to the macro by the refinement procedure, so it is not required in the macro. The -display and -prompt macro options are set by the toggle buttons and need not appear in the macro either.

Interactive dialog

Toggle buttons

Select the crystal, detector and source properties to refine or hold fixed simply by clicking on them. Green means refine, no green means hold fixed. The toggle button labels are self-explanatory.

Sigma

Only reflections with Intensity/SigmaI above this value are used in refinement.

Resolution

Only reflections within the resolution limits in Angstroms are used. If 0.0, 0.0, then all reflections are used.

Rej limits

Reflection with a calculated position that differs by more than the specified value from the observed position are not used in refinement.

Cycles

Maximum number of refinement cycles. Fewer cycles may be used if refinement converged. a spot comple

Rel weight

Relative weight given to difference of rotation angles versus the difference between millimeter positions.

Detector, then all crystal

Refine the detector position, then all the crystal properties, then all but the source properties. Use this macro if you are more sure of the crystal properties than the detector properties.

Crystal, then all detector

Refine the crystal properties first, then all the detector properties, then all but the source properites. Use this macro if you are more sure of the detector properties than the crystal properties.

Low resolution, then all resolution

Refine with low resolution reflection first, then use all reflections.

Custom 4

Same as Low resolution, then all resolution

Custom 5

Same as Custom 4.

Custom 6

Same as Custom 4.

Custom 7

Same as Custom 4.

Rotation axis, crystal, detector

This turns on the SourceRot refinement which is essentially equivalent to refining the tilt of the rotation axis. Use this option with reflections that are widely spaced in the rotation angle when you suspect the rotation axis to be tilted with respect to the source.

Display

If set, then the reflection list filename is sent to dtdisplay for visualization. A vector from the observed centroid to the calculated centroid is drawn for each reflection used in the refinement. If the dtdisplay / Respond to updates / Others is not set, then dtdisplay will not listen for the filename and thus will not display the reflections. NOTE: this is always set and no longer available in the menu.

Tips

If the input reflection list is from a 2D dtfind run, then the crystal mosaicity cannot be refined and the mm and deg residuals will be larger than with a 3D dtfind run. Estimate the crystal mosaicity by trial-and-error at the Predict level by predicting, then displaying the reflnlist with dtdisplay. You may change the mosaicity by editing the header (Edit/Edit header items.../Crystal properties).

If reflections found in a narrow rotation range (from a single image or narrow scan) are used, then Detector Rot1 and Crystal Rot3 are highly correlated. You should not refine the Detector Rot1, but use a value determined from a 3D reflection list.

The detector distance can be refined if you have reflections from a wider rotation range or a spacegroup higher than orthorhombic symmetry.

Wavelength and crystal cell lengths will not be refined simultaneously.

For difficult cases, increase the Sigma to use only the strongest reflections and reduce the Rej limits so only reflection centroids that are close to the calculated ones are used in refinement.

You may wish to exclude low resolution reflections, especially if they are streaked.

You may wish to filter your reflnlist with dtreflnmerge in special ways before refinement. For example, you can remove spots from an ice ring.