dtprocess on-line help

Index spots to get the initial crystal unit cell and crystal orientation

1. Select a header from the top list. Usually this is dtprocess.head.
2. Select a reflection list from the bottom list. Usually this is dtfind.ref.
3. Set the menu options described below.
4. Select Run index
5. View the dtindex log file. If Prompt user is set, you will have to enter your choices for the lattice type and orientation angles in the dtindex window.

Index menu options

Use Fourier method

If set, the direct space cosine Fourier map is calculated within a hemisphere with a radius of Max cell length. This map is searched for 3 non-coplanar peaks which define the crystal lattice. If not set, a reciprocal space algorithm is used. The Fourier method tests for every possible unit cell in every possible orientation up to a maximum cell length (see Max cell length below).

User chooses solution

If set, the user is prompted to choose the solution. If not set, dtindex will pick a solution based on the least squares fit residual, and Spacegroup num if not 0, or if 0, the value of Max residual.

Spacegroup num

If User chooses solution is not set, then a solution consistent with space group number is selected. If User chooses solution is set, and a solution consistent with the input space group number is selected, then the input space group is used in the output header. A Space group number of 0 indicates no user preference.

Max residual

Maximum allowed least squares residual for a solution to be listed. dtindex fits the reduced primitive cell to 44 lattice characters. Only those solutions with a residual less than or equal to Max residual are displayed. Typically, residuals greater than 5 are not valid solutions. This helps simplify the output and make it easier to choose the correct solution.

Max cell length

The maximum cell length in Angstroms to search. If this is 0, then dtindex tries to determine a maximum cell length on its own. The 1D FFT (DPS) method is sensitive to the maximum cell length chosen, so if it fails, determine if the max cell length was reasonable and reset if appropriate.

Resolution

Only reflections within the resolution limits in Angstroms are used in indexing. If either limit is 0.0, then resolution limits are not imposed. WARNING: The resolution is calculated based on the detector position and wavelength which may have been specified incorrectly. If indexing fails, using a lower resolution range (say 100 - 3 Angstrom).

I/sigmI cutoff

Only reflections with I/sigmaI greater than this value are used in indexing. If 0, then an I/sigmaI cutoff is not imposed.

Show advanced options

If set, this shows the more advanced options described below.

Method

3 indexing methods are available:

1. 3D Fourier: A 3D real space cosine Fourier transform
2. 1D FFT (DPS): The DPS algorithm of Steller et al. (1997)
3. Reciprocal space: A reciprocal space algorithm

The default is the 1D FFT (DPS) algorithm.

Max vecs

The maximum number of difference or reciprocal lattice vectors to use in the calculations. With more vectors the calculations take more time and the residuals will be larger. With fewer vectors, the calculations take less time and you may miss solutions. The DPS method seems to work better with more vectors.

No diff vecs, use direct

If set, difference vectors are NOT used. This is the default. Difference vectors are useful if the detector position is not well known. Difference vectors are bad if spots are from a split crystal or twinning. Also difference vectors are grouped, so it is more important to have a reasonable Max cell length.

List detector props

If set, the detector position and other properties are listed in the output.

Grid size

The grid size in Angstroms for the 3D direct space cosine Fourier map. This is not used when the 3D Fourier method is not selected. If 0, then dtindex tries to calculate a reasonable grid size to use.

Use known cell

If set, forces dtindex to look at vectors and peaks hat match a known unit cell found in the input header. Use Edit / Header items.../ Cell props to edit the unit cell in the header.

Cell length errors

If Use known cell is set, then the cell in the header is used and only cell which match within the cell length errors (in Angstroms) set here are reported. If these are 0, then the error is 3% of the actual known cell lengths.

Cell angle errors

If Use known cell is set, then the cell in the header is used and only cells which match within the cell angle errors (in degrees) set here are reported. If these are 0, then the error is 3% of the actual known cell angles.