Space group determination
In case of a crystal with an unknown space group (SPACE_GROUP_NUMBER=0 in XDS.INP), XDS (since version June 2008) helps the user in determination of the correct space group, by suggesting possible space groups compatible with the lattice symmetry of the data, and by calculating the Rmeas for these space groups.
Space group selected by XDS
XDS (or rather, the CORRECT step) makes an attempt to pick the correct space group automatically: it chooses that space group which has the highest symmetry and still a tolerable Rmeas compared to the Rmeas the data have in P1.
In many cases the automatic choice may be the correct one, and re-running the CORRECT step is then not necessary.
Space group selected by user
Even in case the space group selected by XDS should be incorrect, the resulting list (in CORRECT.LP) should give the user enough information to pick the correct space group herself. She may then put suitable lines with SPACE_GROUP_NUMBER=, UNIT_CELL_CONSTANTS= into XDS.INP and re-run the CORRECT step to obtain the desired result. (The REIDX= line is no longer required; XDS figures the matrix out.)
Influencing the selection by XDS
new parameters
The automatic choice is influenced by a number of decision constants that may be put into XDS.INP but which have defaults as indicated below:
- MAX_CELL_AXIS_ERROR= 0.03 ! relative deviation of unconstrained cell axes from those constrained by lattice symmetry
- MAX_CELL_ANGLE_ERROR= 0.3 ! degrees deviation of unconstrained cell angles from those constrained by lattice symmetry
- TEST_RESOLUTION_RANGE= 10.0 5.0 ! resolution range for calculation of Rmeas
- MIN_RFL_Rmeas= 50 ! at least this number of reflections are required
- MAX_FAC_Rmeas= 2.0 ! factor to multiply the Rmeas in P1 with to still be acceptable
The user may experiment with adjusting these values to make the automatic mode of space group determination more successful. However, it is much easier to just input the space group and cell parameters that the user thinks are correct.
alternative indexing
As the old REIDX= input has lost its importance, it is useful to keep in mind that there are two ways to have XDS choose an indexing consistent with some other dataset:
- using REFERENCE_DATA_SET=
- using UNIT_CELL_A-AXIS=, UNIT_CELL_B-AXIS=, UNIT_CELL_C-AXIS= from a previous data collection run with the same crystal (see [1])
Screw axes
The current version makes no attempt to find out about screw axes. It is assumed that the user checks the table in CORRECT.LP entitled "REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*)", and identifies whether the intensities follow the rules
- along each axis in reciprocal space, a two-fold screw axis (theoretically) results in zero intensity for the odd-numbered (e.g., K = 2*n + 1) reflections.
- similarly, a three-fold screw axis (theoretically) results in zero intensity for the reflections of type 3*n+1 and 3*n+2, leaving the 3*n reflections as candidates for medium to strong reflections.
- analogously for four-fold and six-fold axes.
Notes
- There is still the old Wiki page Old way of Space group determination
- To prevent XDS from trying to find a better space group than P1, you could just use MAX_FAC_Rmeas= 1.0