1. Prepare the first input file:
JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
Either of these steps will integrate the frames. Since we did not change the space group (still number 0) xds will automatically select the best space group and use it during integration. To switch to a different space group we will run
4. Once either
Here R-FACTOR, I/SIGMA, COMPL, RES LIMIT, ANOMAL CORR can be found.
Notice: Data set statistics is reported several times, each with a different upper limit on the number of images included. This provides the user with the information for deciding which data images should be excluded from the final data set because of radiation damage or other defects.
This tells as about the quality of integrated intensities.
Also, look at:
and insert this values in
Then run again DEFPIX INTEGRATE CORRECT
6. To determine the right Space Group:
Space group automatically selected by XDS:
- First run only
- Then input the correct spacegroup number and the cell parameters in
From the pointless output, the correct space group should be deduced and
7. Final data optimization:
and re-run the
The 8 Steps of processing X-ray data with XDS:
Rotation data images are processed in 8 steps. [Results and diagnostics from each step are saved in files with the extension .LP attached to the program step name called in succession by XDS]
1) XYCORR. Calculates lookup tables of spatial corrections for each detector pixel which are stored in the files X CORRECTIONS.pck and Y-CORRECTIONS.pck
2) INIT. Determines three lookup tables, saved as files BLANK.pck, GAIN.pck, and BKGINIT.pck, that are required by the subsequent processing steps for classifying pixels in the data images as background or belonging to a diffraction spot ('strong' pixels)
3) COLSPOT. Locates strong diffraction spots occurring in a subset of the data images and saves their centroids on the file SPOT.XDS
4) IDXREF. Uses the initial parameters describing the diffraction experiment as provided by XDS.INP and the observed centroids of the spots from the file SPOT.XDS to find the orientation, metric, and symmetry of the crystal lattice. Refines some of these parameters (input parameter REFINE(IDXREF)=) and returns the complete parameter set via the file XPARM.XDS.
5) DEFPIX. Recognizes regions in the initial background table (file BKGINIT.pck) that are obscured by intruding hardware and marks the shaded pixels as untrusted. In addition, pixels outside a user-defined resolution range (INCLUDE_RESOLUTION_RANGE=) are marked and eliminated from the trusted region. The marked background table thus obtained is saved on file BKGPIX.pck which is needed by the subsequent program steps.
6) XPLAN. Supports the planning of data collection. It is base upon information provided by XPARM.XDS and BKGPIX.pck, both of which are available by processing a few test images. XPLAN estimates the completeness of new reflection data, expected to be collected for each given starting angle and total crystal rotation, and reports the results for a number of selected resolution shells in the XPLAN.LP.
7) INTEGRATE. Determines the intensity of each reflection predicted to occur in the rotation data images (DATA_RANGE=) and saves the results on file INTEGRATE.HKL. The diffraction parameters needed for predicting the reflection positions are initially provided by the file XPARM.XDS. These parameters are either kept constant or refined periodically using strong diffraction spots encountered in the data images. Whether refinement should be carried out at all and which parameters are to be refined can be specified by the user (input parameter REFINE(INTEGRATE)=).
8) CORRECT. Applies correction factors to intensities and standard deviations of all reflections found in the file INTEGRATE.HKL, refines the unit cell constants, reports the quality and completeness of the data set, and saves the final integrated intensities on the file XDS_ASCII.HKL.
Notes on the outputs:
XYCORR.LP. This is the output from the XYCORR program and provides few detector specific informations.
INIT.LP. This provides information about the "Detector_gain" and "Detector_background" calculations.
COLSPOT.LP. Details of the number of spots collected for indexing. The first few lines gives the input parameters used for picking of the spots.
SPOT.XDS. Ascii file with the listing of the spots.
IDXREF.LP. Output from the indexing program. The information about various Bravais lattices including the quality of each solution are given at the end of ths file.
XPARM.XDS. The orintation matrix file.
DEFPIX.LP. Provides information about the "trusted" and "untrusted" regions of the detector.
XPLAN.LP. Data collection strategy information.
INTEGRATE.LP. Output file from integration. The number of reflections written to the reflection file is given at the end of the file.
INTEGRATE.HKL. The reflection file output. First few lines at the beginning provides details of the parameters used for the integration.
CORRECT.LP. The scaling output file. Search for 'R-FACTOR' to see the R-factor and related information. The final statistics including R-factor, number of observations, unique reflections, etc. are given towards the end of the file (Tip: Search for XDS_ASCII.HKL and above informations come just before this). If you are scaling two or more data sets (eg. MAD), look at the "CORRELATION" between two data sets to get an idea about relative scaling.
XDS_ASCII.HKL. The scaled reflection file. The first few lines gives details of the parameters used for scaling.
GXPARM.XDS. The final refined cell parameters and orientation. This file is similar to the "XPARM.XDS" file. If we get a better solution from the refinement in the "CORRECT" step, we could replace the XPARM.XDS file by GXPARM.XDS file and rerun "INTEGRATE" and "CORRECT".