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XDS

1. Prepare the first input file: XDS.INP (example)

Set ORGX and ORGY to half the detector size. In the case of the MAR-CCD  (NXxNY=3072x3072 pixels), this means (as explained in the input):

[...] i.e. ORGX=NX/2, ORGY=NY/2
ORGX=1536.00 ORGY=1536.00


Set: 

DETECTOR_DISTANCE=;
OSCILLATION_RANGE=;
X-RAY_WAVELENGTH=;
SPACE_GROUP_NUMBER=0; This is for unknown crystals, and the UNIT_CELL_CONSTANTS= line is automatically ignored;
FRIEDEL'S_LAW=FALSE if the crystal is supposed to have anomalous scatterers (and always when using XDSCONV see below);
DATA_RANGE= with the numbers of first and last data image collected;
BACKGROUND_RANGE= with the numbers of first and last data image for background (doing 1 20 is a good idea, although suggested is often 1 to 5);
RESOLUTION_SHELLS= (example: 10 6 5 4 3 2 1.5 1.3 1.2)
JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT

2. Run xds_par (to use multiple CPU, if present) or simply xds

2b. Sometime xds stops with the following error message

!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 70%) OF INDEXED REFLECTIONS

in that case run again xds using: 

JOB= DEFPIX INTEGRATE CORRECT

as suggested along with the error message above.

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 JOB= CORRECT only once integration is finished.

3. Check IDXREF.LP and look for DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE 

4. Once either JOB= ALL or JOB= DEFPIX INTEGRATE CORRECT are done, check CORRECT.LP and go to

SUMMARY OF DATA SET STATISTICS FOR VARIOUS SUBSETS OF INCLUDED DATA IMAGES

 
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.

5. Check INTEGRATE.LP for

***** AVERAGE THREE-DIMENSIONAL PROFILE OF xxxx STRONG REFLECTIONS **

This tells as about the quality of integrated intensities.

Also, look at:

***** SUGGESTED VALUES FOR INPUT PARAMETERS ***** 
BEAM_DIVERGENCE=   0.474  BEAM_DIVERGENCE_E.S.D.=   0.047
REFLECTING_RANGE=  1.547  REFLECTING_RANGE_E.S.D.=  0.221

and insert this values in XDS.INP after

!============== INTEGRATION AND PEAK PROFILE PARAMETERS ==================

Then run again DEFPIX INTEGRATE CORRECT

6. To determine the right Space Group:

Option 1

Space group automatically selected by XDS:

Option 2

- First run only INIT COLSPOT IDXREF in spacegroup 0 (which means "unknown") and inspect the tables found in IDXREF.LP and CORRECT.LP
- Then input the correct spacegroup number and the cell parameters in XDS.INP, and 
- Rrun IDXREF DEFPIX INTEGRATE CORRECT

Option 3
 (easiest way)

pointless xdsin XDS_ASCII.HKL 

From the pointless output, the correct space group should be deduced and CORRECT run with appropriate SPACE_GROUP_NUMBER, UNIT_CELL_PARAMETERS


7. Final data optimization:


cp GXPARM.XDS XPARM.XDS
mv CORRECT.LP CORRECT.LP.old
egrep -v 'JOB|REIDX' XDS.INP > XDS.INP.new
echo "! JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT" > XDS.INP
echo "JOB=INTEGRATE CORRECT" >> XDS.INP
cat XDS.INP.new >> XDS.INP
xds_par

and re-run the INTEGRATE and CORRECT steps (this has the advantage that the refined geometry parameters (from CORRECT) are recycled into INTEGRATE, which sometimes leads to better R-factors).


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:

The log files are written with the program name and a "LP" extension.


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".