Quality Control
This is an attempt of putting together a number of datasets with different characteristics (high and low resolution, good and bad crystals, untwinned and twinned), their evaluation with different versions of XDS, and the determination of the quality of the resulting data using refinement and phasing.
The goal of this project is to find generally optimal parameters for XDS data reduction, to monitor the progress of the program, and to discover bugs or regressions.
I'm currently working with Qingping Xu on identifying suitable datasets in the (publicly accessible!) JCSG dataset archive.
PulG (good 2-wavelength MAD data @ 2.8 A)
Raw data: ftp://turn5.biologie.uni-konstanz.de/pub/datasets/
Reference: Köhler, R., Schäfer, K., Müller, S., Vignon, G., Diederichs, K., Philippsen, A., Ringler, P., Pugsley, A.P., Engel, A., Welte, W. (2004) Structure and assembly of the pseudopilin PulG. Molecular Microbiology 54, 647-664. [1]
XDS.INP for remote high (rh) data
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT ! for this experiment: ORGX=1031 ORGY=1010 DETECTOR_DISTANCE=220 OSCILLATION_RANGE=1 X-RAY_WAVELENGTH=0.97857 NAME_TEMPLATE_OF_DATA_FRAMES=images/pulg_semet_D22_2_???.img DIRECT TIFF DATA_RANGE=5 124 SPOT_RANGE=5 124 BACKGROUND_RANGE=5 14 SPACE_GROUP_NUMBER=179 UNIT_CELL_CONSTANTS= 85.5 85.5 145.2 90 90 120 FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE ! parameters with changes wrt default values: VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000. TRUSTED_REGION=0. 0.99 MINIMUM_ZETA=0.05 INCLUDE_RESOLUTION_RANGE=50 0 STRONG_PIXEL=6 REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! parameters specifically for this detector and beamline: NX=2048 NY=2048 QX=0.079092 QY=0.079092 ! MARCCD 165mm version DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=65000 DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0 INCIDENT_BEAM_DIRECTION=0 0 1 ROTATION_AXIS=1 0 0 FRACTION_OF_POLARIZATION=0.99 POLARIZATION_PLANE_NORMAL=0 1 0
XDS.INP for inflection point (ip) data
same as above, except
X-RAY_WAVELENGTH=0.97972 NAME_TEMPLATE_OF_DATA_FRAMES=images/pulg_semet_D22_3_???.img DIRECT TIFF DATA_RANGE=1 120 SPOT_RANGE=1 120 BACKGROUND_RANGE=1 10
XSCALE.INP
RESOLUTION_SHELLS= 10 6 5 4 3 2.9 2.8 SPACE_GROUP_NUMBER=179 UNIT_CELL_CONSTANTS= 85.71 85.71 145.34 90 90 120 OUTPUT_FILE=D22-rh.ahkl FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE INPUT_FILE= ../xds_rh_2008/XDS_ASCII.HKL XDS_ASCII 50 2.8 OUTPUT_FILE=D22-ip.ahkl FRIEDEL'S_LAW=FALSE STRICT_ABSORPTION_CORRECTION=TRUE INPUT_FILE= ../xds_ip_2008/XDS_ASCII.HKL XDS_ASCII 50 2.8
running xdsconv for both rh and ip
cat > XDSCONV.INP<<eof INPUT_FILE=D22-rh.ahkl OUTPUT_FILE=D22-rh.hkl SHELX FRIEDEL'S_LAW=FALSE eof xdsconv cat > XDSCONV.INP<<eof INPUT_FILE=D22-ip.ahkl OUTPUT_FILE=D22-ip.hkl SHELX FRIEDEL'S_LAW=FALSE eof xdsconv
SHELXC and SHELXD
shelxc pulg<<eof INFL D22-ip.hkl HREM D22-rh.hkl CELL 85.71 85.71 145.34 90 90 120 SPAG P6522 MAXM 2 eof cat > pulg_fa.ins <<eof TITL pulg_fa.ins MAD in P6522 CELL 0.98000 85.71 85.71 145.34 90.00 90.00 120.00 LATT -1 SYMM -Y, X-Y, 2/3+Z SYMM -X+Y, -X, 1/3+Z SYMM -X, -Y, 1/2+Z SYMM Y, -X+Y, 1/6+Z SYMM X-Y, X, 5/6+Z SYMM Y, X, 2/3-Z SYMM X-Y, -Y, -Z SYMM -X, -X+Y, 1/3-Z SYMM -Y, -X, 1/6-Z SYMM -X+Y, Y, 1/2-Z SYMM X, X-Y, 5/6-Z SFAC SE UNIT 384 SHEL 999 3.3 PATS FIND 8 MIND -1.5 -0.1 NTRY 100 SEED 1 HKLF 3 END eof shelxd pulg_fa