DEF brno david alpha_rev_70042 xia2_dials 16:19 23/Jun/17 Linux CDataFile True True False CList CUnmergedDataFile 0 *? *? CList CObsDataFile 0 observed data,derived data,reference data True 1,2,3 1 CList CFreeRDataFile 0 True CDataReductionPerformance CBoolean True check_image_files_readable 2 CDataFile Backstop mask General settings CBoolean False Fix geometry Whether or not to refine geometry in dials.index and dials.refine. Most useful when also providing a reference geometry to xia2. 1 CString True Outlier rejection algorithm null,auto,mcd,tukey,sauter_poon 1 auto Centroid outlier rejection CBoolean False Fast mode Set various parameters for rapid processing, compromising on quality 1 CFloat 0.02 Closeness to the spindle cutoff for including reflections in refinement 2 0.0 CInt 0 border The border around the edge of the image. CBoolean True use_trusted_range Use the trusted range to mask bad pixels. CFloat d_min The high resolution limit in Angstrom for a pixel to be accepted by the filtering algorithm. 0.0 CFloat d_max The low resolution limit in Angstrom for a pixel to be accepted by the filtering algorithm. 0.0 CString resolution_range an untrusted resolution range True CInt 0 Panel The panel number CString Circle An untrusted circle (xc, yc, r) CString Rectangle An untrusted rectangle (x0, x1, y0, y1) CString Polygon The pixel coordinates (fast, slow) that define the corners of the untrusted polygon. Spots whose centroids fall within the bounds of the untrusted polygon will be rejected. True CBoolean False filter CString unit_cell The unit cell to generate d_spacings for powder rings. 1 CString space_group The space group used to generate d_spacings for powder rings. 1 CFloat 0.002 width 1 The width of an ice ring (in 1/d^2). 0.0 CFloat d_min The high resolution limit (otherwise use detector d_min) 0.0 Masking 1 CDataFile phil file to pass to dials.find_spots 1 CInt Minimum spot size The minimum number of contiguous pixels for a spot to be accepted by the filtering algorithm. 1 CInt 0 min_local The minimum number of pixels under the image processing kernel that are need to do the thresholding operation. Setting the value between 2 and the total number of pixels under the kernel will force the algorithm to use that number as the minimum. If the value is less than or equal to zero, then the algorithm will use all pixels under the kernel. In effect this will add a border of pixels which are always classed as background around the edge of the image and around any masked out pixels. 2 CFloat Strong pixel sigma cutoff The number of standard deviations above the mean in the local area above which the pixel will be classified as strong. 1 CBoolean False Filter ice rings CInt 3 kernel_size The size of the local area around the spot in which to calculate the mean and variance. The kernel is given as a box 1 CFloat Global threshold cutoff The global threshold value. Consider all pixels less than this value to be part of the background. 1 Spot finding CDataFile phil file to pass to dials.index 1 CString True Indexing method fft1d,fft3d,real_space_grid_search fft3d CFloat 0.0 Maximum cell length Maximum length of candidate unit cell basis vectors (in Angstrom). 1 CInt Number of reciprocal space grid points 2 0 CInt 100 Number of reflections per degree for random subset 1 CString True histogram_binning linear,log Choose between linear or logarithmic bins for nearest neighbour histogram analysis. 2 Indexing CDataFile phil file to pass to dials.refine CBoolean True scan_static 2 CBoolean True Fit a scan-varying model CFloat 36.0 Interval width between checkpoints (if scan-varying) Width of scan between checkpoints in degrees 0.0 CInt 100 Number of reflections per degree for random subset Refinement 1 CDataFile phil file to pass to dials.integrate CString True Outlier rejection method null,nsigma,truncated,normal,tukey,mosflm Outlier rejection performed prior to background fit null CString True Background fit method simple,null,glm glm CBoolean True Include partials Include partial reflections (scaled) in output CString True old,new old mosaic Mosaicity determination method to use 2 Integration 1 DIALS settings CString pointless program reindex CString True intensities summation,profile,combine combine CFloat 0.001 Surface tie CBoolean True Surface link CInt 6 Aimless # secondary harmonics 2 aimless CString True chirality chiral,nonchiral,centrosymmetric pointless CString ctruncate program truncate CCP4 data reduction options 1 CBoolean False Use small molecule settings Assume that the dataset comes from a chemical crystallography experiment 1 CBoolean False Fail over gracefully If processing a sweep fails, keep going 1 CBoolean False Settings for working with multiple crystals Settings for working with multiple crystals 1 CBoolean False Interactive indexing 1 CString AUTOMATIC project A name for the data processing project CString DEFAULT crystal A name for the crystal CString Heavy atom name, optional Set the heavy atom name, if appropriate CString True Separate anomalous pairs in merging True,False,Auto Auto CDataFile Working directory (i.e. not $CWD) 1 CDataFile Path to an image file image=/path/to/an/image_001.img 1 True CDataFile Take headers from json file dxtbx-format datablock.json file which can be provided as an alternative source of images header information to avoid the need to read all the image headers on start-up. 1 True CDataFile Take experimental geometry from json file Experimental geometry from this datablock.json or experiments.json will override the geometry from the image headers. 1 True CDataFile Use xinfo instead of image directory Provide an xinfo file as input as alternative to directory containing image files. 1 CBoolean False Reverse rotation axis Reverse the direction of the phi axis rotation. 1 CFloat Detector gain Detector gain if using DIALS 1 CInt 10 Minimum number of matching images 1 Minimum number of matching images to include a sweep in processing. 1 CInt Minimum oscillation range 1 Minimum oscillation range of a sweep for inclusion in processing. 0 CFloat 1e-06 wavelength The wavelength tolerance 0.0 CFloat 1e-06 direction The direction tolerance 0.0 CFloat 1e-06 polarization_normal The polarization normal tolerance 0.0 CFloat 1e-06 polarization_fraction The polarization fraction tolerance 0.0 CFloat 1e-06 fast_axis The fast axis tolerance 0.0 CFloat 1e-06 slow_axis The slow axis tolerance 0.0 CFloat 0.05 origin The origin tolerance 0.0 CFloat 1e-06 rotation_axis The rotation axis tolerance 0.0 CFloat 1e-06 fixed_rotation The fixed rotation tolerance 0.0 CFloat 1e-06 setting_rotation The setting rotation tolerance 0.0 CFloat 0.01 oscillation The oscillation tolerance for the scan 0.0 Tolerances used to determine shared models 2 CFloat wavelength Override the beam wavelength CString Sample to source direction Override the sample to source direction Beam overrides 1 CInt 0 Panel ID The panel number CString Panel name Override the panel name CString Panel type Override the panel type CString Panel pixel size Override the panel pixel size CString Panel image size Override the panel image size CString Panel trusted range Override the panel trusted range CFloat Panel thickness Override the panel thickness CString Panel material Override the panel material CString Panel fast axis direction Override the panel fast axis. Requires slow_axis and origin. CString Panel slow axis direction Override the panel slow axis. Requires fast_axis and origin. CString Panel origin vector Override the panel origin. Requires fast_axis and slow_axis. CString True Enable parallax correction True,False,None Enable parallax correction. By default in overwrite mode, the value of None does nothing. True CString group name Override the group name CString Panel fast axis direction Override the panel fast axis. Requires slow_axis and origin. CString Panel slow axis direction Override the panel slow axis. Requires fast_axis and origin. CString Panel origin vector Override the panel origin. Requires fast_axis and slow_axis. CString Group ID The group identifier specifying the place in the hierarchy CString Group name Override the group name CString Group fast axis direction Override the group fast axis. Requires slow_axis and origin. CString Group slow axis direction Override the group slow axis. Requires fast_axis and origin. CString Group origin vector Override the group origin. Requires fast_axis and slow_axis. CInt Panel ID The panel id True True CString Beam centre coordinates (mm, mm) using the Mosflm convention Override the beam centre from the image headers, following the mosflm convention. CFloat Detector distance The detector distance (used when mosflm_beam_centre is set) CString Beam centre coordinates (px slow, px fast, [panel id]) Override the beam centre from the image headers, following the slow/fast pixel convention used by dials.image_viewer. The first two values are the slow and fast pixel coordinate. If the third is supplied it specifies a panel number. Detector overrides 1 CString Goniometer axes Override the goniometer axes. Axes must be provided in the order crystal-to-goniometer, i.e. for a Kappa goniometer phi,kappa,omega CString Goniometer angles Override the goniometer angles. Axes must be provided in the order crystal-to-goniometer, i.e. for a Kappa goniometer phi,kappa,omega CString The axis names The multi axis goniometer axis names CInt The scan axis The scan axis CString Fixed rotation matrix Override the fixed rotation matrix CString Setting rotation matrix Override the setting rotation matrix Goniometer overrides 1 CString Image range Override the image range CBoolean False Extrapolate scan When overriding the image range, extrapolate exposure and epoch information from existing images CString Oscillation Override the image oscillation Scan overrides 1 CBoolean False Convert stills into sweeps When overriding the scan, convert stills into sweeps CBoolean False Convert sweeps into stills When overriding the scan, convert sweeps into stills Allow overrides of experimental geometry 2 CBoolean False dynamic_shadowing Enable dynamic shadowing CBoolean False multi_panel Enable a multi-panel detector model. (Not supported by all detector formats) Options to pass to the Format class 2 xia2 input settings CString Id CString Range CBoolean False Exclude xia2 sweep 2 True CString Auto xia2 scale directory CFloat 0.05 1.0 0.0 Fraction of free reflections free_fraction CInt free_total Total number of free reflections 0 CDataFile freer_file Copy freer flags from this file CDataFile reference_reflection_file Reference file for testing of alternative indexing schemes CString *decay *modulation *absorption partiality Scaling models to apply CString True Smoothed or batch scaling rotation,batch rotation CBoolean True Run dials.two_theta_refine Run dials.two_theta_refine to refine the unit cell and obtain estimated standard uncertainties on the cell parameters. Only relevant to DIALS pipeline. Scaling 1 CString Space group Provide a target space group to the indexing program CString Unit cell (requires the space group to be set) Provide a target unit cell to the indexing program CString True Keep all data (default for small molecule mode) True,False,Auto Keep all data regardless of resolution criteria Auto CFloat Low resolution cutoff Low resolution cutoff. 0.0 CFloat High resolution cutoff High resolution cutoff. 0.0 CFloat Outer shell Rmerge 1 Maximum value of Rmerge in the outer resolution shell 0.0 CFloat Outer shell completeness 1 Minimum completeness in the outer resolution shell 0.0 CFloat 0.5 Outer shell CC1/2 1 Minimum value of CC1/2 in the outer resolution shell 0.0 CString True cc_half_method half_dataset,sigma_tau half_dataset CFloat cc_half_significance_level 1 0.0 1.0 CString True cc_half_fit polynomial,tanh 1 polynomial CFloat 0.25 Outer shell unmerged <I/sigI> 1 Minimum value of the unmerged <I/sigI> in the outer resolution shell 0.0 CFloat 1.0 Outer shell merged <I/sigI> 1 Minimum value of the merged <I/sigI> in the outer resolution shell 0.0 CInt 100 Number of resolution bins. Number of resolution bins to use for estimation of resolution limit. 1 CString True counting_sorted,volume counting_sorted Equal-volume or equal #ref binning. Use equal-volume bins or bins with approximately equal numbers of reflections per bin. 1 CBoolean False Keep anomalous pairs separate in merging statistics 1 Resolution CBoolean False Unify crystal orientations For one crystal, multiple orientations, unify U matrix 1 CBoolean False Trust beam centre Whether or not to trust the beam centre in the image header. If false, then labelit.index is used to determine a better beam centre during xia2 setup phase 1 CFloat 5e-05 Wavelength tolerance 1 Tolerance for accepting two different wavelengths as the same wavelength. 0.0 CBoolean True Read all image headers 1 CFloat Detector distance 1 Distance between sample and detector (mm) 0.0 CBoolean False Show template 1 CString Untrusted rectangle for indexing 1 True CBoolean False Check cell deviation in XDS IDXREF 1 CBoolean False Brehm-Diederichs Use the Brehm-Diederichs algorithm to resolve an indexing ambiguity. See: W. Brehm and K. Diederichs, Acta Cryst. (2014). D70, 101-109. 1 CBoolean True Use profile fitting Use profile fitting not summation integration, default yes CBoolean False Exclude ice regions Exclude measurements from regions which are typically where ice rings land Integration 1 CBoolean False use_dials_spotfinder This feature requires the dials project to be installed, and is not currently intended for general use. Use at your peril! CFloat 0.0 pointless_tolerance Tolerance to use in POINTLESS for comparison of data sets 0.0 CString detector_id Override detector serial number information 2 CString True True,False,Auto Auto multi_sweep_indexing Index all sweeps together rather than combining individual results (requires dials indexer) 2 CBoolean False remove_blanks 2 CBoolean False Integrate in P1 1 CBoolean True Reintegrate using a corrected lattice 1 CBoolean True Reject lattice if constraints increase RMSD 2 CFloat 1.5 Threshold for lattice rejection 2 CString True indexer mosflm,labelit,labelitii,xds,xdsii,xdssum,dials 2 CString True refiner mosflm,xds,dials 2 CString True integrater mosflmr,xdsr,mosflm,xds,dials 2 CString True scaler ccp4a,xdsa 2 CString True Software to calculate merging statistics aimless,cctbx Use AIMLESS or cctbx for calculation of merging statistics cctbx CInt 20 Number of bins 1 CBoolean False Use internal variance Use internal variance of the data in the calculation of the merged sigmas CBoolean False Eliminate systematic absences before calculation Eliminate systematically absent reflections before computation of merging statistics. Merging statistics 1 CBoolean False verbose 1 CString True serial,parallel serial mode Whether to process each sweep in serial (using n processes per sweep) or to process sweeps in parallel (using 1 process per sweep). 1 CInt nproc 0 The number of processors to use per job. 1 CInt njob 1 The number of sweeps to process simultaneously. 1 CString True simple,qsub simple type How to run the parallel processing jobs, e.g. over a cluster 1 CString qsub_command The command to use to submit qsub jobs 1 Multiprocessing xia2 settings