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Xds Output Files

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This parameter provides a simple way of defining the acceptable detector surface. For recognizing the obscured regions in the initial background, DEFPIX generates a control image (file ABS.cbf) that contains values around 10000 for unshaded pixels and lower values for shaded pixels. The values outside the range are treated unreliable. The first few lines gives the input parameters used for picking of the spots.

GAIN.cbf codes for the expected variation of the pixel contents in the background region of a data image. An arbitrary number of such ranges may be specified. Example:FRACTION_OF_POLARIZATION=0.9 A typical parameter value for data collection at a synchrotron. Example 2: NAME_TEMPLATE_OF_DATA_FRAMES= ../mckhg_???.image MAR This is the usual method of specifying images for processing images by XDS.

Xds Output Files

Output file from integration. On return, the complete set of parameters are saved in the file XPARM.XDS, and the original file SPOT.XDS is replaced by a file of identical name - now with indices attached I've seen datasets where each reflection had a satellite associated with the main reflection, but separate from it. The number of grid points in this coordinate system used for representing the transformed reflection profile are usually chosen automatically by XDS; the user has the option to override the automatic

  1. The number of profiles is approximately equal to 9 * Total rotation range covered by data set/DELPHI.
  2. Try running with a different INDEX_ORIGIN.
  3. To apply this correction, specify PATCH_SHUTTER_PROBLEM=TRUE.
  4. The actual integration is carried out in the second pass by profile fitting with respect to the spot shape determined in the first pass.
  5. ERROR !!!

Default is to omit specification of the parameter value. The format keyword applies to all data images with the given generic file name template. DIRECTION_OF_SEGMENT_X-AXIS=EDS(1,1) EDS(2,1) EDS(3,1) DIRECTION_OF_SEGMENT_Y-AXIS=EDS(1,2) EDS(2,2) EDS(3,2) define "fast" and "slow" pixel directions, respectively. Xds Correct After initial refinement based on the reflections in the largest subtree, all spots which can now be indexed are included.

Replace CCP4_F with CNS or SHELX. Xds Tutorial Consequently, the default parameter value is REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL If none of the above KEYWORDS is given, the diffraction parameters are not refined during the INTEGRATE step and remain as Otherwise, the table is derived in the following order. Parameter is used by CORRECT PATCH_SHUTTER_PROBLEM= The mean intensity of the reflections in the data set should not correlate with the angular position of their diffraction maxima within the rotation/oscillation

Inspect the control image FRAME.cbf to find out whether this has been the case. Kabsch, W. Xds. Acta Cryst. D66, 125-132 (2010) The pixel at IX, IY is in the background region, if the variation in contents of pixels within the region IX-NBX,IX+NBX; IY-NBY,IY+NBY does not exceed the expected variation by more than If you do insist on processing these images, swich off refinement REFINE(INTEGRATE)=! The reference space group will be extracted from the header of the mtz multirecord file in the first autoxds processing subdirectory in the list.

Xds Tutorial

Computed reflection indices deviating from integers by more than INDEX_ERROR= or indices of an absolute value larger than INDEX_MAGNITUDE= are … diffraction parameters are not refined during the INTEGRATE step and Thus, running XDS amounts to just editing a few parameter values in the selected input file template (for example XDS-ADSC.INP if data images were recorded by the ADSC detector) and renaming Xds Output Files Specifies the parameters to be refined during indexing (IDXREF program). Error Cannot Open Or Read Xds Inp This is mandatory for the SIEMENS, BRUKER, and CCDD2AM detectors.

DEFPIX defines the trusted region of the detector, recognizes and removes shaded areas, and eliminates regions outside the resolution range defined by the user. These R-factors as well as the intensities of all reflections with indices of type h00, 0k0, and 00l and those expected to be systematically absent provide important information for identification of The …

Problems From XDSwiki Jump to: navigation, search This is a collection of problems and their solutions. Indexing and Integration The XDS program can be started from any of the data processing machines by typing xds (Program name "xds" is case sensitive). For most of the detectors presently used the image format is recognized automatically by XDS and a format keyword, like MAR or GENERIC in the examples below, is not needed. NOTE: This option is … xds_par > $workdir.log #Was there an error in the autoindexing?

The default value is 6.0. Xds Integrate x=QX*(IX-ORGXS)*EDS(1,1)+QY*(IY-ORGYS)*EDS(1,2)+FS*EDS(1,3) y=QX*(IX-ORGXS)*EDS(2,1)+QY*(IY-ORGYS)*EDS(2,2)+FS*EDS(2,3) z=QX*(IX-ORGXS)*EDS(3,1)+QY*(IY-ORGYS)*EDS(3,2)+FS*EDS(3,3) Each segment of the detector is specified by its own set of 7 parameters. Please go to the various sections of the input file to change their values.

Up to 10 such ranges may be specified.

All SSRL beamlines except beamline 7-1 use an omega angle of 270 degree. The default value works fine and hardly needs to be changed. If specified, the given value overrides the default settings for SIEMENS, BRUKER, or CCDD2AM detectors. Xds_par Change it to "0" for auto indexing.

We encourage you to report any errors you … +XDS Error - "Cannot Configure Requested Transport" RS232 communications can be adversely affected in a number of different ways. Both values must be odd and positive numbers <22. Parameter is used by CORRECT SPACE_GROUP_NUMBER= Space-group number of the crystal. Example:SPOT_MAXIMUM-CENTROID=2.0 This is the default value for the parameter.

If the data cannot be read successfully, XDS assumes that there are no such data available. IDXREF prints!!! All parameters in XDS.INP are named by keywords containing an equal sign as the last character, and many of them will be mentioned here in context to clarify their meaning. As described in this chapter, rotation data images are processed in 8 steps XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT which are called in succession by XDS.

Example:SEPMIN=6.0 This is the default value for the parameter.