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XDS.INP: Difference between revisions
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A minimal XDS.INP needs at least these keywords and their parameters: | A minimal XDS.INP needs at least these keywords and their parameters: | ||
* Keywords that describe the detector: | |||
DETECTOR NX NY QX QY - for a list of supported detectors and possible geometries, see [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#Table%20of%20supported%20detectors Table of supported detectors] | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_X-AXIS= DIRECTION_OF_DETECTOR_X-AXIS] - often 1 0 0 | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_Y-AXIS= DIRECTION_OF_DETECTOR_Y-AXIS] - often 0 1 0 | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCIDENT_BEAM_DIRECTION= INCIDENT_BEAM_DIRECTION] - often 0 0 1 | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS= ROTATION_AXIS] - often 1 0 0 at a synchrotron | |||
* Keywords that describe your particular dataset: | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ORGX= ORGX ORGY] - in pixels '''The most critical parameters for a successful data reduction''' . See [[Obtaining ORGX ORGY]] | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ORGX= ORGX ORGY] - in pixels '''The most critical parameters for a successful data reduction''' . See [[Obtaining ORGX ORGY]] | ||
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[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DATA_RANGE= DATA_RANGE] - numbers of frames to be reduced | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DATA_RANGE= DATA_RANGE] - numbers of frames to be reduced | ||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#BACKGROUND_RANGE= BACKGROUND_RANGE] - same for initial calibration | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#BACKGROUND_RANGE= BACKGROUND_RANGE] - same for initial background calibration, "1 5" is usually enough, and "1 20" should be ample. | ||
== Keywords for space group assignment == | == Keywords for space group assignment == | ||
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The way how to determine a space group (and unit cell parameters) is described in [[space_group_determination|space group determination]]. | The way how to determine a space group (and unit cell parameters) is described in [[space_group_determination|space group determination]]. | ||
== Keywords | == Keywords that additionally describe your experiment == | ||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html# | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#FRACTION_OF_POLARIZATION= FRACTION_OF_POLARIZATION] and [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#POLARIZATION_PLANE_NORMAL= POLARIZATION_PLANE_NORMAL=] should be specified for detectors at synchrotron sites. If they are not specified, their effect will mostly be absorbed by the scale factors determined in [[CORRECT]]. | |||
== Keywords which affect which detector pixels will be used == | |||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html# | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCLUDE_RESOLUTION_RANGE= INCLUDE_RESOLUTION_RANGE] - the default is "20.0 0.0" but it would be good to change this to sensible values for your data set, e.g. 50.0 for the lower resolution limit and the limiting resolution, where the average signal-to-noise ratio drops below 1, for the upper limit (the latter number could be obtained from [[CORRECT.LP]]). | ||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html# | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS] - the default is "7000. 30000." but the first number is probably on the low side. | ||
[[MINIMUM_ZETA]] - the default of 0.15 is rather on the safe side. A lower value increases completeness. | [[MINIMUM_ZETA]] - the default of 0.15 is rather on the safe side. A lower value increases completeness. | ||
... | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#TRUSTED_REGION= TRUSTED_REGION] - The default is "0.00 1.05" but if you have a square detector, and their are reflections visible in the corners, you may go as high as "0. 1.4142". Depending on the symmetry of your crystal, this may give you useful high-resolution data. | ||
== Keywords which affect aspects of parameter refinement == | |||
... | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(IDXREF)= REFINE(IDXREF)] - The defaults (REFINE(IDXREF)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK, but '''only if''' COLSPOT has seen '''all''' (or rather, a significant fraction of the) frames. If only a small SPOT_RANGE was used (which is not the best way, but possible), one should use REFINE(IDXREF)= AXIS BEAM ORIENTATION CELL . (The next thing to omit would be AXIS) | ||
== | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)] - The defaults (REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL) could be modified by omitting DISTANCE, because one should assume that the distance is constant. Furthermore, by fixing the distance one can better see from the results of the refinement whether the cell parameters are stable, or whether they change due to radiation damage. | ||
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html# | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(CORRECT)= REFINE(CORRECT)] - The defaults (REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK | ||
== Keywords which affect the speed of data reduction == | |||
... | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] - speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine. | ||
... | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS] - speeds up XDS by chopping the DATA_RANGE into pieces, and feeding each piece to a new process. That process may run on the local machine, or a different one (but this needs to be configured by the system administrator). Unless you know what you are doing, use MAXIMUM_NUMBER_OF_JOBS=1 - or at least don't set ''both'' MAXIMUM_NUMBER_OF_PROCESSORS ''and'' MAXIMUM_NUMBER_OF_JOBS to values >1! | ||
== What can go wrong with this file? == | == What can go wrong with this file? == | ||
The most important pitfalls are: | The most important possible pitfalls are: | ||
* Lines longer than 80 characters are truncated silently (FIXME: is this still true?). This happens most often with the NAME_TEMPLATE_OF_DATA_FRAMES keyword line, because the path to the directory with the frames may be long. Fix: use a symlink to the directory with the frames. | * Lines longer than 80 characters are truncated silently (FIXME: is this still true?). This happens most often with the NAME_TEMPLATE_OF_DATA_FRAMES keyword line, because the path to the directory with the frames may be long. Fix: use a symlink to the directory with the frames. | ||
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* There may be decoding errors in the parameter which may lead to obscure error messages. E.g., see what happens if you provide only one cell parameter instead of six! | * There may be decoding errors in the parameter which may lead to obscure error messages. E.g., see what happens if you provide only one cell parameter instead of six! | ||
Written by --[[User:Kay|Kay]] 14:44, 8 November 2007 (CET) | Written by --[[User:Kay|Kay]] 14:44, 8 November 2007 (CET) | ||