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XDS.INP: Difference between revisions
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XDS.INP is a user-provided file that is read by [[XDS]]. Each line consists of one or more <keyword>=<parameter(s)> pairs. Anything after a "!" is a comment. | XDS.INP is a user-provided file that is read by [[XDS]]. Each line consists of one or more <keyword>=<parameter(s)> pairs. Anything after a "!" is a comment. | ||
Complete documentation is at http:// | * Complete documentation is at http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html . | ||
Templates for various detectors are at http:// | * Templates for various detectors are at http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html . | ||
A small and expandable script to generate XDS.INP is called [[generate_XDS.INP]] . | * A small and expandable script to generate XDS.INP is called [[generate_XDS.INP]]. | ||
* Define a [[custom syntax in VIM]] for better legibility of XDS.INP. | |||
== Required keywords == | == Required keywords == | ||
| Line 17: | Line 19: | ||
* Keywords that describe the detector: | * Keywords that describe the detector: | ||
DETECTOR NX NY QX QY - for a list of supported detectors and possible geometries, see [http:// | DETECTOR NX NY QX QY - for a list of supported detectors and possible geometries, see [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#Table%20of%20supported%20detectors Table of supported detectors] | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_X-AXIS= DIRECTION_OF_DETECTOR_X-AXIS] - often 1 0 0 | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_Y-AXIS= DIRECTION_OF_DETECTOR_Y-AXIS] - often 0 1 0 | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#INCIDENT_BEAM_DIRECTION= INCIDENT_BEAM_DIRECTION] - often 0 0 1 | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#ROTATION_AXIS= ROTATION_AXIS] - often 1 0 0 at a synchrotron | ||
* Keywords that describe your particular dataset: | * Keywords that describe your particular dataset: | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#ORGX= ORGX ORGY] - in pixels '''The most critical parameters for a successful data reduction''' . See [[Obtaining ORGX ORGY]] | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DETECTOR_DISTANCE= DETECTOR_DISTANCE] - in millimeters | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE] - in degrees | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#X-RAY_WAVELENGTH= X-RAY_WAVELENGTH] - in Ã
ngström | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= NAME_TEMPLATE_OF_DATA_FRAMES] - path and name of frames, with wildcards for numbers, plus type of frames (e.g. "CBF") | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DATA_RANGE= DATA_RANGE] - numbers of frames to be processed. Missing frames will be ignored (thus if you want certain frames to not be processed, just change their name e.g. by appending a .x to their name - the Unix ''rename'' command is handy for this). | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#BACKGROUND_RANGE= BACKGROUND_RANGE] - numbers of frames to be used for initial background estimation, "1 5" is usually enough, and "1 20" should be ample. | ||
== Keywords that additionally describe your experiment == | == Keywords that additionally describe your experiment == | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#FRACTION_OF_POLARIZATION= FRACTION_OF_POLARIZATION] and [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#POLARIZATION_PLANE_NORMAL= POLARIZATION_PLANE_NORMAL] should be specified for detectors at synchrotron sites. If they are not specified (or inaccurate), their effect will to some extent be absorbed by the scale factors determined in [[CORRECT]]. | ||
== Keywords for space group assignment == | == Keywords for space group assignment == | ||
A dataset with unknown space group can be reduced by XDS in space group P1. The decision about the possible space group(s) is then deferred until the CORRECT step. If you know the space group and unit cell parameters of your crystal you just need these two keywords: | A dataset with unknown space group can be reduced by XDS in space group P1. The decision about the possible space group(s) is then deferred until the CORRECT step. If you know the space group and unit cell parameters of your crystal you just need these two keywords: | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#SPACE_GROUP_NUMBER= SPACE_GROUP_NUMBER] | ||
:If you don't know the space group, put a 0 or comment out the line. The space group will then [[Space_group_determination|be automatically determined]] in the CORRECT step. A mapping of space group names against their numbers is available from [[IDXREF.LP]] and [[CORRECT.LP]]. | :If you don't know the space group, put a 0 or comment out the line. The space group will then [[Space_group_determination|be automatically determined]] in the CORRECT step. A mapping of space group names against their numbers is available from [[IDXREF.LP]] and [[CORRECT.LP]]. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#UNIT_CELL_PARAMETERS= UNIT_CELL_PARAMETERS] | ||
:If you don't know the space group, put six | :If you ''don't'' know the space group (and thus use SPACE_GROUP_NUMBER=0) and cell parameters, put six arbitrary numbers or comment out the line. Unit cell parameters need to respect the constraints of the Laue group, e.g. all angles must be exactly 90.0 for orthorhombic and tetragonal space groups, a and b must be equal for trigonal and tetragonal, and so on. | ||
If you want to assign a space group and unit cell parameters to a dataset that was reduced in P1, you just have to put that space group and those unit cell parameters into [[XDS.INP]], and re-run [[CORRECT]]. | If you want to assign a space group and unit cell parameters to a dataset that was reduced in P1, you just have to put that space group and those unit cell parameters into [[XDS.INP]], and re-run [[CORRECT]]. | ||
If the space group is given as 0, the file REMOVE.HKL is not used | '''If the space group is given as 0, the file REMOVE.HKL is not used! | ||
''' | |||
== Keywords which affect completeness and resolution limits == | == Keywords which affect completeness and resolution limits == | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/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. If you change the values, you'll have to re-run INIT and DEFPIX to make INTEGRATE use the changed region. IDXREF however does not require re-running of INIT, so if you just want to exclude the high-resolution reflections from indexing, it is enough to change TRUSTED_REGION and then to run the IDXREF step. | :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. If you change the values, you'll have to re-run INIT and DEFPIX to make INTEGRATE use the changed region. IDXREF however does not require re-running of INIT, so if you just want to exclude the high-resolution reflections from indexing, it is enough to change TRUSTED_REGION and then to run the IDXREF step. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/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. See [[Determining_VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]]. | :the default is "7000. 30000." but the first number is probably on the low side. See [[Determining_VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]]. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_ZETA= MINIMUM_ZETA] | ||
:the default of 0.05 is good. A lower value increases completeness. See [[MINIMUM_ZETA]]. | :the default of 0.05 is good. A lower value increases completeness. See [[MINIMUM_ZETA]]. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/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]]). | :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:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#EXCLUDE_RESOLUTION_RANGE= EXCLUDE_RESOLUTION_RANGE] | ||
:to exclude reflections in [[Ice_rings|ice rings]] ([[CORRECT]] step). Whether [[Ice_rings|ice rings]] are a problem should be obvious by looking at individual frames (often later frames are affected more than earlier ones), FRAME.pck and the "alien" statistics at the end of [[CORRECT.LP]]. Also see [[Wishlist]], and [[VIEW]] misfits.pck (produced by [[XDSSTAT]]). | :to exclude reflections in [[Ice_rings|ice rings]] ([[CORRECT]] step). Whether [[Ice_rings|ice rings]] are a problem should be obvious by looking at individual frames (often later frames are affected more than earlier ones), FRAME.pck and the "alien" statistics at the end of [[CORRECT.LP]]. Also see [[Wishlist]], and [[VIEW]] misfits.pck (produced by [[XDSSTAT]]). | ||
== Keywords which affect aspects of geometry parameter refinement == | == Keywords which affect aspects of geometry parameter refinement == | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REFINE(IDXREF)= REFINE(IDXREF)] | ||
:The | :The default (REFINE(IDXREF)=POSITION BEAM ORIENTATION CELL AXIS i.e. refine everything) could be used, but '''only if''' COLSPOT has seen '''all''' (or rather, a significant fraction of the) frames (see SPOT_RANGE below). 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 . This is also a good choice because at modern beam lines the distance should be accurately known. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]. | ||
:The defaults (REFINE(INTEGRATE)= | :The defaults (REFINE(INTEGRATE)= POSITION BEAM ORIENTATION CELL) could be modified by omitting POSITION, because one should assume that the distance is constant. This is particularly recommended if SPACE_GROUP_NUMBER=0 or 1. 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. An even more robust way is to omit CELL instead of POSITION. There are situations when one wants to reduce the number of parameters to be refined even more, see [[Optimization]]. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REFINE(CORRECT)= REFINE(CORRECT)] | ||
:The defaults (REFINE(CORRECT)= | :The defaults (REFINE(CORRECT)= POSITION BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK. For low resolution datasets the distance refinement may not be stable (i.e. refined distance differs more than a few mm from expected distance). In this case one should remove POSITION from the list. If that is the case, one should also not refine POSITION in IDXREF and INTEGRATE. | ||
== Keywords which affect whether indexing will succeed == | == Keywords which affect whether indexing will succeed == | ||
Again, the most important parameters are [[Obtaining ORGX ORGY|ORGX ORGY]]. Often the software which writes the frames puts these numbers into the headers of the frames. However, these numbers are sometimes wrong, | Again, the most important parameters are [[Obtaining ORGX ORGY|ORGX ORGY]]. Often the software which writes the frames puts these numbers into the headers of the frames. However, these numbers are sometimes wrong, which is why old versions of XDS did not read and interpret headers of frames at all (update: since 2009 XDS tries to extract NX NY QX QY from the header, but nothing else). How to obtain estimates for ORGX ORGY from frames is described in [[Obtaining ORGX ORGY]]. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#SPOT_RANGE= SPOT_RANGE] | ||
:If this line is omitted (''and SECONDS=0''), the whole DATA_RANGE is used. This is usually a good way to proceed. If there is radiation damage, I would advise to use the first half of the DATA_RANGE as SPOT_RANGE. The SPOT_RANGE in principle may comprise a single frame. <br />Attention: if SECONDS= has a parameter >0, a small SPOT_RANGE will be used if SPOT_RANGE is not explicitly provided! | :If this line is omitted (''and SECONDS=0''), the whole DATA_RANGE is used. This is usually a good way to proceed. If there is radiation damage, I would advise to use the first half of the DATA_RANGE as SPOT_RANGE. The SPOT_RANGE in principle may comprise a single frame. <br />Attention: if SECONDS= has a parameter >0, a small SPOT_RANGE will be used if SPOT_RANGE is not explicitly provided! | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#STRONG_PIXEL= STRONG_PIXEL] | ||
:the default is 3, but | :the default is 3, but 4 may be more appropriate, to prevent many noise pixel from being picked up. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_NUMBER_OF_PIXEL_IN_A_SPOT= MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT] | ||
:the default is 6, but 3 is usually more appropriate for synchrotron data (small reflections). | :the default is 6, but 3 is usually more appropriate for synchrotron data (small reflections). For Pilatus data, 2 or even 1 may be required. | ||
;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#SEPMIN= SEPMIN] | |||
:minimum pixel distance between spots (default: 6). This setting results in an upper limit to the longest primitive cell axis that IDXREF would find, so SEPMIN should be less than X-RAY_WAVELENGTH*DETECTOR_DISTANCE/(longest_primitive_cell_axis*QX). For Pilatus data one might need to lower this to 4 or even 2, for long axes. You can check what the longest permitted axis is, by taking the reciprocal of what is printed out in IDXREF.LP as the value of "MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS". | |||
;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#CLUSTER_RADIUS= CLUSTER_RADIUS] | |||
:should be half of SEPMIN (or less); the default is 3. This should be an integral value, so for Pilatus one should use 2 or even 1. | |||
See also the article [[Ice_rings]]. | See also the article [[Ice_rings]]. | ||
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== Keywords which affect the speed of data reduction == | == Keywords which affect the speed of data reduction == | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] | ||
:speeds up XDS by use of several ( | :speeds up XDS by use of several (2-99) CPUs within a single machine. | ||
;[http:// | ;[http://xds.mpimf-heidelberg.mpg.de/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 | :speeds up XDS by chopping the DATA_RANGE into (2-99) 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). Unless specifically set up for a given computer environment (e.g., at a synchrotron site), usually don't set ''both'' MAXIMUM_NUMBER_OF_PROCESSORS ''and'' MAXIMUM_NUMBER_OF_JOBS to values >1 ! | ||
Some amount of "overcommiting of resources" is OK, i.e. if you are the sole user of a Dual-core workstation, you may set both parameters to 2. Wolfgang Kabsch found that this utilizes the machine even a bit better than either MAXIMUM_NUMBER_OF_PROCESSORS=2 or MAXIMUM_NUMBER_OF_JOBS=2. | Some amount of "overcommiting of resources" is OK, i.e. if you are the sole user of a Dual-core workstation, you may set both parameters to 2. Wolfgang Kabsch found that this utilizes the machine even a bit better than either MAXIMUM_NUMBER_OF_PROCESSORS=2 or MAXIMUM_NUMBER_OF_JOBS=2. | ||
| Line 114: | Line 121: | ||
The most important possible pitfalls are: | The most important possible pitfalls are: | ||
* | * Blanks in the parameter of the NAME_TEMPLATE_OF_DATA_FRAMES keyword. Fix: use a symlink to the directory with the frames. | ||
* Error due to omitting the "=" directly after the keyword (i.e. having an intervening blank). | * Error due to omitting the "=" directly after the keyword (i.e. having an intervening blank). | ||
| Line 120: | Line 127: | ||
* 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! | ||
See also [[Problems]]. | |||
== Example XDS.INP files for ADSC, MarCCD and Pilatus detectors == | == Example XDS.INP files for ADSC, MarCCD and Pilatus detectors == | ||
| Line 246: | Line 254: | ||
SENSOR_THICKNESS=0.32 | SENSOR_THICKNESS=0.32 | ||
UNTRUSTED_RECTANGLE= 487 495 1 2527 ! these do not have to be specified | UNTRUSTED_RECTANGLE= 487 495 1 2527 ! these do not have to be specified | ||
UNTRUSTED_RECTANGLE= 981 989 1 2527 ! but it | UNTRUSTED_RECTANGLE= 981 989 1 2527 ! but it is better | ||
UNTRUSTED_RECTANGLE=1475 1483 1 2527 ! ... | UNTRUSTED_RECTANGLE=1475 1483 1 2527 ! ... | ||
UNTRUSTED_RECTANGLE=1969 1977 1 2527 ! | UNTRUSTED_RECTANGLE=1969 1977 1 2527 ! painstakingly checked KD 2012-01-14 | ||
UNTRUSTED_RECTANGLE= 1 2463 195 213 ! ... | UNTRUSTED_RECTANGLE= 1 2463 195 213 ! ... | ||
UNTRUSTED_RECTANGLE= 1 2463 407 425 ! ... | UNTRUSTED_RECTANGLE= 1 2463 407 425 ! ... | ||