https://wiki.uni-konstanz.de/xds/api.php?action=feedcontributions&user=DaveL&feedformat=atomXDSwiki - User contributions [en]2024-03-29T08:49:22ZUser contributionsMediaWiki 1.39.6https://wiki.uni-konstanz.de/xds/index.php?title=Finding_out_ORGX_ORGY&diff=3210Finding out ORGX ORGY2015-09-03T19:50:09Z<p>DaveL: ORGY ORGY changed to ORGX ORGY</p>
<hr />
<div>The mathematically correct definition of ORGX ORGY is: "the point of the detector (in pixels) closest to the crystal". However, in practice (namely for the standard setup of a beam perpendicular to the detector plane) the best way to come up with good values of ORGX ORGY is to find out where the direct beam would hit the detector.<br />
<br />
There are different possibilities to find out where the direct beam would hit the detector:<br />
<br />
# visualize BKGINIT.cbf (from [[INIT]]), or FRAME.cbf (from [[COLSPOT]]) with [[XDS-Viewer]], and click (left-mouse) into the middle of the beamstop shadow (or the attenuated direct beam itself, if it is recorded). Use the pixel coordinates displayed by [[XDS-Viewer]] as ORGX ORGY (in principle you should add 1 to both numbers, because for XDS-Viewer the pixels go from 0 to NX-1 whereas for XDS they go from 1 to NX).<br />Instead of these files written by XDS, one could directly use a measured frame. (If XDS-Viewer does not know the format, it will ask for NX, NY, and the size of the header. The latter is usually <size of frame in bytes>, minus 2*NX*NY .)<br />
# use [[adxv]] for visualization. Otherwise the same as with XDS-Viewer. (1.9.7beta version works for the PILATUS detector at SLS)<br />
# use MOSFLM for visualization. It prints out X BEAM and Y BEAM from the frame header, and you may click on the hypothetical direct beam position. However, ''x and y are swapped in MOSFLM when compared to XDS'', and the coordinates are in mm, not in pixels (so one has to divide by QX). Sometimes the X BEAM and Y BEAM from the header are not reliable.<br />
# use ice rings to find out (in [[XDS-Viewer]], and with paper and pencil) where the direct beam would be. This should be rather accurate but may be tedious.<br />
# use the Unix command line tools to look at the header of the frame. E.g. "strings <frame-name>|more" would should you the (hopefully correct) information stored in the header, like wavelength, delta-phi, X and Y beamcentre and so on.<br />
<br />
The error you make in the determination of ORGX ORGY should in principle be less than half of the distance between two spots. If you have a reasonable estimate (from one of the methods above), but the error is bigger than that, ''you can still find out the true ORGX ORGY by inspecting [[IDXREF.LP]] . This works best if [[COLSPOT]] has seen a significant fraction of all frames.'' This procedure is [[Thaumatin_ACA2014#Digression:_a_computational_investigation_into_the_robustness_of_the_indexing|documented]].<br />
<br />
<br />
== The case of a swung-out detector ==<br />
<br />
<br />
In the case of a swung-out detector, there is a large discrepancy between the direct beam position and (ORGX,ORGY). E.g. assuming the detector is swung out by 2theta in the horizontal, then ORGX has to be adjusted w.r.t. the value obtained in steps 1-5 (above), by an amount given by basic geometry: <br />
# the third component of DIRECTION_OF_DETECTOR_X-AXIS= is sin(2theta), let's call this S2T.<br />
# in the right-angled triangle of crystal, (ORGX,ORGY), and (Xbeam,Ybeam), we can find the distance (ORGX-Xbeam) by taking tan(2theta)*|DETECTOR_DISTANCE|/QX .<br />
# now since sin(2theta)~tan(2theta) we can approximate the adjustment by S2T*|DETECTOR_DISTANCE|/QX<br />
# for large 2theta one obviously has to take the arc sine of S2T, and calculate tan(2theta) from that.<br />
<br />
Second method: if you feel you would rather like to find ORGX, ORGY by smart trial-and-error, then you just need to realize that in the output of IDXREF.LP you can check the lines<br />
<br />
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 361.92 533.30 ! should be close to XDS-Viewer findings<br />
DETECTOR ORIGIN (PIXELS) AT 512.37 533.63 ! should be close to specified ORGX, ORGY<br />
<br />
i.e. you have to ''change ORGX, ORGY in XDS.INP to make the upper line show the values you expect'' from clicking the direct beam position in XDS-Viewer.</div>DaveLhttps://wiki.uni-konstanz.de/xds/index.php?title=XDS.INP&diff=3209XDS.INP2015-09-03T19:49:06Z<p>DaveL: Misspelling of ORGX as ORGY -- happens several times</p>
<hr />
<div>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.<br />
<br />
Complete documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html .<br />
<br />
Templates for various detectors are at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html .<br />
<br />
A small and expandable script to generate XDS.INP is called [[generate_XDS.INP]] .<br />
<br />
== Required keywords ==<br />
<br />
These keywords have no default parameters and must be given with the correct values.<br />
<br />
The values may be obtained from logfiles of the beamline software, your notes, or (for many types of frames) from the headers of the frames (using 'strings <filename>|more'). A good way to retrieve them is by using MOSFLM.<br />
<br />
A minimal XDS.INP needs at least these keywords and their parameters:<br />
<br />
* Keywords that describe the detector:<br />
<br />
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]<br />
<br />
[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<br />
<br />
[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<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCIDENT_BEAM_DIRECTION= INCIDENT_BEAM_DIRECTION] - often 0 0 1<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS= ROTATION_AXIS] - often 1 0 0 at a synchrotron<br />
<br />
* Keywords that describe your particular dataset:<br />
<br />
[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]] <br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DETECTOR_DISTANCE= DETECTOR_DISTANCE] - in millimeters<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE] - in degrees<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#X-RAY_WAVELENGTH= X-RAY_WAVELENGTH] - in Ångström<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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")<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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).<br />
<br />
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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.<br />
<br />
== Keywords that additionally describe your experiment ==<br />
<br />
[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 (or inaccurate), their effect will to some extent be absorbed by the scale factors determined in [[CORRECT]].<br />
<br />
== Keywords for space group assignment ==<br />
<br />
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:<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SPACE_GROUP_NUMBER= SPACE_GROUP_NUMBER]<br />
: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]].<br />
<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#UNIT_CELL_PARAMETERS= UNIT_CELL_PARAMETERS]<br />
: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.<br />
<br />
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]].<br />
<br />
'''If the space group is given as 0, the file REMOVE.HKL is not used!<br />
'''<br />
<br />
== Keywords which affect completeness and resolution limits ==<br />
<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#TRUSTED_REGION= TRUSTED_REGION]<br />
: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.<br />
;[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]<br />
:the default is "7000. 30000." but the first number is probably on the low side. See [[Determining_VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]].<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MINIMUM_ZETA= MINIMUM_ZETA]<br />
:the default of 0.05 is good. A lower value increases completeness. See [[MINIMUM_ZETA]].<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCLUDE_RESOLUTION_RANGE= INCLUDE_RESOLUTION_RANGE]<br />
: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]]).<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#EXCLUDE_RESOLUTION_RANGE= EXCLUDE_RESOLUTION_RANGE]<br />
: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]]).<br />
<br />
== Keywords which affect aspects of geometry parameter refinement ==<br />
<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(IDXREF)= REFINE(IDXREF)]<br />
: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 (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 . (The next thing to omit would be AXIS) <br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]<br />
:The defaults (REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL) could be modified by omitting DISTANCE, 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. There are situations when one wants to reduce the number of parameters to be refined even more, see [[Optimization]].<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(CORRECT)= REFINE(CORRECT)]<br />
:The defaults (REFINE(CORRECT)=DISTANCE 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 DISTANCE from the list.<br />
<br />
== Keywords which affect whether indexing will succeed ==<br />
<br />
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]].<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SPOT_RANGE= SPOT_RANGE]<br />
: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!<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#STRONG_PIXEL= STRONG_PIXEL]<br />
:the default is 3, but 4 may be more appropriate, to prevent many noise pixel from being picked up.<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MINIMUM_NUMBER_OF_PIXEL_IN_A_SPOT= MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT]<br />
: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.<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SEPMIN= SEPMIN]<br />
: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".<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#CLUSTER_RADIUS= CLUSTER_RADIUS]<br />
: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.<br />
<br />
See also the article [[Ice_rings]].<br />
<br />
== Keywords which affect the speed of data reduction ==<br />
<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS]<br />
:speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine. <br />
<br />
;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS]<br />
: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 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 !<br />
<br />
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.<br />
<br />
See also: [[performance]].<br />
<br />
== How to tweak data quality ==<br />
<br />
See [[Optimization#Final_polishing]].<br />
<br />
== What can go wrong with this file? ==<br />
<br />
The most important possible pitfalls are:<br />
<br />
* Lines longer than 80 characters are not allowed. 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.<br />
<br />
* Error due to omitting the "=" directly after the keyword (i.e. having an intervening blank).<br />
<br />
* 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!<br />
<br />
<br />
== Example XDS.INP files for ADSC, MarCCD and Pilatus detectors ==<br />
<br />
Please note that the task of setting up these files may be simplified with the [[generate_XDS.INP]] script.<br />
<br />
=== ADSC Quantum Q315r @ ESRF ID23-1 ===<br />
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT<br />
<br />
! for this experiment:<br />
ORGX= 1541 ORGY= 1550<br />
DETECTOR_DISTANCE=350<br />
OSCILLATION_RANGE=0.25<br />
X-RAY_WAVELENGTH=1.0001<br />
NAME_TEMPLATE_OF_DATA_FRAMES=../mk/mk04_1_???.img <br />
DATA_RANGE=1 720<br />
SPOT_RANGE=1 360 ! SPOT_RANGE= first half of DATA_RANGE; that is ample<br />
BACKGROUND_RANGE=1 10<br />
<br />
SPACE_GROUP_NUMBER=0<br />
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90<br />
<br />
! remove the exclamation marks if anomalous signal is present or expected <br />
! FRIEDEL'S_LAW=FALSE <br />
! STRICT_ABSORPTION_CORRECTION=TRUE ! but read Tips_and_Tricks in XDSwiki<br />
<br />
! parameters with changes wrt default values: <br />
TRUSTED_REGION=0.00 1.35 <br />
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok<br />
MINIMUM_ZETA=0.05<br />
INCLUDE_RESOLUTION_RANGE=50 0<br />
STRONG_PIXEL=6<br />
REFINE(INTEGRATE)=CELL BEAM ORIENTATION<br />
<br />
! parameters specifically for this detector and beamline:<br />
DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000<br />
!NX= 3072 NY= 3072 QX= 0.10260 QY= 0.10260 ! XDS finds this out by itself<br />
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0<br />
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0<br />
INCIDENT_BEAM_DIRECTION=0 0 1<br />
ROTATION_AXIS=1 0 0 <br />
FRACTION_OF_POLARIZATION=0.98<br />
POLARIZATION_PLANE_NORMAL=0 1 0<br />
<br />
=== MarCDD (e.g. @ SLS, APS, ... ) ===<br />
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT ! XPLAN<br />
<br />
! for this experiment:<br />
ORGX=1533 ORGY=1536 ! if unknown estimate beam position visually using XDS-Viewer or adxv<br />
DETECTOR_DISTANCE=350<br />
OSCILLATION_RANGE=0.25<br />
X-RAY_WAVELENGTH=1.0001<br />
NAME_TEMPLATE_OF_DATA_FRAMES=../mk/mk04_1_???.img DIRECT TIFF<br />
DATA_RANGE=1 720<br />
SPOT_RANGE=1 360 ! for very accurate geometry determination use half of dataset<br />
BACKGROUND_RANGE=1 10<br />
<br />
SPACE_GROUP_NUMBER=0 ! 0 if unknown, in that case UNIT_CELL_CONSTANTS do not matter<br />
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90<br />
<br />
! remove the exclamation mark in next line if anom signal is expected/present <br />
! FRIEDEL'S_LAW=FALSE <br />
! STRICT_ABSORPTION_CORRECTION=TRUE ! usually no need to change - see Tips_and_Tricks in XDSwiki<br />
<br />
! parameters with changes wrt default values: <br />
TRUSTED_REGION=0.00 1.35 ! take corners into account<br />
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok<br />
MINIMUM_ZETA=0.05 ! integrate reflections close to rotation axis<br />
INCLUDE_RESOLUTION_RANGE=50 0<br />
STRONG_PIXEL=6<br />
REFINE(INTEGRATE)=CELL BEAM ORIENTATION<br />
<br />
! parameters for this detector and beamline: <br />
DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD=65500 <br />
! XDS picks up NX, NY, QX, QY automatically; possibilities are:<br />
!NX=3072 NY=3072 QX=0.073242 QY=0.073242 !MARCCD 225mm version<br />
!NX=2048 NY=2048 QX=0.079092 QY=0.079092 !MARCCD 165mm version<br />
!NX=4096 NY=4096 QX=0.079346 QY=0.079346 !MARCCD 325mm version<br />
!NX=4096 NY=4096 QX=0.073242 QY=0.073242 !MARCCD 300mm at APS (22-ID)<br />
<br />
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0<br />
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0<br />
INCIDENT_BEAM_DIRECTION=0 0 1<br />
ROTATION_AXIS=1 0 0 ! at e.g. SERCAT ID-22 this needs to be -1 0 0<br />
FRACTION_OF_POLARIZATION=0.99 <br />
POLARIZATION_PLANE_NORMAL=0 1 0<br />
<br />
=== Pilatus 6M @ SLS, BL X06SA ===<br />
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT<br />
<br />
! for this experiment:<br />
ORGX=1330 ORGY=1321<br />
DETECTOR_DISTANCE=550<br />
OSCILLATION_RANGE=0.25<br />
X-RAY_WAVELENGTH=1.0001<br />
NAME_TEMPLATE_OF_DATA_FRAMES=../mk/mk04_1_0????.cbf CBF<br />
DATA_RANGE=1 720<br />
SPOT_RANGE=1 720<br />
BACKGROUND_RANGE=1 10<br />
<br />
SPACE_GROUP_NUMBER=0<br />
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90<br />
<br />
! remove the exclamation marks if anom signal is present <br />
! FRIEDEL'S_LAW=FALSE <br />
! STRICT_ABSORPTION_CORRECTION=TRUE ! but read Tips_and_Tricks in XDSwiki<br />
<br />
! parameters with changes wrt default values: <br />
TRUSTED_REGION=0.00 1.15 <br />
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok<br />
MINIMUM_ZETA=0.05<br />
INCLUDE_RESOLUTION_RANGE=50 0<br />
STRONG_PIXEL=6<br />
REFINE(INTEGRATE)=CELL BEAM ORIENTATION<br />
<br />
! parameters specifically for this detector and beamline <br />
! (e.g. for the PILATUS 6M, XDS picks up NX=2463 NY=2527 automatically)<br />
<br />
DETECTOR=PILATUS QX=0.172 QY=0.172<br />
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0<br />
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0<br />
INCIDENT_BEAM_DIRECTION=0 0 1<br />
ROTATION_AXIS=1 0 0 <br />
FRACTION_OF_POLARIZATION=0.99 <br />
POLARIZATION_PLANE_NORMAL=0 1 0<br />
SENSOR_THICKNESS=0.32<br />
UNTRUSTED_RECTANGLE= 487 495 1 2527 ! these do not have to be specified<br />
UNTRUSTED_RECTANGLE= 981 989 1 2527 ! but it is better<br />
UNTRUSTED_RECTANGLE=1475 1483 1 2527 ! ...<br />
UNTRUSTED_RECTANGLE=1969 1977 1 2527 ! painstakingly checked KD 2012-01-14<br />
UNTRUSTED_RECTANGLE= 1 2463 195 213 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 407 425 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 619 637 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 831 849 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 1043 1061 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 1255 1273 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 1467 1485 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 1679 1697 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 1891 1909 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 2103 2121 ! ...<br />
UNTRUSTED_RECTANGLE= 1 2463 2315 2333 ! ...<br />
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 !used by: INTEGRATE<br />
! NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9 !used by: INTEGRATE</div>DaveL