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FAQ: Difference between revisions
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=== The background range is defined as first 5 degrees by default. Is this an assumption that the background (used in Integrate?) remains consistent over the entire dataset valid? The spots over the entire dataset still have background corrected based on first 5 degrees? === | === The background range is defined as first 5 degrees by default. Is this an assumption that the background (used in Integrate?) remains consistent over the entire dataset valid? The spots over the entire dataset still have background corrected based on first 5 degrees? === | ||
No. The INIT step uses the first 5 degrees (by default) for a number of purposes (check out the files written by INIT !). BKGINIT.cbf is | No. The INIT step uses the first 5 degrees (by default) for a number of purposes (check out the files written by INIT !). BKGINIT.cbf is used for scaling purposes and beamstop masking (in DEFPIX); the ''real'' background calculation just requires those frames which have the reflections that are integrated. | ||
=== I can see many diffraction spots in the BKGINIT.cbf when the BACKGROUND_RANGE is set default (first 5 degree images). When this value is set large (eg. 50 degree), no diffraction spots can be seen. It seems that only the large value produces a "real" background image. But both these two scenarios produce nearly the same results (data statistics). Do I need to always change the BACKGROUND_RANGE so that there are no diffraction spots in the BKGINIT.cbf? === | |||
No. Again, BKGINIT.cbf is used only for scaling purposes and masking the beamstop (in DEFPIX); the ''real'' background calculation just requires those frames which have the reflections that are integrated. Normally you don't worry about BACKGROUND_RANGE; just use the default! You need only increase the BACKGROUND_RANGE if you have so low background that a) even 5° of data produces many zero pixels in BKGINIT.cbf (but this is highly unlikely), or b) if shadowed parts of the detector are not visible in BKGINIT.cbf when viewed with xds-viewer. | |||
== COLSPOT == | == COLSPOT == | ||
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=== How does one define the beam stop shadow? Is it possible to develop a simple method, e.g. the ignore circle and ignore rectangle of HKL2000? === | === How does one define the beam stop shadow? Is it possible to develop a simple method, e.g. the ignore circle and ignore rectangle of HKL2000? === | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=] masks shaded portions, and variation of its first parameter (values between 6000 and 9000) may be used to obtain the desired result (check with "XDS-Viewer BKGPIX.cbf"). [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#UNTRUSTED_RECTANGLE= UNTRUSTED_RECTANGLE=] is probably the same as is available in HKL2000. [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#UNTRUSTED_ELLIPSE= UNTRUSTED_ELLIPSE=] is also available, and there's also [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#UNTRUSTED_QUADRILATERAL= UNTRUSTED_QUADRILATERAL=]. Furthermore, you could set [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_VALID_PIXEL_VALUE= MINIMUM_VALID_PIXEL_VALUE] such that all shaded pixels are below that number, and all background values above it. | ||
== INTEGRATE == | == INTEGRATE == | ||
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=== Is it possible to exclude images inside the frame range from integration? === | === Is it possible to exclude images inside the frame range from integration? === | ||
just remove them from the directory, or change their name. Or create a directory with symlinks only to those file you want XDS to use. | Use EXCLUDE_DATA_RANGE. It is also possible to just remove them from the directory, or change their name. Or create a directory with symlinks only to those file you want XDS to use. | ||
== CORRECT == | == CORRECT == | ||
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xscale_par | xscale_par | ||
XSCALE.LP now has the table for the I > 3sigma observations (even if the header of the table says that it's for the SIGNAL/NOISE >= -3.0 data) | XSCALE.LP now has the table for the I > 3sigma observations (even if the header of the table says that it's for the SIGNAL/NOISE >= -3.0 data) | ||
== XSCALE == | |||
=== Just wondering if the XDS_ASCII.HKL file needs to be scaled using XSCALE or its not required? === | |||
It is not required. XDS_ASCII.HKL is scaled in the CORRECT step. If you want to scale two (or more, even >1000 !) XDS_ASCII.HKL files together, or if you want to use zero-dose extrapolation, or determine resolution shells yourself, then you need [[XSCALE]]. | |||
== other questions == | == other questions == | ||
=== any comments on compatibility with Pilatus detector? === | === any comments on compatibility with Pilatus detector? === | ||
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=== the URL for detector templates on slide 6 denied my visits === | === the URL for detector templates on slide 6 denied my visits === | ||
http:// | http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html | ||
=== for anomalous dataset, if there is radiation damage, how do I find out where to best cut off the frames for processing? === | === for anomalous dataset, if there is radiation damage, how do I find out where to best cut off the frames for processing? === | ||
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=== Could you give recommendation for MAD data processing, to get best anomalous?? How to process the 3 data sets with the same orientation matrix, should we use reference datataset? === | === Could you give recommendation for MAD data processing, to get best anomalous?? How to process the 3 data sets with the same orientation matrix, should we use reference datataset? === | ||
First question: | First question: Scale them in a single XSCALE run, using one OUTPUT_FILE for each wavelength. See also this wiki: [[Optimisation]] and [[Tips and Tricks]]. Second question: yes, you may use a REFERENCE_DATA_SET - this simplifies getting the right setting in space groups like P3, P4 and so on. | ||
== See also == | == See also == | ||
[[Problems]] | [[Problems]] | ||