FAQ: Difference between revisions
/* 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 o... |
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=== How accurate need to be the ORGX, ORGY? Can XDS optimize the beam position? === | === How accurate need to be the ORGX, ORGY? Can XDS optimize the beam position? === | ||
ideally, the error should be less than half the minimum spot separation. If the error is larger than that, you'll have to inspect the table in IDXREF.LP which investigates alternative origin positions. XDS does optimize the beam position (or rather the beam direction, but that determines the beam position). | ideally, the error should be less than half the minimum spot separation. If the error is larger than that, you'll have to inspect the table in IDXREF.LP which investigates alternative origin positions (the one that has the heading "***** SELECTION OF THE INDEX ORIGIN OF THE REFLECTIONS *****"). XDS does optimize the beam position (or rather the beam direction, but that determines the beam position). See [[Finding out ORGX ORGY]] for a program that estimates ORGX, ORGY from ice rings. | ||
=== can I use xdisp (part of denzo) to find out the beamstop position and use it for xds? === | === can I use xdisp (part of denzo) to find out the beamstop position and use it for xds? === | ||
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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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=== 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? === | ||