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-These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010 (available at http://www.rigaku.com/protein/kay-diederichs/). Some answers were given during the webinar; these are not repeated here.
+These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010 (available at http://www.rigaku.com/protein/kay-diederichs/), or in emails. If possible, they are grouped here with the appropriate processing step.
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+== INIT ==
+=== 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 essentially used only for scaling purposes; the ''real'' background calculation just requires those frames which have the reflections that are integrated.
+== COLSPOT ==
+== IDXREF ==
+=== What is LATTICE-CHARACTER in IDXREF.LP  and CORRECT.LP ? ===
+the definitive answer is in [http://it.iucr.org/Ab/ch9o2v0001/sec9o2o5/ 9.2.5. Lattice characters, in International Tables A].
+=== 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).
-Q: 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?
+== DEFPIX ==
-A: 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"). UNTRUSTED_RECTANGLE= is probably the same as is available in HKL2000. UNTRUSTED_ELLIPSE= is also available.
+=== 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? ===
-----
+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"). UNTRUSTED_RECTANGLE= is probably the same as is available in HKL2000. UNTRUSTED_ELLIPSE= is also available.
-Q: Can one apply the corrections in CORRECT without deleting outliers (i.e. waiting for a later program e.g. SCALA to do outlier rejection).
+== INTEGRATE ==
-A: you could set WFAC1 to a higher value, like 2 (default is 1).
+== CORRECT ==
-----
+=== Can one apply the corrections in CORRECT without deleting outliers (i.e. waiting for a later program e.g. SCALA to do outlier rejection). ===
-Q: What is LATTICE-CHARACTER in CORRECT.LP ?
+you could set WFAC1 to a higher value, like 2 (default is 1).
-A: the definitive answer is in [http://it.iucr.org/Ab/ch9o2v0001/sec9o2o5/ 9.2.5. Lattice characters, in International Tables A].
-----
+== other questions ==
-Q: any comments on compatibility with Pilatus detector?
+=== any comments on compatibility with Pilatus detector? ===
-A: fully compatible, well tested, daily used (namely at the SLS in Villigen, Switzerland).
+fully compatible, well tested, daily used (namely at the SLS in Villigen, Switzerland).
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-Q: How accurate need to be the ORGX, ORGY? Can XDS optimize the beam position?
-A: 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).
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-Q: 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?
-A: 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 essentially used only for scaling purposes; the ''real'' background calculation just requires those frames which have the reflections that are integrated.
 == See also ==
 [[Problems]]