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FAQ: Difference between revisions
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== COLSPOT == | == COLSPOT == | ||
=== All my crystals are split, and HKL200 has a hard time indexing the unit cell using sequential frames. However, iMOSFLM does a really good job indexing using orthogonal frames. Can XDS index the unit cell using orthogonal frames? === | |||
yes. You can define several SPOT_RANGE= keyword/parameter pairs, e.g. SPOT_RANGE=1 1 SPOT_RANGE=90 90 . Most likely it will be even better with SPOT_RANGE= 1 90 . Also see [[Indexing]]. | |||
== IDXREF == | == IDXREF == | ||
=== What is LATTICE-CHARACTER in IDXREF.LP and CORRECT.LP ? === | === 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]. | the definitive answer is in [http://it.iucr.org/Ab/ch9o2v0001/sec9o2o5/ 9.2.5. Lattice characters, in International Tables A]. | ||
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yes. Unfortunately, the conventions of the different data reduction programs are not the same, but there is always a simple transformation between them, like x' = y; y' = x (which often works!) or some such. The transformation may be different for different detectors. For a given detector, you can easily find the transformation out for yourself, by noting the values from xdisp and comparing them with those from [[adxv]] or [[XDS-Viewer]]. After that, you can always find the beamstop position with xdisp, and put the transformed values into XDS.INP . | yes. Unfortunately, the conventions of the different data reduction programs are not the same, but there is always a simple transformation between them, like x' = y; y' = x (which often works!) or some such. The transformation may be different for different detectors. For a given detector, you can easily find the transformation out for yourself, by noting the values from xdisp and comparing them with those from [[adxv]] or [[XDS-Viewer]]. After that, you can always find the beamstop position with xdisp, and put the transformed values into XDS.INP . | ||
== DEFPIX == | == DEFPIX == | ||
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do you mean the *** stars appear in the output of mtzdump? That would be a problem of mtzdump output only, and irrelevant for the use of the MTZ file. The XDS/XSCALE/XDSCONV route should not produce these stars (the proper Fortran formats are used throughout). | do you mean the *** stars appear in the output of mtzdump? That would be a problem of mtzdump output only, and irrelevant for the use of the MTZ file. The XDS/XSCALE/XDSCONV route should not produce these stars (the proper Fortran formats are used throughout). | ||
=== How does one check you've got the ice-rings excluded correctly ? (ie is there a visual way of | === How does one check you've got the ice-rings excluded correctly ? (ie is there a visual way of checking?) === | ||
checking?) === | |||
look at the Wilson plot, and the list of outliers at the bottom of CORRECT.LP. | look at the Wilson plot, and the list of outliers at the bottom of CORRECT.LP. | ||
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http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html | http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html | ||
=== for anomalous dataset, if there is radiation damage, how do I find out where to best cut off the | === for anomalous dataset, if there is radiation damage, how do I find out where to best cut off the frames for processing? === | ||
frames for processing? === | |||
there are no hard rules. One possibility is to look at the anomalous correlation printed in CORRECT.LP for subsets of the data. If those numbers drop after frame X, you should probably not use frames after X. | there are no hard rules. One possibility is to look at the anomalous correlation printed in CORRECT.LP for subsets of the data. If those numbers drop after frame X, you should probably not use frames after X. | ||
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REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.= | REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.= | ||
(take the values from INTEGRATE.LP after a first pass) in XDS.INP, and to use REFINE(INTEGRATE)= to refine only those geometrical parameters that actually change. | (take the values from INTEGRATE.LP after a first pass) in XDS.INP, and to use REFINE(INTEGRATE)= to refine only those geometrical parameters that actually change. | ||
For challenging datasets, a single pass of data processing is often not enough - you'll have to experiment yourself. | For challenging datasets, a single pass of data processing is often not enough - you'll have to experiment yourself. | ||