FAQ: Difference between revisions
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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? | 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? | ||
A: VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= and UNTRUSTED_RECTANGLE= | 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_CIRCLE may be implemented soon. | ||
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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). | 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). | ||
A: you could set WFAC1 to | A: you could set WFAC1 to a higher value, like 2 (default is 1). | ||
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Q: What is LATTICE-CHARACTER in CORRECT.LP ? | Q: What is LATTICE-CHARACTER in CORRECT.LP ? | ||
A: the definitive answer is | 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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Q: any comments on compatibility with Pilatus detector? | Q: any comments on compatibility with Pilatus detector? | ||
A: fully compatible | A: 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? | 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. XDS does 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: can I use xdisp (part of denzo) to find out the beamstop position and use it for xds? | Q: can I use xdisp (part of denzo) to find out the beamstop position and use it for xds? | ||
A: 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 or some such. | A: 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 that out for yourself. | ||
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Q: What about overlapping reflections in XDS? | Q: What about overlapping reflections in XDS? | ||
A: If I understand your question correctly: reflections that occur on the same position of the detector, and on the same frame, are not deconvoluted by XDS (there are programs which may be able to do this but I have not used them so far, and cannot comment on them). Reflections that are either spatially (x,y) or rotationally (in phi) separated are not a problem, they are treated quite adequately by XDS (read about the pixel-labelling method!) | A: If I understand your question correctly: reflections that occur on the same position of the detector, and on the same frame, are not deconvoluted by XDS (there are programs which may be able to do this but I have not used them so far, and cannot comment on them). Reflections that are either spatially (x,y) or rotationally (in phi) separated (even if it's only a small distance) are not a problem, they are treated quite adequately by XDS (read about the pixel-labelling method!) | ||
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Q: if one compares data integrated with the different programs (XDS, mosflm, hkl2000...): is there any difference in the final quality of the data set? | Q: if one compares data integrated with the different programs (XDS, mosflm, hkl2000...): is there any difference in the final quality of the data set? | ||
A: yes, because the programs implement different ideas. | A: yes, because the programs implement different ideas, the results differ. For good datasets, the differences are minor, but for bad datasets, the differences may be large. Don't rely on anecdotal evidence only - try for yourself! | ||
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Q: Is there a way to automatically set the high resolution limit based on | Q: Is there a way to automatically set the high resolution limit based on an I/sigma cutoff? | ||
A: no. | A: no. Different purposes require different cutoffs: refinement and MR may be done with data down to 1 to 2 sigma; sulfur SAD needs 30 sigma. | ||
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What about very low resolution data, 5 to 10 A range with the rather high mosaicity of few degrees? Any experience with processing of such data with the XDS? | What about very low resolution data, 5 to 10 A range with the rather high mosaicity of few degrees? Any experience with processing of such data with the XDS? | ||
A: yes, | A: yes, it should be possible to process these data. You may want to specify | ||
BEAM_DIVERGENCE= BEAM_DIVERGENCE_E.S.D.= | BEAM_DIVERGENCE= BEAM_DIVERGENCE_E.S.D.= | ||
REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.= | REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.= | ||
in XDS.INP, and to use REFINE(INTEGRATE)= | (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. | |||
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reference datataset? | reference datataset? | ||
A: First question: see XDSwiki. Second question: yes. | A: First question: was answered in webinar, and see XDSwiki. Second question: yes, you may use a reference dataset - this simplifies getting the right setting in space groups like P3, P4 and so on. | ||
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Q: It would be nice to have a Table with Rfactors for each | Q: It would be nice to have a Table with Rfactors for each image to identify xtal damage. | ||
I meant Table with Ractor over Image in CORRECT.LP | I meant Table with Ractor over Image in CORRECT.LP | ||
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Q: how to identify whether the data processed had a good anomalous signal? | Q: how to identify whether the data processed had a good anomalous signal? | ||
A: look at anomalous correlation: if it is > 90% at low resolution it is definitely good. | A: look at anomalous correlation: if it is > 90% at low resolution it is definitely good. Down to 30% the signal is useful, according to T. Schneider and G. Sheldrick (2002). | ||
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index the unit cell using orthagonal frames? | index the unit cell using orthagonal frames? | ||
A: yes. You can define several SPOT_RANGE= keyword/parameter pairs, e.g. SPOT_RANGE=1 1 SPOT_RANGE=90 90 . | A: 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]]. | ||
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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? | 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 | 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. | ||
Revision as of 16:58, 28 February 2010
These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010. Some answers were given during the webinar; these are not repeated here.
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?
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_CIRCLE may be implemented soon.
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).
A: you could set WFAC1 to a higher value, like 2 (default is 1).
Q: What is LATTICE-CHARACTER in CORRECT.LP ?
A: the definitive answer is in 9.2.5. Lattice characters in International Tables A.
Q: any comments on compatibility with Pilatus detector?
A: fully compatible, well tested, daily used (namely at the SLS in Villigen, Switzerland).
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).
Q: I can not find generate_XDS.INP in XDSwiki page
A: try http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
Q: the url for detector templates on slide 6 denied my visits
A: try http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html
Q: can I use xdisp (part of denzo) to find out the beamstop position and use it for xds?
A: 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 that out for yourself.
Q: for anomalous dataset, if there is radiation damage, how do I find out where to best cut off the frames for processing?
A: 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.
Q: How do you interpret the DECAY.cbf file?
A: Using XDS-Viewer: along the x direction, you find the "integration batches" (first frames to the left; last frames to the right). Along the y direction, you find the resolution ranges (bottom: low res; top: high res). The shades of gray correspond to numbers. Move the mouse across them to find the numbers which are simply the scalefactors multiplied with 1000.
Q: What about overlapping reflections in XDS?
A: If I understand your question correctly: reflections that occur on the same position of the detector, and on the same frame, are not deconvoluted by XDS (there are programs which may be able to do this but I have not used them so far, and cannot comment on them). Reflections that are either spatially (x,y) or rotationally (in phi) separated (even if it's only a small distance) are not a problem, they are treated quite adequately by XDS (read about the pixel-labelling method!)
Q: if one compares data integrated with the different programs (XDS, mosflm, hkl2000...): is there any difference in the final quality of the data set?
A: yes, because the programs implement different ideas, the results differ. For good datasets, the differences are minor, but for bad datasets, the differences may be large. Don't rely on anecdotal evidence only - try for yourself!
Q: Is there a way to automatically set the high resolution limit based on an I/sigma cutoff?
A: no. Different purposes require different cutoffs: refinement and MR may be done with data down to 1 to 2 sigma; sulfur SAD needs 30 sigma.
What about very low resolution data, 5 to 10 A range with the rather high mosaicity of few degrees? Any experience with processing of such data with the XDS?
A: yes, it should be possible to process these data. You may want to specify BEAM_DIVERGENCE= BEAM_DIVERGENCE_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. For challenging datasets, a single pass of data processing is often not enough - you'll have to experiment yourself.
Q: You said that the XDS deals with high mosaicity. How high mosaicity is still manageable?
A: I don't have exact numbers. Maybe up to ten degrees?
Q: 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?
A: First question: was answered in webinar, and see XDSwiki. Second question: yes, you may use a reference dataset - this simplifies getting the right setting in space groups like P3, P4 and so on.
Q: It would be nice to have a Table with Rfactors for each image to identify xtal damage. I meant Table with Ractor over Image in CORRECT.LP
A: XDSSTAT produces this table.
Q: Is it possible to exclude images inside the frame range from integration?
A: 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.
Q: how to identify whether the data processed had a good anomalous signal?
A: look at anomalous correlation: if it is > 90% at low resolution it is definitely good. Down to 30% the signal is useful, according to T. Schneider and G. Sheldrick (2002).
Q: 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 orthagonal frames. Can XDS index the unit cell using orthagonal frames?
A: 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.
Q: What is the best way to create mtz files? With the Xscale/xdsconv I often obtain intensity values that are marked *** stars - probably overshooting a formatting limit.
A: do you mean the *** stars appear in the output of mtzdump? That would be a problem of mtzdump 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).
Q: How does one check you've got the ice-rings excluded correctly ? (ie Is there a visual way of checking?)
A: look at the Wilson plot.
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.