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Revision as of 22:35, 27 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: Is there a way to automatically set the high resolution limit based on an I/sigma cutoff?
A: no.
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= are the primary means. 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 may set WFAC1 to 100 (default is 1)
Q: What is LATTICE-CHARACTER in CORRECT.LP ?
A: the definitive answer is at 9.2.5. Lattice characters in International Tables A.
Q: any comments on compatibility with Pilatus detector?
A: fully compatible & well tested
Q: How accurate need to be the ORGX, ORGY? Can XDS optimize the beam position?
A: the error should be less than half the minimum spot separation. XDS does optimize 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 or some such. 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" (last frames on the right). Along the y direction, the resolution ranges. The shades of gray correspond to numbers - move the mouse across them. The numbers are 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 are not a problem, they are treated very 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.
Q: Is there a way to automatically set the high resolution limit based on and I/sigma cutoff?
A: no.
Colin Levy What is the best way to deal with weak data with a long cell axis (ie. very close spots)
Alice Douangamath Have been told that XDS does not deal well with ice rings. Is it true? What is the problem there? What other way beside excluding the ice rings?
Nick Sennett How do you interpret the DECAY.cbf file?
Alejandro Buschiazzo There are ‘several’ R-factor figurest in the logs: could you comment on their
differences/advantages?
Aleksander Roszak 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?
You said that the XDS deals with high mosaicity. How high mosaicity is still manageable?
Roberto Steiner What is the best way in XDS to understand whether particular frames should be rejected? Is there an Rmerge/frame table in CORRECT.LP?
Jose Casasnovas 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?
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
Pius Padayatti how well XDS will handle weakly diffracting images?especially highly mosaic patterns, is there an option to play with mosaicity etc like in the case of HKL?
Loannis Manolaridis Thank you for the very useful seminar.
Bartholomeus Kuettner Is it possible to exclude images inside the frame range from integration?
Lirong Chen how to identify whether the data processed had a good anomalous signal?
Donal Raymond 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?
Ulrich Englich What is the best way to vreate mtz files? With the Xscale/xdsconv I often obtain intensity values that are marked *** stars - probably overshooting a formatting limit.
Xiaoyun Ji Which command lines should be refered to when dealing with really weak data?
Is there a way if the diffraction is kind of multple latticed? I mean when the automatic procedure failed due to the weak diffraction.
Nikolina Sekulic I wold like to be added to e-mail list on when slides will be available
When evaluating the processing results in CORRECT.LP, what should be done if chi2is is far fom 1.0 ? Is there any help to that?
Jonathan Grimes How does one check youve got the ice-rings excluded correctly ? (ie Is there a visual way of checking?)
Lynn Gregory-Pauron Which Rfactor do you use for publishing the structure? Do I use the Rmeas at -3 sigma (from XSCALE.LP), and why?
Karthik Sathiyamoorthy 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?