FAQ

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.

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

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

What is LATTICE-CHARACTER in IDXREF.LP and CORRECT.LP ?

the definitive answer is in 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).

can I use xdisp (part of denzo) to find out the beamstop position and use it for xds?

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

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.

INTEGRATE

What about overlapping reflections in XDS?

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!)

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.

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).

you could set WFAC1 to a higher value, like 2 (default is 1).

Is there a way to automatically set the high resolution limit based on an I/sigma cutoff?

no. Different purposes require different cutoffs: refinement and MR may be done with data down to 1 or 2 sigma; sulfur SAD needs 30 sigma for finding the S sites.

How do you interpret the DECAY.cbf file?

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.

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

XDSSTAT produces this table.

how to identify whether the data processed had a good anomalous signal?

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).

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.

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 checking?)

look at the Wilson plot, and the list of outliers at the bottom of CORRECT.LP.

other questions

any comments on compatibility with Pilatus detector?

fully compatible, well tested, daily used (namely at the SLS in Villigen, Switzerland).

I can not find generate_XDS.INP in XDSwiki page

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP

the URL for detector templates on slide 6 denied my visits

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 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.

if one compares data integrated with the different programs (XDS, mosflm, hkl2000...): is there any difference in the final quality of the data set?

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!

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?

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.

You said that the XDS deals with high mosaicity. How high mosaicity is still manageable?

I don't have exact numbers. Maybe up to ten degrees?

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?

First question: short answer was given in the webinar, and see this wiki: Optimisation and Tips and Tricks. Second question: yes, you may use a reference dataset - this simplifies getting the right setting in space groups like P3, P4 and so on.

See also

Problems