XDS.INP

XDS.INP is a user-provided file that is read by XDS. Each line consists of one or more <keyword>=<parameter(s)> pairs. Complete documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html .

The most important keywords to get data reduction running

These keywords have no default parameters and must be given with the correct values. A minimal XDS.INP needs at least these keywords and their parameters.

ORGX ORGY

DETECTOR_DISTANCE

X-RAY_WAVELENGTH

NAME_TEMPLATE_OF_DATA_FRAMES

DATA_RANGE

DETECTOR NX NY QX QY - see http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#Table%20of%20supported%20detectors

The parameters may be obtained from logfiles of the beamline software, your notes, or (for many types of frames) from the headers of the frames (using 'strings <filename>|more'). A good way to retrieve them is by using MOSFLM.

Keywords which influence the success, outcome and quality of data reduction

REFINE(IDXREF) - The defaults (REFINE(IDXREF)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK, but only if COLSPOT has seen all (or rather, a significant fraction of the) frames. If only a small SPOT_RANGE was used (which is not the best way, but possible), one should use REFINE(IDXREF)= AXIS BEAM ORIENTATION CELL . (The next thing to omit would be AXIS)

REFINE(INTEGRATE) - The defaults (REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL) could be modified by omitting DISTANCE, because one should assume that the distance is constant. Furthermore, by fixing the distance one can better see from the results of the refinement whether the cell parameters are stable, or whether they change due to radiation damage.

REFINE(CORRECT)- The defaults (REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK

MINIMUM_ZETA - see separate entry MINIMUM_ZETA

Keywords whose default parameters rarely need to be changed

MAXIMUM_NUMBER_OF_PROCESSORS - speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine.

MAXIMUM_NUMBER_OF_JOBS - speeds up XDS by chopping the DATA_RANGE into pieces, and feeding each piece to a new process. That process may run on the local machine, or a different one (but this needs to be configured by the system administrator). Unless you know what you are doing, use MAXIMUM_NUMBER_OF_JOBS=1 - or at least don't set both MAXIMUM_NUMBER_OF_PROCESSORS and MAXIMUM_NUMBER_OF_JOBS to values >1!

What can go wrong with this file?

The most important pitfalls are:

a) Lines longer than 80 characters are truncated silently (FIXME: is this still true?). This happens most often with the NAME_TEMPLATE_OF_DATA_FRAMES keyword line, because the path to the directory with the frames may be long. Fix: use a symlink to the directory with the frames.

b) Error due to omitting the "=" directly after the keyword (i.e. having an intervening blank).

c) There may be decoding errors in the parameter which may lead to obscure error messages. E.g., see what happens if you provide only one cell parameter instead of six!

Written by --Kay 14:44, 8 November 2007 (CET)