Pointless

The pointless program (see Scaling and Assessment of Data Quality, Philip Evans, Acta Cryst D 62, 72-82) serves to identify space group possibilities from unmerged data.

HTML documentation is at http://www.ccp4.ac.uk/html/pointless.html . The pre-release version may be obtained from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/ .

Typical usage for space group determination is

pointless xdsin XDS_ASCII.HKL

("xdsin" can be left out)

Typical usage for converting to multi-record MTZ file (for scaling with SCALA or AIMLESS) is

pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz

(the -copy option does not seem to be required for the latest versions)

More complicated operations may be scripted:

#!/bin/csh -f
pointless <<eof
xdsin XDS_ASCII.HKL
centre
eof

will make an R-factor search for the correct origin.

Attention: the space group number that pointless writes into the logfile (e.g. "17") is the generic one (as in the International Tables vol A), not the specific one (which could be 17, 1018 or 2017) that is used as a special convention within CCP4 to encode which of a,b and c is the two-fold screw axis. At the same time, pointless re-indexes orthorhombic such that a<b<c : this is what is called "cell-based setting" in the pointless documentation, and unfortunately it's the default. However, users of XDSCONV want the "symmetry-based setting" because XDSCONV does not understand 1017 and 2017 (and those numbers are not even in the logfile, only in the MTZ file which is not used by XDSCONV anyway). This also affects the distinction between space groups C2 and I2.

This is discussed under the headings "A note on setting conventions" and "SETTING CELL_BASED || SYMMETRY-BASED || C2" in the pointless documentation.

The upshot is: for space groups 5, 17 and 18, XDS users want to use the "symmetry-based setting". It does not hurt to always (i.e. for all 65 space groups that proteins crystallize in) use it, so an easy way is e.g.:

echo -e SETTING SYMMETRY-BASED\\n CHIRALITY CHIRAL | pointless xdsin XDS_ASCII.HKL

which also shows how to send several commands to pointless.

See also:

xprep

Space group determination

Scaling with SCALA