Pointless: Difference between revisions

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 Typical usage for space group determination is
-  pointless xdsin XDS_ASCII.HKL
+  echo SETTING SYMMETRY-BASED | pointless XDS_ASCII.HKL
-("xdsin" can be left out)
+One may send several commands to pointless:
+ echo -e SETTING SYMMETRY-BASED\\n CHIRALITY CHIRAL | pointless XDS_ASCII.HKL
 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
+  pointless -copy XDS_ASCII.HKL hklout XDS_ASCII.mtz
-(the -copy option does not seem to be required for the latest versions)
+(the -copy option is not required)
 More complicated operations may be scripted:
   #!/bin/csh -f
   pointless <<eof
+ SETTING SYMMETRY-BASED
   xdsin XDS_ASCII.HKL
   centre
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 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, 1017 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.
+Why "SETTING SYMMETRY-BASED"? 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, 1017 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 [[XDS]], [[XSCALE]] and [[XDSCONV]] want the "symmetry-based setting" because these programs do not understand 1017 and 2017 (and those numbers are not even in the logfile, only in the MTZ file). This also affects space group 18 ("P 21 21 2"), and in space group 5 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 [http://www.ccp4.ac.uk/html/pointless.html 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.:
+The upshot is: for space groups 5, 17 and 18, XDS users want to use the "symmetry-based setting", and it does not hurt to ''always''  use it, i.e. for all 65 space groups that proteins crystallize in. This deviation from the default of pointless has several advantages (avoiding the ambiguity, and avoiding change of space group assignment upon small change of axes), and no disadvantage.
- 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: