Hi Ralf I tried supplying the space group in the command line using the --symmetry I think there is another bug there - the command line symmetry does not override the (wrong) symmetry that the routine gets from the .sca file cheers Peter M Ralf W. Grosse-Kunstleve wrote:
iotbx.reflection_statistics returns space group 195 for a scalepack 'no merge original index' .sca file for space group 123 (i.e space group 197)
the first line of the .sca file is 12 i23
You are right, this is a bug. Sorry. However, it went unnoticed because we usually supply the correct space group (along with the missing unit cell parameters) via
--symmetry=some_other_file
You could also use
--unit_cell=10,20,30,90,90,90 --space_group=197
Mostly I prefer --symmetry because there is less of a chance to mistype. Also, quite often the space group in a reflection file is not correct anyway (e.g. P222 vs. P212121).
the CCP4 program scala can output a 'no merge original index' format file, which has all 24 i23 symmetry operators in the header - but iotbx.reflection_statistics cannot read that either
I think you should be able to use the .sca file with the --symmetry or --space_group option. I've never tried to work with scala 'no merge original index' files. If you could send me your files I will look into fixing both problems.
Peter Zwart wrote:
Note that iotbx.reflection statistics itself performs a merging step, which is less sophisticated then those available in SCALA or scalepack. Therefor, it might be worthwile considering supplying merged data to iotbx.reflection_statistics.
That's right. The simple merging in the cctbx is meant to be a stop-gap measure. It is best to merge externally with a program specifically designed for this purpose.
Thanks for reporting the bug!
Cheers, Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb