[phenixbb] bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
peter.metcalf at auckland.ac.nz
Mon Mar 6 14:05:00 PST 2006
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
the (wrong) symmetry that the routine gets from the .sca file
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
>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
>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!
>phenixbb mailing list
>phenixbb at phenix-online.org
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