Dear Kay,

> Concerning usage of programs, everybody has his/her preferences, but what could be simpler than a 2-liner XDSCONV.INP like
> INPUT_FILE=XDS_ASCII.HKL
> OUTPUT_FILE=temp.hkl CCP4  ! or CCP4_F or CCP4_I or SHELX or CNS
> and then running XDSCONV by running "xdsconv"? At least there's not much room for mistakes.

Exactly!

>> I beg to disagree, and this was the point of my question. The output of XDSCONV literally says that 190093 reflections are read, and [of those, my interpretation] 44047 are accepted. I may be a pedant but I can't read that output in any other way. To me it looks like it is reading only the reflections that already fall into the asymmetric unit and is ignoring all the others. So if XDSCONV is really doing what it is supposed to, I would suggest rephrasing that output line.
> 
> good point about the rephrasing. I'll see to making the wording consistent between XDSCONV and XDS.

Thanks for that.

> But irrespective of the wording, it does take all observations into account when calculating the intensity (and amplitude) of the unique reflections (as it should - ignoring reflections would not make sense, and would produce significantly worse data).

Great, this was just the reassurance I was looking for.

> However, it does so not by calculating the geometric mean (which you seem to assume), but by calculating the weighted mean. Weighting is done with the variances, and here it also does not differ from (c)truncate or other programs.

Sorry, that was a typo born of thinking I could quote the manual from memory.

>> But yes, pedantry aside, I will start using pointless in my csh pipelines.
> 
> please report back whether that changes (or even improves) your results! It is always very good when people compare programs in a meaningful way, but from my own experience I can say that meaningful comparisons are sometimes not entirely straightforward to get right. (for the German-speaking: "wer misst, misst Mist!")

Probably I will still be in too much of a hurry each time to make a meaningful and thorough comparison, but if time allows I will compare XDSCONV with pointless/scala.

/Derek