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
