Hi, I am a long time user of XDS (20 years this year) but all the same I find that I have constant angst about losing observations because I don't understand what goes in in the conversion steps to get to CCP4 format. I used to believe that XSCALE was always necessary, and I always use it in my workflow even if there is only one dataset (after all, there's nothing to lose), but my Ph.D. students pointed out to me that XDSCONV could take output directly from CORRECT, and they often do it this way. The XDS wiki and XDSCONV docs seems to confirm this: using MERGE=TRUE in XDSCONV should output the geometrical mean of the observations. However I am worried by what the XDSCONV output says. For today's example CORRECT gives me this:
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 190093 NUMBER OF REJECTED MISFITS 3842 NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 34 NUMBER OF ACCEPTED OBSERVATIONS 186217 NUMBER OF UNIQUE ACCEPTED REFLECTIONS 44059 XDSCONV says the following: FRIEDEL'S_LAW=TRUE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT FILE 190093 NUMBER OF IGNORED REFLECTIONS (I< -3.0*SIGMA) 19 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE 44047 To my literal mind this says it is throwing away most of the observations. Now if I merge the reflections in XSCALE first it says this: FRIEDEL'S_LAW=TRUE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT FILE 44046 NUMBER OF IGNORED REFLECTIONS (I< -3.0*SIGMA) 0 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE 44046 which makes more sense. If I compare the first few reflections of the output file with structure factor amplitudes from XDSCONV for each scenario they are different, but I believe that is because XSCALE has put the intensities on an absolute scale and CORRECT has not. Basically all I want to know is that the output from XDSCONV is misleadingly worded, i.e. that even if it appears to say that only the asymmetric unit has been accepted, actually all observations have gone in and the geometric mean is indeed output. That would put my mind to rest! /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden
