Hi Tim, > I would actually recommend using pointless (or xprep) instead of > xdsconv. It is much easier to use and maybe even less error prone.
I take the point about pointless but XPREP is commercial software sold by Bruker and costs €700 (as I remember), so is not really an option for everyone. > All your quotes from the output are perfectly consistent. The first > table tells you there are 190093 unmerged reflections in total, but > only 44059 unique reflections. Hence if you ask xdsconv to merge the > output (MERGE=TRUE), it will do so and only write 44047 (a few less > than 44059 because it rejects those 19 unmerged reflections with > I<-3sigma). 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. > The documentation tells you: > "MERGE=TRUE means that the weighted mean of symmetry equivalent > reflection intensities appearing in the input file will be determined > and used in the output file." Yes, I paraphrased this in my original mail. I like to believe that the manual describes what the program is doing, but the output isn't consistent with this in my view. > xscale does not scale data in a crystallographic sense since scaling > is already done in the CORRECT step of XDS. It put the data on a > common scale (in a sophisticated manner), i.e. if you only have one > data set there is no need to run xscale except for the thinner shells > for the statistics table compared to CORRECT. No need indeed, except that including XSCALE doesn't leave me sleepless about the data having been merged. And maybe correction for radiation damage when you have sufficient multiplicity? But yes, pedantry aside, I will start using pointless in my csh pipelines. Best wishes Derek > On 02/14/2014 03:57 PM, Derek Logan wrote: >> 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 >> >> >> >> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFS/jWBUxlJ7aRr7hoRAk0NAJ4nlKwfBMUdnbkpXzNz92+XtX1FXACfQTwJ > S92/lRMo5Jn9YHUJqLVi9mA= > =UiLX > -----END PGP SIGNATURE-----
