Dear Doo Nam Kim, actually the results of XDS processing are deterministic for all practical purposes (to be nitpicking, the multi-processor version xds_par may result in slighly different output each time it is run, because for a few calculations the order of operations is influenced by the operating system's scheduler, but this only typically affects the last digit and is of no practical importance).
XDS needs to know the starting and end angle of each frame. It calculates these values internally, from STARTING_ANGLE and OSCILLATION_RANGE and the frame number (you specify the frames to process with DATA_RANGE for INTEGRATE, and with SPOT_RANGE for COLSPOT and IDXREF). If you don't specify STARTING_ANGLE, it will use 0 as the default. This does not affect the success of indexing, nor the data quality. There is no corresponding ENDING_ANGLE, because - as I said - the ENDING_ANGLE is anyway calculated internally; it is the end angle of the last frame. Concerning completeness: if your DATA_RANGE is specified correctly, AND the indexing succeeds, AND the space group is found (or given) correctly, then I see no reason why the completeness should not result in 60% for you, if someone else got 60%. Apart from http://xds.mpimf-heidelberg.mpg.de, there is documentation and examples in XDSwiki at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_page Hope this helps, Kay On Fri, 9 Oct 2020 07:43:22 +0100, Doo Nam Kim <doonam....@pnnl.gov> wrote: >Thank you Tim and Kay. > > > >"the indexing procedure is independent of the starting angle of the first >frame." >--> I see, since XDS does indexing, I think that XDS is independent of the >starting angle of the first frame > > >"Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree >per frame during data collection?" > >--> As I see >http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE= > >OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) >appears to designate 1 value, rather than 2 values (like min and max, e.g. >-60, 60). > >Since I don't know correct value of OSCILLATION_RANGE, I just changed to the >example value (0.1) from (0.899999976, I know it is not a positive multiple of >0.0001, but worked for ketone data). > >Then, xds ran without error. > >Then, according to recommendtion, I changed from >JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT >to >JOB= DEFPIX INTEGRATE CORRECT > >and ran again. > >This time, it generated CORRECT.LP, but I see COMPLETENESS is only ~6%, while >my predecessor achieved ~60% > >I think that results of XDS are somehow random (not 100% deterministic). But I >didn't expect this big difference of COMPLETENESS (6% vs 60%). > >I think that I still entered a wrong option value somewhere in my XDS.INP. > >I think that I need to use well documented (with respect to needed xds.INP >parameters) microED dataset but I can't download from >https://cryoem.ucla.edu/MicroED > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
