Dear everyone, I also want to thank Andrew for imosflm to give me the right direction. I have also successfully indexed the data with imosflm.
Thanks! Best wishes, Shen On Mon, Oct 5, 2020 at 8:50 AM Xu, Shenyuan <x...@miamioh.edu> wrote: > Dear everyone, > > Thanks for all the suggestions! I am sorry if I did not respond to your > emails and say thanks individually. > > For the dataset 1, the data has been successfully indexed with Dials and > XDS after readjusting beam center and rotation axis handedness. Thanks > David for providing me the Dials commands and Kay for giving me the XDS > codes. > > I really appreciate the help from all of you! > > Thanks, > > Shen > > On Fri, Oct 2, 2020 at 11:04 AM Xu, Shenyuan <x...@miamioh.edu> wrote: > >> Dear CCP4 community, >> >> I have two challenging datasets for indexing, one has very strong >> diffraction, the other one has very weak spots. I know both crystals are >> not very good, knocked down from a big chunk of crystal. >> >> For the dataset 1, first I use iMosflm to index it, but it can not refine >> it as "Detector tilt and twist parameters vary substantially". Based on the >> penalty value and RMSD, the index solution is not satisfactory. Then I >> moved to Xia2 from CCP4i, no index solution was found. Then I use Dials, it >> can successfully index the data, but only about 25% spots have been >> indexed, and the rmsd is not very good. I forced it to proceed, and after >> integration, the statistics seem to be good, but I can not use MR to solve >> the structure (If the index is good, I think MR can solve it as I did it >> before). I have gone through all the troubleshooting suggestions that are >> available online for iMosflm and Dials, but no improvement. >> >> For the dataset 2, I think the main reason is because of the weak >> diffraction. Both iMosflm and Dials can not give good results. >> >> The best way may be to optimize the crystal. But I feel like there may be >> a better way to optimize the parameters to index it. The datasets are >> large, I can send you privately by email if you are interested to take a >> look. >> >> I really appreciate your suggestions. >> >> Thanks, >> Shen >> >> > ######################################################################## 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/
