After inspecting the log files it is obvious the problem is in the data integration. (Wilson B negative! highest resolution shell stronger than low res, etc..) I think you used XDS for that? Do you have an alternative set of integrated unmerged data, eg done with DIALS? If so I would use that, or download a new version of XDS and try again..
On Wed, 28 May 2025 at 07:56, Janani Ganesh <[email protected]> wrote: > Dear Martin, > > Thank you for your suggestion. I will try it out and let you know. > > Regards, > Janani Ganesh > > On Tue, 27 May 2025 09:01:06 +0100, Martin Malý <[email protected]> > wrote: > > >Dear Janani, > > > >There has been recently a significant development in twin refinement > >algorithms in Servalcat. Could you try this program and let us know if > >it helps? > >You can find Servalcat in i2 in the most recent version of CCP4. You can > >also run it in terminal/CCP4Console: > >servalcat refine_xtal_norefmac --hklin data.mtz --model model.pdb -s > >xray --labin I,IMEAN,FreeR_flag --twin > >(Assuming your MTZ data file has columns I,IMEAN,FreeR_flag.) > > > >Full list of options: > >servalcat refine_xtal_norefmac -h > > > >Please feel free to ask if anything was not clear. > >Cheers, > >Martin > > > > > >On 27/05/2025 07:00, Janani Ganesh wrote: > >> Hello, > >> > >> I recently collected diffraction data and I was able to do the data > processing upto 1.88 Å. I observed the R-merge remained the same throughout > the resolution bins. I could solve the structure using Phaser in the space > group P32 2 1 (no. 154). But when I refined the structure the R-factors > remained ~ 35 % even after several cycles of refinement and model building. > >> > >> Then I looked for twinning in my data using Xtriage, Detwin, Pointless, > etc which indicated twining. Subsequently, I started twin refinement with > Refmac using twin law (-h, -k, l). The R-factors came down to ~25%. > However, the B-factors refined to 0.5 for all the atoms. I tried redoing > the data processing at lower symmetry space groups, P3, P31, P32, followed > by twin refinement but the issue with the B-factors persisted. > >> > >> I would appreciate any suggestions and advice towards resolving this > problem. > >> > >> Regards, > >> Janani Ganesh > >> > >> ######################################################################## > >> > >> 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/ > > ######################################################################## > > 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/
