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
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