Dear Peter and Pavel, Thank you very much for your replies. I just didn't know that the target function is limited to lsq in case of twinning, not suspect that as a bug. Currently, R-work and R-free are 22%, 24%, respectively (with twin_law) at 2.5 Angstrom resolution. In my understanding, least square target function has very poor convergence since it is much biased to the current model. I'm afraid refinement couldn't converge correctly with twin_lsq_f. This is why I thought it could be better to refine without twin_laws for first several cycles. (But if ignoring twinning, the targeted amplitudes should be inappropriate... I have no idea which way to turn.)
The next CCN (Computational Crystallography Newsletter; http://www.phenix-online.org/newsletter/) that comes out beginning of January will contain an article about using ML target in twin refinement, which will be implemented in some (hopefully near) future.
I'm looking forward to using it. Will it be different formulation from Refmac?
Not sure, can you send (off-list) logfile of that run? This is weird... If you could send me the inputs that I can use to reproduce this problem then I will be able to explain what is going on.
I'm sorry, the model under refinement must be kept confidential so I could not give it to you. But in log file, twin_law keyword is definitely accepted:
Command line parameter definitions: refinement.input.xray_data.labels = F,SIGF
refinement.refine.strategy = individual_sites+individual_adp
refinement.twinning.twin_law = -k,-h,-l
However, the refinement target is still ml:
=============================== refinement start ============================== ... | maximum likelihood estimate for coordinate error: 0.37 A | | x-ray target function (ml) for work reflections: 6.900796 | |-----------------------------------------------------------------------------|
Does phenix.refine read some informations from pdb file other than coordinates? Thank you very much, Keitaro