Hi Keitaro, phenix.refine uses ml target all the time by default (or mlhl if experimental phases are available). If you ask phenix.refine to use information about twinning (by providing a twin law) then phenix.refine will use a least-squares target function called "twin_lsq_f". So what you observe is expected. Therefore I'm not sure I understand what exactly you suspect as a bug... 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. Also, when using "twin_lsq_f" some of refinement statistics is not available and this is why you see "None" for some of those - this is nothing to worry about but just a matter of fact. May be you can explain some more what you believe is not right?
When I tried to refine using the model refined without twin_law, the target function was still ml, not twin_lsq_f although I specified twin_law. Is this a bug?
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. Thanks! Pavel. On 12/24/10 9:21 PM, Keitaro Yamashita wrote:
Dear Phenix developers,
I'm working with pseudo-merohedrally twinned data (fraction 45%), using Phenix-dev-616.
I have three questions about phenix.refine with twin_law. (running on the command line)
During refinement with twin_law, the log file says x-ray target function is set to "twin_lsq_f". Does it mean, we cannot use maximum likelihood target for twinned data? If so, is it recommended to refine without twin_law at first several cycles?
When I tried to refine using the model refined without twin_law, the target function was still ml, not twin_lsq_f although I specified twin_law. Is this a bug?
When I used twin_law option, in the table "R-free likelihood based estimates", "Scale factor" were None in all resolution bins. Cannot scale factor be calculated during twin refinement?
Thanks in advance and Wishing you the best holidays,
Keitaro _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb