[phenixbb] Questions about phenix.refine with twin_law

Pavel Afonine pafonine at lbl.gov
Fri Dec 24 23:32:58 PST 2010


  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
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