[phenixbb] Questions about phenix.refine with twin_law

Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp
Sun Dec 26 04:47:04 PST 2010

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,


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