[phenixbb] Twinned Refinement

Axelrod, Herbert haxelrod at slac.stanford.edu
Mon Mar 19 15:55:27 PDT 2007

Hi Petrus,
 Thank You for your e-mail. Yesterday I tried out phenix.refine for one of the twinned targets here at JCSG. The results are quite encouraging!
  The resolution of this target is 1.9 Ang was refined with SHELXL to an Rfree of ~22%. Implementing your phenix.refine twin protcol, the Rfree dropped to 17% with better geometry than SHELXL.
 I can keep you informed on our findings at this end.

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Petrus H Zwart
Sent: Monday, March 19, 2007 12:20 PM
To: PHENIX user mailing list
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Twinned Refinement

Hi Herbert,

I did test it a bit, mainly because I implemented it.

See below some details of the manual that deal with twinning.

make sure you choose your free flags in a proper manner. The easiest way to do this, is by letting phenix.refine take care of it.

You can do it manually as well:

iotbx.reflection_file_converter --generate-r-free-flags --use-lattice-symmetry-in-r-free-flag-generation <other keywords>

I have seen  that in some cases the automatic weighting between restraints and xray terms performs poorly (R and R free both go up during refinement, mainly during the ADP refinement), this is being adressed now. 
A not so user friendly way of dealing with this is by manualling optimising wxu.  Please let us know if this happens and we can provide more clues how to get things going.



phenix.refine for the refinement of twinned data

phenix.refine can handle the refinement of hemihedrally twinned data (two twin domains). Least square twin refinement can be carried out using the following commands line instructions::

  % phenix.refine data.hkl model.pdb twinning=True twin_law=="-k,-h,-l"

The twin law (in this case -k,-h,-l) can be obtained from phenix.xtriage. If more than a single twin law is possible for the given unit cell and space group, using phenix.twin_map_utils might give clues which twin law is the most likely candidate to be used in refinement.

Other twinning options are defined in the following scope::

    twin_law = None
      mode = algebraic proportional *auto
      local_scaling = False
        twofofc = *two_m_dtfo_d_fc two_dtfo_fc
        fofc = m_dtfo_d_fc *gradient m_gradient
        aniso_correct = False

At this giving moment, it is best to leave the map types alone, although correcting for anisotropy might be usefull (detwin.map_types.aniso_correct=True).

The detwinning mode is auto by default: it will perform algebraic detwinning for twin fraction below 40%, and detwinning using proportionality rules (SHELXL style) for fractions above 40%.

Please note that the gradient maps (fofc=gradient) are detwinned by
nature: no detwinning is needed. At this point in time, the gradient maps are the best choice for picking waters or building missing ligands.

An important point to stress is that phenix.refine will only deal properly with twinning that involves two twin domains. The refinement of more than two domains will be dealth with at the appropriate juncture.

----- Original Message -----
From: "Axelrod, Herbert" <haxelrod at slac.stanford.edu>
Date: Monday, March 19, 2007 10:57 am
Subject: [phenixbb] Twinned Refinement
To: phenixbb at phenix-online.org

> Hi,
> I was wondering if anyone has tested the new version of 
> phenix.refine for the refinement of twinned diffraction data. Last 
> week at Asilomar, Pavel presented a nice talk at Asilomar on the 
> capabilities of phenix.refine to handle twinned data.
> Best wishes,
> Herbert L. Axelrod
> Stanford Synchrotron Radiation Lab 
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> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
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