[phenixbb] Twinned Refinement

Petrus H Zwart PHZwart at lbl.gov
Mon Mar 19 16:06:43 PDT 2007


Very nice to know.

You might want to include a TLS model if you have multiple chains inthe ASU.
Besides that, it is not a bad idea to play with the threshold values of water picking. The gradient maps can be more noisy than your average FO-FC map, resulting in phenix.refine picking out more 'breadcrums' than 'buns'.
The mFO-DFC maps one currently can put out, have some problems, so beter leave those alone for now. It is on the top of my list.

Cheers

Peter




 


----- Original Message -----
From: "Axelrod, Herbert" <haxelrod at slac.stanford.edu>
Date: Monday, March 19, 2007 2:55 pm
Subject: Re: [phenixbb] Twinned Refinement
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 
> 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.
> Thanks,
> Herb
> 
> -----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.
> 
> Cheers
> 
> Peter
> 
> 
> -------------------------------------------------------------------
> 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::
> 
>  refinement.twinning{
>    twin_law = None
>    detwin{
>      mode = algebraic proportional *auto
>      local_scaling = False
>      map_types{
>        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 
> > 
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> > 
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