[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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