[phenixbb] rigid body refinement with electron density as a model

Edward A. Berry BerryE at upstate.edu
Thu Apr 5 13:00:28 PDT 2018

I'm mostly using .eff files, and I do seem to have a line defining
that parameter:     solution_origin_ensemble = None
So I would replace "None" with the ID of the ensemble if it is
nearly in the right place? Like solving a structure using
the structure from an  almost-isomorphous crystal.

I'm asking mainly for future reference, but I will use this
feature with atomic models to get the same AU for different crystals.
Would it have a larger radius of convergence than
conventional rigid-body refinement?

On 04/05/2018 03:12 PM, Randy Read wrote:
> Hi,
> In the Phaser-MR GUI in Phenix, this is relatively easy for a PDB model, though I see it’s not set up properly for a map ensemble!  You choose “Refinement and phasing” for the Phaser mode.  You define a PDB file for the model in the right place as the ensemble and check the box saying “Ensemble is fixed partial solution”.  You still have to define the composition, but for this mode you don’t specify a search procedure because there’s no search taking place.
> In principle it should work basically the same way for a map ensemble, but I guess I’ve always done that from a script file!  Now I see there isn’t a check box for “fixed partial solution” when the model is defined with a map.  So you have to set up a script to run Phaser, in the same way as for a coordinate file, but you use the ENSEMBLE <MODLID> HKLIN command to define the model through map coefficients.  One trick here is that when you cut out the density, you have to make sure not to shift it away from its current position to the origin — this is one of the things controlled by “for_phaser=True” in phenix.cut_out_density.  Then you can say that it’s already in about the right position with the command “SOLU ORIGIN ENSEMBLE <MODLID>”.
> Let me know if you need any more help? In the meantime, we should change the GUI so that this option can be selected with a check box…
> Randy
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research    Tel: +44 1223 336500
> Wellcome Trust/MRC Building                         Fax: +44 1223 336827
> Hills Road                                                            E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk
>> On 5 Apr 2018, at 18:41, Edward A. Berry <BerryE at upstate.edu> wrote:
>> Is it possible to tell phaser to just do rigid body refinement?
>> Or how do you do rigid body with electron density?
>> On 04/05/2018 04:52 AM, Randy Read wrote:
>>>   you can cut that density out and use it to phase the native crystal by molecular replacement.  (Actually, just rigid-body refinement usually works

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