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

[Randy Read]

Hi,

I had to run some test jobs to check how this would work in a .eff file.  So, actually, what you need to do is to go to the ensemble section of the .eff file where the model to be fixed is defined, and set "solution_at_origin = True".  That works for both models specified as PDB files or as density, as long as they're close to being in the correct position.

Our experience with the rigid-body refinement in Phaser has been very good in terms of radius of convergence, though we haven't done systematic tests against phenix.refine and Refmac to see how they would compare.  Definitely it's a good option to try first if you have a crystal that should be reasonably isomorphous and it will usually work in those circumstances.  If it doesn't work, then you can go back to trying a full MR search.  Even in that case (at least if you're running Phaser from a script) you can use the SOLU TEMPLATE command to indicate the start of a target solution that you would like the answer to match to as closely as possible, which should work even if there are several components being allowed to move.  However, I don't see a way at the moment of specifying that from phil .eff files!

Randy

> On 5 Apr 2018, at 21:00, Edward A. Berry <BerryE at UPSTATE.EDU> wrote:
> 
> 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
>> 
>> 

------
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