[phenixbb] Q. Phase extension

[Mark J van Raaij]

Can't you just refine the poly-Ala model against the 1.5A native data? (Perhaps after rigid body refinement or even molecular replacement if the data is too non-isomorphous). And then run Autobuild with these phases?

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 26 Jun 2013, at 10:44, Randy Read wrote:

> Hi John,
> 
> Tom Terwilliger will have to answer the question of whether there's a better way to extend to the high resolution data set than the defaults in AutoSol/AutoBuild.  If there is, then I imagine he'll want to change those defaults!
> 
> I just thought I would check whether you're confident that the Os and native data sets are truly isomorphous.  It doesn't take a lot of non-isomorphism before you run into problems transferring the phase information from one crystal to another.
> 
> If there is significant lack of isomorphism (e.g. a cell dimension change as big as 1A or more) then it might be worth using cross-crystal averaging to transfer the phase information.  We've used this for a recent structure solution, where we cut out the density for the protein from the SAD-phased map, then used the density as a molecular replacement model where rigid-body refinement was enough to determine the small shift in rotation and translation required to place that density correctly in the native cell.  Cutting out the density and preparing a corresponding MTZ file for Phaser can be accomplished fairly easily using Tom's phenix.cut_out_density tool, if you have a PDB file that can be used to define the envelope for the protein density.  Once you've phased the native data with that map, then you can use Tom's phenix.multi_crystal_average to average between the two forms.  You'd probably want to follow that up by phase extension of the native crystal, but now starting from the phases obtained from the multi-crystal averaging.
> 
> Best wishes,
> 
> Randy Read
> 
> On 26 Jun 2013, at 03:58, John Rose <rose at bcl4.bmb.uga.edu> wrote:
> 
>> Hi,
>> 
>> I have a 3.5 angstrom Os SAD phased map from AutoSol that looks real good (~50% fitted as poly ALA) and a 1.5 Angstrom set of native data.  I would like to try phase extension in steps to see if the map improves enough for AutoBuild to fit the sequence.
>> 
>> What AutoSol files/flags do I need for AutoBuild in addition to the high res data to get the best results.
>> 
>> Thanks,
>> 
>> John
>> 
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> 
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
> 
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