[phenixbb] Q. Phase extension

[Terwilliger, Thomas C]

I would just run autobuild with the experimental data and hl coeffs as "data" and the high resolution data as "hires" data and your current model and sequence file.  Specify "rebuild_in_place=False" and that should work well.  You might cut off the resolution at 1.8 A to speed it up and slightly improve the model-building but I expect that wouldn't make too much difference. The phase extension should automatically be carried out in steps in autobuild density modification.

All the best,
-Tom T
On Jun 26, 2013, at 3:05 AM, Mark J van Raaij wrote:

> 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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