Re: [phenixbb] Q. Phase extension

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 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 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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