[phenixbb] Molecular replacement with fixed solution
rjr27 at cam.ac.uk
Fri Jan 16 12:06:48 PST 2015
There are two ways to do this, and I’ve just tested them both using the beta-lactamase:BLIP tutorial from the Phenix distribution.
1. The easy way, which is what users are generally meant to do. Define all the necessary background information (data, both ensembles: beta and blip, composition with sequence files). Specify one search for one component, e.g. beta. When this finishes, go to the main “Input and general options” pane of the GUI and, in the “Use partial solution from previous job” pulldown, choose the job that placed the beta component. Now go to the “Search procedure” pane and uncheck “beta” for the search model and check “blip” instead. Run the search, and it will place the blip component in the context of the already placed beta-lactamase component. This could go wrong if the user is obsessively tidy and deletes the definition for the “beta” ensemble between the first and second jobs, because the partial solution information specifies how to place a defined ensemble (which therefore still has to be defined), but it does not store the placed ensemble.
2. The harder way, which is probably what you were trying to do. After placing the first component, define a new ensemble, giving the PDB file from the phaser subdirectory created in the first search (I called this ensemble “beta_placed”). For this one, check the box labelled “Ensemble is fixed partial solution”. Again, in the “Search procedure” pane, uncheck “beta” and check “blip”, then run the search. Note that you’re not specifying any search for the already placed component. This way of doing things was really only created so people could come in halfway through a structure solution with another molecular replacement program, not as the way you would choose to do it with Phaser.
Actually, the very easiest way, which I hope most users do by default, is to decide at the beginning what you are hoping to find in the structure solution and specify all the copies of all the components you’re looking for in one job. That approach gives Phaser the most flexibility to use an adaptive search strategy. So, in the tutorial, users are instructed to set up two searches in the one job, searching for both “beta” and “blip”.
Let me know if that doesn’t clarify things.
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 16 Jan 2015, at 18:56, Muhammed bashir Khan <muhammad.bashir.khan at UNIVIE.AC.AT> wrote:
> Hi There;
> I want to solve the structure with molecular replacement using phaser in
> phenix GUI. When I get solution from the one, how I can use as it as
> already solution using phenix in the next run. I use the "ensamble is
> fixed partial solution" but seems its not working. Any suggestion will be
> highly appreciated. Thanks
> Muhammad Bashir Khan
> Department for Structural and Computational Biology
> Max F. Perutz Laboratories
> University of Vienna
> Campus Vienna Biocenter 5
> A-1030 Vienna
> Phone: +43(1)427752224
> Fax: +43(1)42779522
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> phenixbb at phenix-online.org
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