[phenixbb] Molecular replacement with fixed solution

[Muhammed bashir Khan]

Thanks Randy for your detail reply. Its worked out..


On Fri, January 16, 2015 21:06, Randy Read wrote:
> Hi,
>
> 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 Read
>
> -----
> 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
>>
>> Regards
>>
>>
>> --
>> Muhammad Bashir Khan
>> **************************************************
>> Department for Structural and Computational Biology
>> Max F. Perutz Laboratories
>> University of Vienna
>> Campus Vienna Biocenter 5
>> A-1030 Vienna
>> Austria
>>
>> Austria
>>
>> Phone: +43(1)427752224
>> Fax: +43(1)42779522
>>
>>
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>
>


-- 
Muhammad Bashir Khan
**************************************************
Department for Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

Austria

Phone: +43(1)427752224
Fax: +43(1)42779522