[phenixbb] Running Phaser with a already placed solution from a previous job

Randy Read rjr27 at cam.ac.uk
Thu Oct 5 05:37:18 PDT 2017

Dear Vincent,

What is stored in the database for the partial solution is the name of the ensemble(s) already placed, and the manipulations applied to them (rotation, translation, potentially B-factor).  However, the coordinates are not stored, and what is expected in a subsequent search is that you will provide the same ensemble definition(s) for the component(s) already placed.

Defining what has been placed already as a new ensemble and calling that a fixed partial solution is an alternative (but, in my opinion somewhat less convenient) way of doing the same thing, but then you shouldn't select the option to use a partial solution from a previous job.

I hope that helps!

Randy Read

> On 5 Oct 2017, at 12:55, vincent Chaptal <vincent.chaptal at ibcp.fr> wrote:
> Dear everyone, 
> this sounds trivial but I somehow can't make it work so I would appreciate any pointer. 
> I have placed a component using phaser and would like to expand my search using this already placed component as partial solution.
> I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there).
> I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for.  I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". 
> Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" 
> but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. 
> Any help would be greatly appreciated. 
> Thanks
> Vincent
> I'm using phenix 1.12-2829.
> -- 
> Vincent Chaptal, PhD
> Institut de Biologie et Chimie des Protéines
> Drug Resistance and Membrane Proteins Laboratory
> 7 passage du Vercors 
> 69007 LYON
> +33 4 37 65 29 01
> http://www.ibcp.fr <http://www.ibcp.fr/>
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Randy J. Read
Department of Haematology, University of Cambridge
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