[phenixbb] ENSEmble parameters when the model is an EM map

Randy Read rjr27 at cam.ac.uk
Thu Jul 23 08:51:53 PDT 2009

Dear Peter,

There's a new Phenix GUI for Phaser that's under development, and when  
that 's finished you'll be able to run all possible Phaser jobs from  
the GUI.  In the meantime, it's probably easiest to use command scripts.

A number of the practical issues of using EM maps are the same as  
using density cut out from an X-ray
electron density map, e.g. making sure the cell is big enough (so that  
the interpolation of the transform of the density works) and knowing  
where the centre of the object is.  These are discussed on our web  
page, at http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html 

Assuming that your large P1 cell is at least 2.5 times as big in all  
directions as the small cell, then your approach sounds reasonable.

For EM maps, there's an extra issue.  It seems that there is generally  
an uncertainty of several percent in the magnification factor, so you  
will want to adjust that up and down -- steps of 0.5% would probably  
be fine enough.  The easiest way to do this is to scale the cell  
dimensions in the MTZ file containing the structure factors derived  
from the EM map.  You could do that easily in sftools, and then run  
searches with all the scaled MTZ files.

Good luck!  I'd be interested in hearing how you get on, and don't  
hesitate to ask any further questions.

Best wishes,

Randy Read

On 23 Jul 2009, at 16:08, Peter Grey wrote:

> Dear benevolent experts,
> I am trying to use Phaser for molecular replacement with EM-map as a  
> model.
> The EM map, originally in a small P1 cell, was put in large P1 using  
> CCP4's MAPROT and a mask that was defined by a certain cut-off level.
> Could you please advise me how to derive the EXTEnt and CENTre  
> parameters needed for ENSEmble building ?
> Does the simple way of giving the size of the original P1 as the  
> EXTEnt and its centre as CENTre sound reasonable ?
> I would be grateful for any advice and comments,
> Peter.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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- 

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