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

[Peter Grey]

Dear Prof. Read,

Thank you for the swift and kind reply. I would like to mention than there
are several  difficult issues in using EM maps. For example it would be wise
to use a temperature factor to sharpen/blur the map so that the histogram
of  amplitudes vs. resolution would look similar to that of the measured
structure factors (better for MR). In addition one needs to determine
visually the cut-off level for the mask. Visual inspection is also required
to determine the magnification because many maps are deposited in the EMDB
with absolutely arbitrary magnification. EMDB is not run like PDB and
standartization is not really practiced (sadly) - All these parameters
should have been given by the microscopist.

I am familiar with the Phaser example you mentioned but there the problem of
finding the origin and extent is easy  because you start from a pdb file (to
obtain the mask). The approach I suggested is very primitive. Is there a
program that can determine more precisely the "box" that contains the
particle and its centre of  mass ? It should be easy becasue at this stage
you already have the mask (whose cut-off was determined by visual
inspection) that dictates what is "particle" and what is not in the map.

Peter.



On Thu, Jul 23, 2009 at 5:51 PM, Randy Read <rjr27 at cam.ac.uk> wrote:

> 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.
>
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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: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
>
>
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