[phenixbb] Phaser searching with density: how do I place my model on the solution?

Randy Read rjr27 at cam.ac.uk
Sun Jul 31 04:44:03 PDT 2011

Hi Pietro,

Just back from a holiday where internet access was very patchy.

If you have an atomic model that fits into the density corresponding to the MTZ file you used for the density model, then applying the same rotation and translation should put that model into the corresponding density in the other crystal form.  Things can go wrong with the book-keeping if, when you cut out the density from the first crystal form, you changed the location of that density by, say, centering it on the origin.

For dmmulti, you want to define a mask for one crystal form (P43212 is probably easier in your case) and the NCS operator you want is the one that would fetch the density from the other crystal form.  So the rotation and translation that Phaser applied to the density (assuming you haven't changed the origin!) should be the operator you need for multi-crystal averaging.  This operator transforms points in the mask to get the points in the other map with which they should be averaged.

By the way, I've been meaning to revise the web page on using density as a model.  Tom Terwilliger has made a one-line procedure that replaces the whole horrible set of shell scripts documented on that page, so now all you need is phenix.cut_out_density.  More recently, Kevin Cowtan has done something similar to go in the CCP4 package, but I don't think his routine has been released yet.

Also, as an alternative to dmmulti, you can also use Tom's phenix.multi_crystal_average procedure.

Let me know if you still have any problems with any of this.

Best wishes,


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 29 Jul 2011, at 19:50, Pietro Roversi wrote:

> Dear all,
> I succeded in finding a molecular replacement
> solution searching with the density I have in P43212
> against a C2221 dataset, using the Phaser procedure documented in:
> http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model
> Question: what operators should I use for dmmulti now?
> Or put it another way, how do I put onto the C2221 placement
> my P43212 model?
> I tried using the Euler and xyz numbers fro0m the phaser sol file
> but they do not seem to produce a model that goes with the C2221 
> Phaser density.
> Any help is greatly appreciated
> Thanks
> Pietro 
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