[phenixbb] Phaser with fixed solution

R.D. Oeffner rdo20 at cam.ac.uk
Wed Jan 30 09:49:32 PST 2013

Hi Ursula,

If I understand you correctly you have two fragments and want to place them one by one with Phaser.

If you use Phaser-MR in the automated molecular replacement mode then you shouldn't have to specify the search order of components for Phaser. Nor would you have to specify which placed fragment should be fixed and used in subsequent MR searches for the next fragment. Phaser will take care of this by itself. 

Simply specify the other search fragments as another ensemble by clicking on the "Add Ensemble" button on the "Ensembles" tabbed sheet. Then click on the "Search Procedure" tabbed sheet and add that ensemble to the MR search. You'll want to let Phaser determine the search order of your fragments as it does this better than humans. So don't alter the defaults.

As for the packing test more info can be found on http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#PACK
In your case I should probably try and play with the cutoff value for a start.

Hope this helps,


On Jan 30 2013, Ursula Schulze-Gahmen wrote:

>I am trying to solve a structure by molecular replacement  in phaser using
>2 model fragments. I think I may have placed the 1st fragment correctly. I
>don't quite understand how to best proceed with a fixed ensemble searching
>for the second fragment in phaser-MR. If I select "use partial solution
>from previous job", do I still need to read in the coordinates of that
>previous solution for one ensemble? And If I do, should I read in the
>starting coordinates or the placed output from this 1st molecular
>The second question is about how to relax the restraints fr the packing. In
>the "other settings" sub window is a section for packing. Could someone
>explain to me what the different options in this packing section mean?
>Which of them should I change to allow for more close contacts?

Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162

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