[phenixbb] phaser for long thin molecule

Randy Read rjr27 at cam.ac.uk
Fri Feb 8 09:32:41 PST 2013

Dear Ursula,

If you click on the button "Other settings" at the end of the Phaser mode line in the Phaser-MR GUI, then select Developer for User level, you should get access to every parameter that would be available through the command line.  At the bottom of the page that comes up, there's a line labelled "Fix the radius for decomposition of the Patterson", where you can enter the desired Patterson cutoff.

We've hidden this because, in the tests we've done so far with elongated models (e.g. single helices) it doesn't seem to be necessary to play with it.  As long as the fast rotation function generates the correct orientation in the list, the likelihood rescoring should give it the proper score.  The likelihood score is, essentially, a direct rotation function where there's no Patterson decomposition, so it doesn't matter what the shape of the molecule is.

However, if you find that setting the Patterson radius explicitly makes a difference in a real problem, then we'd be very interested in hearing about it!

Best wishes,

Randy Read

On 7 Feb 2013, at 20:42, Ursula Schulze-Gahmen <uschulze-gahmen at lbl.gov> wrote:

> I am doing molecular replacment for a very elongated molecule in phaser. I would like to try different values for the maximum patterson cutoff but I am not sure which parameter I need to change in the phenix version of phaser. Does somebody have experience with this?
> Thanks
> Ursula
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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