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 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 _______________________________________________ phenixbb mailing list [email protected] http://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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk