Hi Francois, If you're going to use the ccp4 almn program for calculating the your rotation function (I understand it's a cross-rotation function between an experimental and model-based Patterson) the parameters SPHMAX and SPHMIN (under the keyword SELF, but they hold for the cross RF too) will do the job for you, i.e. they'll define the inner & outer limits of the radii for both of your Patterson. It's best to experiment with those values until you get some consistent solutions, this has been the experience over the years, I think. If you check some summaries from past ccp4 meetings you'll find some on rotation function searches, I'm sure.
http://www.ccp4.ac.uk/dist/html/almn.html#self http://www.ccp4.ac.uk/dist/html/almn.html#self http://www.ccp4.ac.uk/dist/html/almn.html#self Good luck, Boaz ----- Original Message ----- From: Francois Berenger <beren...@riken.jp> Date: Monday, April 5, 2010 14:11 Subject: Re: [ccp4bb] question about rotation search To: CCP4BB@JISCMAIL.AC.UK > By the way, > > Is there a tool in ccp4 to remove the origin peak in a Patterson map? > > If I do so for both the experimental and the calculated > Patterson maps, > should I only worry about the maximum** radius after? > I mean, could I correlate both maps from 0 to maximum** after origin > peak removal? > > Thanks, > Francois. > > Francois Berenger wrote: > > Hello, > > > > While doing a rotation search with Patterson maps, > > what is the standard way to find the minimum* and maximum** > > radius to be used while correlating maps? > > > > * to avoid the origin peak > > ** to avoid inter molecular-vectors > > > > Is there a CCP4 tool to give me this if I provide it with > > a model? > > > > If you know a good paper describing a smart way to find these > > 2 limits automatically, I would be happy to know about it. > > > > Thank you, > > Francois. > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
