> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs > Sent: 02 December 2007 10:07 > To: [EMAIL PROTECTED] > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rotation search using the Patterson in > a non-spherical neighbourhood of the origin > > Pietro Roversi schrieb: > > Dear everyone, > > is any of the currently available > > molecular replacement programs capable of accepting a > > description of an ellipsoid (rather than the radius > of a sphere) > > to define the portion of the Patterson around the > origin to be > > used in a Molecular > > Replacement rotation search? Our search model is an > elongated > > object and we are searching in a cell with a=205 b=100 c=21 > > Angstrom ... ;-) > > > > Ciao > > > > Pietro > > Pietro, > > I believe that the "direct rotation function" in CNS should > circumvent the > problem entirely - there are no cutoffs AFAIK. > > sorry for answering late! > > HTH, > > Kay > -- > Kay Diederichs http://strucbio.biologie.uni-konstanz.de > email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 > Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz >
Unlike the Rossman & Blow, Crowther and related rotation functions, the "direct rotation function" doesn't use any kind of radius cutoff. However the problem then is obviously that a spherical or ellipsoidal radius cutoff, which serves to reduce the noise level by removing intermolecular vectors in the Patterson, may be essential to improve the discrimination of the correct solution relative to wrong ones in order for the correct solution to appear reasonably close to the top of the list. This has certainly been my experience. In the "direct rotation function" no attempt is made to remove these intermolecular vectors, either those between instances of the search model related by lattice translations, or those between symmetry/lattice-related instances of the target molecule. The direct RF is easier to compute because you only need to compute normalised SF's for the model, and you don't have to worry about the complexities of spherical harmonics & Bessel functions, but otherwise it's not clear to me what its advantage is. -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
