Re: [ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

[Kay Diederichs]

Ian Tickle schrieb:

-----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



Pietro Roversi schrieb:

Subject: Re: [ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

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,



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

I believe that the "direct rotation function" in CNS should circumvent the problem entirely - there are no cutoffs AFAIK.

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


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Ian,

I agree with your description, but not quite with your conclusion. In the original poster's problem one of the cell axes is so short that at most a < 20 Angstrom Patterson outer radius can be used in a Patterson-based rotation function. This will inevitably lead to loss of many interesting Patterson vectors, and probably a low signal-to-noise ratio. So in this particular situation the "direct rotation function" (http://dx.doi.org/10.1107/S0907444995001284) might have a distinct advantage compared to Patterson methods, which is why I suggested it. Whether this is enough to solve Pietro's problem remains to be seen. For me it's a case of "know your options, and try them".

best,

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

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