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

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CCP4bb <-- 2007 <-- December 2007 <-- 02 December 2007
Previous message:
Subject: Re: Rotation search using the Patterson in a non-spherical neighbourhood of the origin
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-12-02 		Next message:
Subject: Registration and Abstract submission for Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2007-12-02


Subject: Re: Rotation search using the Patterson in a non-spherical neighbourhood of the origin
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-12-02
Ian Tickle schrieb:
<... interesting information about AMORE deleted ...>
>
> Anyway this is all academic now, I always use Phaser which does all this properly (I have no experience using it for highly ellipsoidal models though).
>
> Cheers
>
> -- Ian

My understanding is that Phaser by default does the full-blown maximum
likelihood calculations (which are very slow) _only_ for the peaks identified in
a "fast rotation function" (a scaled and variance-weighted version of the
Patterson overlap function used in the traditional Crowther (1972) fast rotation
function). Therefore the same "radius cutoff caveats" apply to this calculation;
only if the correct peak is in the list that is scored with MLRF then it may be
identified as such.

It appears to me that you if you choose "brute rotation function" then the fast
rotation function will not be calculated by Phaser.

Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz


CCP4bb navigation

CCP4bb <-- 2007 <-- December 2007 <-- 02 December 2007
Previous message:
Subject: Re: Rotation search using the Patterson in a non-spherical neighbourhood of the origin
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-12-02 		Next message:
Subject: Registration and Abstract submission for Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2007-12-02


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