Re: [ccp4bb] Highest shell standards

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CCP4bb <-- 2007 <-- March 2007 <-- 26 March 2007

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Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-26

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From: artem {- at -} XTALS {- dot -} ORG artem {- at -} XTALS {- dot -} ORG
Date: 2007-03-26

Subject: Re: Highest shell standards
From: "Fred {- dot -} Vellieux" vellieux {- at -} IBS {- dot -} FR
Date: 2007-03-26

On Fri, 23 Mar 2007, Edward Berry wrote:

> I believe fft does not by default do this- only if you use the "fillin"
> keyword? One place where it might be important is in density
> modification/ molecular averaging. Molecular averaging can be seen
> as a numerical solution of the MR equations, finding a density map
> which (A) obeys the NCS/intercrystal symmetry and (B) yields the
> observed F's upon Fourier transformation. Now if on each cycle
> you set the missing F's to zero, you are requiring it to have
> as part of (B) zero amplitude for the missing reflections, which is
> more restrictive and incorrect. If instead you allow the missing F's
> to "float", calculating them on each cycle from the previous map
> using the fillin option, someone has shown (don't have the
> reference handy at the moment) that the F's tend toward the true F's
> (in the case that they weren't really missing but omitted as part
> of the test).
>
> Ed

You have phase scatter plots in Acta Cryst. D51, 575-589 (1995) that show
just that: the map inversion phases from NCS averaging tend toward the
true phases. Since F's are phased quantities and since phases are more
important than amplitudes, non random amplitudes plus non random phases
(both from map inversion of averaged maps) lead to better electron density
maps.

Fred.

--

Fred. Vellieux, esq.

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CCP4bb <-- 2007 <-- March 2007 <-- 26 March 2007

Previous message:
Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-26

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Subject: Re: Nature policy update regarding source code
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Date: 2007-03-26