<aa8297f160771e4da7fba29578ebaba2018ba...@nt-mail3.astex-technology.com>
<[email protected]>
<[email protected]>
From: "Ian Tickle" <[email protected]>
To: =?iso-8859-1?Q?Andreas_Förster?= <[email protected]>,
<[email protected]>
Cc: <[email protected]>
Return-Path: [email protected]
X-OriginalArrivalTime: 29 Jan 2009 16:27:43.0581 (UTC)
FILETIME=[831110D0:01C9822E]
Yes I agree with that!
-- Ian
> -----Original Message-----
> From: Andreas Förster [mailto:[email protected]]
> Sent: 29 January 2009 16:26
> To: [email protected]; Ian Tickle
> Cc: [email protected]
> Subject: Re: [ccp4bb] Small lines in diffraction pattern (more info)
>
> Ian and Herman,
>
> does one want to convolute the electron density at all? I
> was under the
> impression that current thinking favors convolution of the model
> instead, i.e. placing both the helices in both orientations
> at partial
> occupancy and letting the refinement program figure things out?
>
>
> Andreas
>
>
> [email protected] wrote:
> > Dear Ian and Margriet,
> >
> > You are right, the correction needs to be done on F, not on
> |F|^2. If I recall correctly (I did not do it myself), the
> assumption was that Fobs = 0.5*Fobs(A) + 0.5*Fobs(B), so
> Fcorrected(A) = 2*Fobs - Fcalc(B) where A and B are the two
> orientations. Since one does not have an observed phase, one
> would have to take calculated phases. I am unsure though, if
> that was done in practise and one did not just subtract the
> absolute values. Since the inhibitor is usually only a small
> part of the total scattering mass, the phases might not
> differ too much and therefore the error would not be too big.
> In case of superposition of base pairs, I guess that the
> differences in scattering between the different base-pairs is
> not too much, so one might also be able to get away with not
> using phases, but here you are the expert.
> >
> > Using this method, one could much better interpret the
> convoluted electron density, but one has to be very careful
> not introducing severe model bias. I would look in the
> literature in detail, what people from the HIV protease field
> had done to solve this problem.
> >
> > Cheers,
> > Herman
> >
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>
>
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