Re: [ccp4bb] difference density ripples around Hg atoms

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: difference density ripples around Hg atoms
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-01

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Subject: Re: difference density ripples around Hg atoms
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-08-01

Subject: Re: difference density ripples around Hg atoms
From: "David J {- dot -} Schuller" djs63 {- at -} CORNELL {- dot -} EDU
Date: 2007-08-01

On Wed, 2007-08-01 at 09:35 +0200, Klemens Wild wrote:
> Dear friends of the Fourier transform,
>
> I am refining a structure with 2 adjacent Hg atoms bound to cysteines of
> different monomers in the crystal contacts, which means I need to refine
> them as well. While the structure nicely refines (2.2 A data), I do not
> get rid of negative density ripple layers next to them (-10 sigmas). My
> question: is this likely due to anistropy of the soft mercury atoms
> (anisotropic B refinement decreases the ripples) or is this likely a
> summation truncation effect prominent for heavy atoms? Can I just
> anistropically refine the mercuries while I keep the rest isotropic?

Yes, that sounds worth a try. At 2.2 A you probably don't have the
data/parameter ratio to justify anisotropic refinement for the whole
molecule, but since you know the mercury atoms are not being treated
adequately, adding an extra ~ 10 parameters to refine them as
anisotropic is worth a try. Don't expect it to completely eliminate the
ripples, but hopefully you can get some improvement on R/Rfree.

Cheers,

--
=======================================================================
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome guest - R.G. Ingersoll
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
djs63@cornell.edu

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: difference density ripples around Hg atoms
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-01

Next message:
Subject: Re: difference density ripples around Hg atoms
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-08-01