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Re: [ccp4bb] difference density ripples around Hg atoms
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: how to bring back the missing density for half of the structure
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: "David J {- dot -} Schuller" djs63 {- at -} CORNELL {- dot -} EDU
Date: 2007-08-01


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

Well - there will be a ripple, but is it there in the difference map as
well? that is meantto be less affected.

REFMAC5 claims to be able to refine some atoms anisotropically and
that would be a good place to start

Maybe you will need to read the documentation! There is some way of
requesting the option..
The PDB doesinclude structures with some anisotropic/ some isotropic B
values., usually waters
Eleanor


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? Never saw this in a PDB. Suggestions are very welcome.
>
> Greetings
>
> Klemens Wild
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: how to bring back the missing density for half of the structure
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: "David J {- dot -} Schuller" djs63 {- at -} CORNELL {- dot -} EDU
Date: 2007-08-01
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