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Re: [ccp4bb] How can I refine Mg2+ with REFMAC?5.2
 

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CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007
Previous message:
Subject: How can I refine Mg2+ with REFMAC?5.2
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-09 		Next message:
Subject: Re: How can I refine Mg2+ with REFMAC?5.2
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-09


Subject: Re: How can I refine Mg2+ with REFMAC?5.2
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-09
You just put on the element column of pdb MG+2 instead of MG (you can
do it on the atom name column also but if you have the element column
then that will
be used to interpret element name with its oxidation state)

Garib

On 9 May 2007, at 13:41, Dirk Kostrewa wrote:

> Dear CCP4ers,
>
> I try to refine a protein structure with a Mg2+ bound. In the
> REFMAC5.2 dictionary, I only found a neutral Mg and several
> (strange) entries of different water-coordinated Mg2+ with some
> predefined water naming that I don't want to use. I would just like
> to refine a Mg2+ with whatever oxygen ligands around. In my
> coordinate file, the residue and atom names are "MG ", and REFMAC
> really takes this as a neutral Mg, because when I add the
> formfactors Sum_i(a_i)+c, I get 12 electrons, which is not what I
> want. How can I refine Mg2+ (or any other ion) with REFMAC?
>
> Best regards,
>
> Dirk.
>
> --
>
> ****************************************
> Dirk Kostrewa
> Paul Scherrer Institut
> Biomolecular Research, OFLC/110
> CH-5232 Villigen PSI, Switzerland
> Phone: +41-56-310-4722
> Fax: +41-56-310-5288
> E-mail: dirk.kostrewa@psi.ch
> http://sb.web.psi.ch
> ****************************************
>

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CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007
Previous message:
Subject: How can I refine Mg2+ with REFMAC?5.2
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-09 		Next message:
Subject: Re: How can I refine Mg2+ with REFMAC?5.2
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-09


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