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

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007

Previous message:
Subject: references for TLS refinement
From: "Nalam, Madhavi" Madhavi {- dot -} Nalam {- at -} UMASSMED {- dot -} EDU
Date: 2007-05-09

Next message:
Subject: Re: references for TLS refinement
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: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-09

Many thanks!

Dirk.

Garib Murshudov wrote:
> 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
>> ****************************************
>>

--

****************************************
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
****************************************

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 09 May 2007

Previous message:
Subject: references for TLS refinement
From: "Nalam, Madhavi" Madhavi {- dot -} Nalam {- at -} UMASSMED {- dot -} EDU
Date: 2007-05-09

Next message:
Subject: Re: references for TLS refinement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-09