Re: [ccp4bb] reifine metal with phenix

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

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Subject: expression of single chain variable fragment
From: Matt Colins matt {- dot -} colins2009 {- at -} YAHOO {- dot -} COM
Date: 2009-02-17

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Subject: Re: expression of single chain variable fragment
From: Karl Schmitz karl {- dot -} schmitz {- at -} GMAIL {- dot -} COM
Date: 2009-02-17

Subject: Re: reifine metal with phenix
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-02-17

Hi Lisa,

in addition to what Joern suggested, there are two other options:

1) You can run "phenix.metal_coordination" that will create additional
restraints for Mg atoms:

phenix.metal_coordination model.pdb

2) Not the best ways of doing this, but just to mention so you have a
complete list of options. After you have added Mg atoms and optimized
them in electron density, you can continue refining your structure with
phenix.refine while keeping the coordinates of Mg atoms fixed. You can
do this, for example, as following:

phenix.refine model.pdb data.hkl refine.sites.individual="not element Mg"

Pavel.

On 2/16/2009 11:39 AM, Lisa Wang wrote:
> Hi all,
> The resolution of my structure is 3.1A. There are three Mg binds in
> this structure. I try to refine it with phenix. There are cleare
> extrea density before I add Mg atoms. But when I put Mg in the
> central of density with good coordination and try to refine it by
> phenix, those Mg move away.Does phenix need addiational paramters file
> to refine Mg and keedp it 2.1A 2.1A from it coordinated atom?
> Thanks.
> Lisa

CCP4bb navigation

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

Previous message:
Subject: expression of single chain variable fragment
From: Matt Colins matt {- dot -} colins2009 {- at -} YAHOO {- dot -} COM
Date: 2009-02-17

Next message:
Subject: Re: expression of single chain variable fragment
From: Karl Schmitz karl {- dot -} schmitz {- at -} GMAIL {- dot -} COM
Date: 2009-02-17