Re: [ccp4bb] reifine metal with phenix

[Pavel Afonine]

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] reifine metal with phenix

[Lisa Wang]

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

Re: [ccp4bb] reifine metal with phenix

[Joern Krausze]

Dear Lisa,

you can specify custom bond and angle restraints by using the option 
refinement.geometry_restraints.edits. Best is to save them to a file (e.g. 
restraints_edits.params) and use this as input for your next 
phenix.refine run. Assuming the ideal distance for your Mg is 2.1A and the 
amino acid is asp113 of chain A, the according file entry could look like 
this:

refinement.geometry_restraints.edits {
  bond {
action = *add
atom_selection_1 = name MG01 and chain G and resname MG and resseq 1
atom_selection_2 = name OD2 and chain A and resname ASP and resseq 113
distance_ideal = 2.1000
sigma = 0.01
  }

You can check the phenix hompage for detailed documentation:

http://phenix-online.org/documentation/refinement.htm

Yours,

Joern


**
Address:
Joern Krausze
University of Leipzig
Centre for Biotechnology and Biomedicine
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04103 Leipzig
Germany

eMail:  krau...@bbz.uni-leipzig.de
Phone:  +49 (0)341 9731312
Fax:+49 (0)341 9731319
**

On Mon, 16 Feb 2009, 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