Hi,
Looks as if you want to do rigid body refinement 'a la CORELS'.
What about rigid body refinement in Phenix? From the Phenix manual:
"
If one have many rigid groups, a lot of typing in the command line may not be
convenient, so creating a parameter file rigid_body_selections, containing the
following lines, may be a good idea:
refinement.refine.sites {
rigid_body = chain A
rigid_body = chain B
}
The command line will then be:
% phenix.refine data.hkl model.pdb strategy=rigid_body
rigid_body_selections.params
"
You would have to create this file once and only once... Easily done using vi
for example if you know that editor.
You will have to check in the Phenix manual how to specify single residues...
instead of having chains. I had a quick look and could not find this
information. Or you could also ask Pavel Afonine (who is currently in
Strasbourg). Or perhaps someone else on the bb will know.
Fred.
> Message du 01/12/09 21:30
> De : "Jason Porta"
> A : CCP4BB@JISCMAIL.AC.UK
> Copie à :
> Objet : [ccp4bb] Refining residues as rigid bodies
>
>
> Hi everybody,
>
> I am currently refining a 3 ang structure and would like to do rigid body
> refinement treating each residue as a separate rigid body. I have looked
> through several refinement packages, but do not see a way to do this without
> having to type each residue in manually (there are 512 residues total).
> Preferably, I would carry out the refinement in Refmac5, but any advice
> pertaining to any program would be greatly appreciated.
>
> Thanks in advance for any help.
>
> Jason Porta
> Graduate Student
> Eppley Structural Biology Facility
> Dept. Biochemistry & Molecular Biology
> University of Nebraska Medical Center
> Omaha, NE 68198
> (402) 559-5533
>
>
