Dear Rex,
Here (
http://www.phenix-online.org/documentation/reference/refinement.html#refinem...)
is some documentation for the command line version.
Basically
1.
One rigid body group per chain (default behavior):
% phenix.refine data.hkl model.pdb strategy=rigid_body
2.
Multiple groups (requires a basic knowledge of the PHENIX atom selection
language, see below):
% phenix.refine data.hkl model.pdb strategy=rigid_body \
sites.rigid_body="chain A" sites.rigid_body="chain B"
This will refine the chain A and chain B as two rigid bodies. The rest
of the model will be kept fixed.
3.
If there are many rigid groups to define, typing them in the command
line may be a tedious exercise. In this case a better alternative is to
create a parameter file rigid_body_selections containing the following
lines:
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
Files like this can be created, for example, by copy-and-paste from the
complete list of parameters (phenix.refine --show-defaults=all).
And here (
http://www.phenix-online.org/documentation/reference/refine_gui.html#refinem...)
is some documentation for the GUI.
So "Modify selections for" (choose Rigid body from the dropdown menu) will
let you define the selections, either with text (e.g. "chain A and resseq
1:100"), or by using the "View/Pick" GUI, where you can select atoms.
Hope this helps!
Best regards,
Folmer
2015-11-11 12:38 GMT+01:00 Rex Palmer
We have 1.5A resolution data for a heterodimeric protein with linked A and B chains. Phenix MR has produced a promising solution. We would now like to perform an initial refinement using Phenix with the A chain and B chain individually treated as rigid bodies. Is this possible with Phenix and if so how?
Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4614-3954-7
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