[phenixbb] Rigid body refinement

Folmer Fredslund folmerf at gmail.com
Wed Nov 11 23:56:59 PST 2015

Dear Rex,

Here (
is some documentation for the command line version.


   One rigid body group per chain (default behavior):

   % phenix.refine data.hkl model.pdb strategy=rigid_body


   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.

   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

   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 \

   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 (
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,


2015-11-11 12:38 GMT+01:00 Rex Palmer <rex.palmer at btinternet.com>:

> 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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Folmer Fredslund
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