[phenixbb] phenix.refine special positions

Pavel Afonine PAfonine at lbl.gov
Thu Aug 13 22:29:42 PDT 2009

Hi Simon,

yes, as Folmer suggested, you can use atom selections to define the 
rigid body groups such that they do not include the atoms at special 
positions. For example:

phenix.refine model.pdb data.mtz rigid.params

where the file rigid.params contains lines like these:

refinement.refine {
    sites {
      rigid_body = chain A and not (resseq 123 and (name XX or name ZZ))
      rigid_body = chain B and not (resseq 456 and element Fe)
      rigid_body = chain Y or chain Z

However, since the large-scale movements of the rigid groups are 
expected during rigid body refinement, it may happen that they will move 
away from fixed atoms (and therefore breaking the bonds), but may be it 
is ok at the level of accuracy at rigid body refinement stage.


On 8/13/09 7:14 AM, Simon Kolstoe wrote:
> Dear Pavel et al.
> Is there any way of defining a residue for rigid body refinement if a  
> couple of the atoms are sitting on a symmetry axis? i.e. can I define  
> the rigid body to be chain L but not the atoms that are giving the  
> problems? I keep on getting the error:
> ================== Extract refinement strategy and selections  
> =================
> Some atoms selected for rigid body refinement are in special positions  
> (listed
>   below). Please remove these atoms from the rigid body selection and  
> run
>   refinement again.
>      "ATOM      4  C4  A12 L   2 .*.     C  "
> Sorry:
> Atoms at special positions are within rigid groups.
> Thanks,
> Simon
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