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. Pavel. 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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb