Hi, while you can exclude any atoms from refinement, refinement { refine { sites { individual = not (chain Z and resseq 1:123) } } } that will refine coordinates of everything but atoms in "chain Z and resseq 1:123", I guess you can handle this situation more elegantly. Can you please send me PDB file or its portion containing relevant residues (before and after refinement, so I see how they pushed apart), and I might be able to suggest a better solution. Pavel On 5/22/14, 9:13 PM, Murpholino Peligro wrote:
Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups.
Can I tell phenix.refine not to move only those two residues?
It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 }
Thank you very much
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