On Wed, Jan 25, 2012 at 2:31 AM, Christian Roth
I modified the .link.edits file accordingly for the sugars like this ---------- refinement.geometry_restraints.edits { apply_cif_link { data_link = ALPHA1-4 atom_selection_1 = name O4 and chain B and resname GLC and resseq 1 atom_selection_2 = name C1 and chain B and resname GLC and resseq 2
} } ------------ And applied a trans link for the peptide bond
Okay, looking at this more closely, I think the parameter scope is wrong - it should be: refinement.pdb_interpretation { apply_cif_link { ... } } This would explain why it isn't working - the parameters are being discarded because they're not recognized. Details here: http://www.phenix-online.org/version_docs/dev-968/refinement.htm#anch88
Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening?
Just to double-check, could you please send me (off-list) the .eff file for the run? I suspect I know what is going on - probably an inconsistency in GUI behavior, which I recently changed because the old way was just broken. -Nat