Hi, i am refining a perdeuterated neutron structure and have noticed a lot of positive density aside the D atoms on aliphatic and aromatic side chains. just in the alignment of C-D bonds (C-D then +), suggesting that phenix.refine constraints these bond lengths too short in my case. i tried automatic weights for geometry refinement and unrestrained specific C-D refinement but it is not satisfactory. then i found the following funny distances (angströms) in the pdb database neutron structures: 3KYX: program: Phenix.refine D-prot Distances: C-D aromatics = 0.93-0.94 C-D aliph. = 0.98 1CQ2 Program : xplor3.1 D-protein (despite the atoms being labelled as H according to abstract) Distances: C-D aromatics = 1.06-1.08 C-D aliph. = 1.08 4FC1 H-protein Distances: program: Phenix.refine C-H aromatics = 0.93 C-H aliph. = 0.97 1VCX H-protein program: CNS Distances: C-H aromatics = 1.06-1.10 C-H aliph. = 1.09 those neutron C-D/C-H bond lengths in pdb seem pretty much inconsistentto me. So it seems that phenix.refine uses C-D/ C-H bonds restrains that are different to other programs to below 1.0 Ang. ( ca. 0.10 A differences) how can i change the restraints to make it all longer bond lengths for C-D only? with a .cif file? i saw that phenix uses the CCP4 monomer library but the one in : /usr/local/phenix-.../chem_data/mon_lib/list only seem to be applying modifications. any clue on how to specifically modify the restraints parameters on C-D bonds would be very appreciated. Thanks, Maxime