From 077bd524c2340dc180712d05d91823b99a61f4bf Mon Sep 17 00:00:00 2001 From: keitaroyam Date: Thu, 23 Jan 2020 13:38:15 +0900 Subject: [PATCH] Correct base pair definitions in bondlength_defaults.py Only single hydrogen bonds were defined for symmetric homo purine/pyrimidine pairs. --- mmtbx/monomer_library/bondlength_defaults.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/mmtbx/monomer_library/bondlength_defaults.py b/mmtbx/monomer_library/bondlength_defaults.py index c81d7fbc21..ceda209269 100644 --- a/mmtbx/monomer_library/bondlength_defaults.py +++ b/mmtbx/monomer_library/bondlength_defaults.py @@ -3314,10 +3314,10 @@ def generic_metal_run(metal_element, # # Canonical Watson-Crick base pairings #homo purine -1:[('A','A'), ("N6","N1",2.99,0.14,0.07) ], -2:[('A','A'), ("N6","N7",2.95,0.20,0.06) ], -3:[('G','G'), ("N1","O6",2.86,0.12,0.01) ], -4:[('G','G'), ("N2","N3",3.10,0.22,0.13) ], +1:[('A','A'), ("N6","N1",2.99,0.14,0.07), ("N1","N6",2.99,0.14,0.07) ], +2:[('A','A'), ("N6","N7",2.95,0.20,0.06), ("N7","N6",2.95,0.20,0.06) ], +3:[('G','G'), ("N1","O6",2.86,0.12,0.01), ("O6","N1",2.86,0.12,0.01) ], +4:[('G','G'), ("N2","N3",3.10,0.22,0.13), ("N3","N2",3.10,0.22,0.13) ], 5:[('A','A'), ("N6","N1",2.93,0.18,0. ), ("N7","N6",3.07,0.17,0. ) ], 6:[('G','G'), ("O6","N1",2.88,0.16,0. ), ("N7","N2",2.91,0.15,0. ) ], 7:[('G','G'), ("N7","N1",2.93,0.17,0. ), ("O6","N2",2.76,0.24,0. ) ], @@ -3325,10 +3325,10 @@ def generic_metal_run(metal_element, 9:[('A','G'), ("N6","O6",2.70,0.08,0. ), ("N7","N1",3.08,0.08,0. ) ], 10:[('A','G'), ("N6","N3",3.15,0.11,0. ), ("N1","N2",3.02,0.19,0. ) ], 11:[('A','G'), ("N6","N3",3.23,0.15,0. ), ("N7","N2",3.00,0.16,0. ) ], -12:[('U','U'), ("N3","O4",2.86,0.05,0.12) ], -13:[('U','U'), ("O2","N3",2.74,0.05,0.03) ], -14:[('C','C'), ("N3","N4",2.72,0.05,0.6 ) ], -15:[('C','C'), ("O2","N4",2.83,0.01,0. ) ], +12:[('U','U'), ("N3","O4",2.86,0.05,0.12), ("O4","N3",2.86,0.05,0.12) ], +13:[('U','U'), ("O2","N3",2.74,0.05,0.03), ("N3","O2",2.74,0.05,0.03) ], +14:[('C','C'), ("N3","N4",2.72,0.05,0.6 ), ("N4","N3",2.72,0.05,0.6 ) ], +15:[('C','C'), ("O2","N4",2.83,0.01,0. ), ("N4","O2",2.83,0.01,0. ) ], 17:[('C','U'), ("N3","N3",2.98,0.05,0. ), ("N4","O2",2.91,0.07,0. ) ], 18:[('C','U'), ("N4","O4",3.19,0.07,0. ), ("N3","N3",3.16,0.06,0. ) ], 19:[('C','G'), ("N4","O6",2.96,0.17,0. ), ("N3","N1",2.89,0.11,0. ), ("O2","N2",2.77,0.15, 0.)],