Hello Nat,
Thank you so much for your suggestion. I did run phenix refinement in nightly build phenix version with "
intra_chain = True " command. This time refinement worked but again in out put pdb no disulfide bond is estabilished between cys and BME. I provided .pdb, .mtz and .cif files as input. Well can you please suggest me how i can provide both BME and Cys-BME
(SS bond) restrains in .cif file? if that happens then i feel refinement should work. I am attaching my .cis file below please have a look and tell me if anything wrong with this?
BME.cif
# electronic Ligand Builder and Optimisation Workbench (eLBOW)
# - a module of PHENIX version 1.8.1-1168 (Mon Sep 28 16:48:00 2012)
# - file written: Sat Jan 26 17:25:31 2013
#
# Input file: Ref226_154-331-VLD2-BME.pdb
# Random seed: 3628800
# Residue: BME
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
BME BME 'Unknown ' ligand 10 4 .
#
data_comp_BME
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
BME S S S2 . -19.3229 -20.3986 17.2400
BME H5 H H . -18.1988 -20.0550 17.0819
BME C1 C CH2 . -19.3558 -21.8852 18.1928
BME H3 H HCH2 . -18.8480 -21.7572 19.0093
BME H4 H HCH2 . -18.9637 -22.6079 17.6781
BME C C CH2 . -20.7668 -22.2261 18.5333
BME H1 H HCH2 . -21.1200 -21.5643 19.1482
BME H2 H HCH2 . -20.7965 -23.1021 18.9488
BME O O OH1 . -21.5280 -22.2370 17.3822
BME H H HOH1 . -22.3435 -22.5247 17.5704
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
BME S H5 single 1.186 0.020
BME S C1 single 1.766 0.020
BME C1 H3 single 0.970 0.020
BME C1 H4 single 0.970 0.020
BME C1 C single 1.491 0.020
BME C H1 single 0.970 0.020
BME C H2 single 0.970 0.020
BME C O single 1.380 0.020
BME O H single 0.885 0.020
#
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
BME C1 S H5 109.48 3.000
BME C C1 H4 109.47 3.000
BME C C1 H3 109.47 3.000
BME H4 C1 H3 109.47 3.000
BME C C1 S 109.47 3.000
BME H4 C1 S 109.47 3.000
BME H3 C1 S 109.47 3.000
BME O C H2 109.47 3.000
BME O C H1 109.47 3.000
BME H2 C H1 109.47 3.000
BME O C C1 109.47 3.000
BME H2 C C1 109.47 3.000
BME H1 C C1 109.47 3.000
BME H O C 109.48 3.000
#
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
BME Var_01 O C C1 S 52.25 30.0 3
BME Var_02 H1 C C1 S -67.75 30.0 3
BME Var_03 H2 C C1 S 172.25 30.0 3
BME Var_04 O C C1 H3 172.25 30.0 3
BME Var_05 O C C1 H4 -67.75 30.0 3
#
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
CYS-BME CYS DEL-HG . BME DEL-HS . SS-bridge
#
Thanks