Dear Scientific community, Paul and Bernhard,
With the help of ccp4 people I created link records to build a large
ligand from smaller monomers.
One link is FTT-MYR. Cif file attached.
I also put this record in the pdb file
LINKR O3 FTT E 2 C1 MYR E 3
FTT-MYR
and did
Import CIF dictionary in coot with the FTT-MYR.cif
However doing sphere_refine the restraints seem to be not applied,
because the residues are repelled.
What am I doing wrong?
Why do I have to import the cif file via File --> Import CIF dictionary
in coot and can't just past the cif files in
C:\CCP4-7\7.1\Lib\data\monomers\list ?
Many thanks and best regards, Georg.
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#ACEDRG_VERSION 222
#ACEDRG_DB_VERSION 11
#RDKit_VERSION 2017.03.2
#REFMAC_VERSION 5.8.0267
#
data_mod_list
loop_
_chem_mod.id
_chem_mod.name
_chem_mod.comp_id
_chem_mod.group_id
FTTm1 "3-HYDROXY-TETRADECANOIC ACID" FTT .
MYRm1 "MYRISTIC ACID" MYR .
data_link_list
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
FTT-MYR FTT FTTm1 non-polymer MYR MYRm1
non-polymer FTT-MYR
data_mod_FTTm1
loop_
_chem_mod_atom.mod_id
_chem_mod_atom.function
_chem_mod_atom.atom_id
_chem_mod_atom.new_atom_id
_chem_mod_atom.new_type_symbol
_chem_mod_atom.new_type_energy
_chem_mod_atom.new_charge
FTTm1 delete HO3 . H H 0
FTTm1 change O3 . O O2 0
loop_
_chem_mod_bond.mod_id
_chem_mod_bond.function
_chem_mod_bond.atom_id_1
_chem_mod_bond.atom_id_2
_chem_mod_bond.new_type
_chem_mod_bond.new_value_dist
_chem_mod_bond.new_value_dist_esd
FTTm1 delete O3 HO3 single .
.
FTTm1 change C3 O3 single 1.462
0.0100
loop_
_chem_mod_angle.mod_id
_chem_mod_angle.function
_chem_mod_angle.atom_id_1
_chem_mod_angle.atom_id_2
_chem_mod_angle.atom_id_3
_chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
FTTm1 delete C3 O3 HO3 . .
loop_
_chem_mod_tor.mod_id
_chem_mod_tor.function
_chem_mod_tor.atom_id_1
_chem_mod_tor.atom_id_2
_chem_mod_tor.atom_id_3
_chem_mod_tor.atom_id_4
_chem_mod_tor.new_value_angle
_chem_mod_tor.new_value_angle_esd
FTTm1 delete C2 C3 O3 HO3 .
.
data_mod_MYRm1
loop_
_chem_mod_atom.mod_id
_chem_mod_atom.function
_chem_mod_atom.atom_id
_chem_mod_atom.new_atom_id
_chem_mod_atom.new_type_symbol
_chem_mod_atom.new_type_energy
_chem_mod_atom.new_charge
MYRm1 delete O2 . O OC -1
loop_
_chem_mod_bond.mod_id
_chem_mod_bond.function
_chem_mod_bond.atom_id_1
_chem_mod_bond.atom_id_2
_chem_mod_bond.new_type
_chem_mod_bond.new_value_dist
_chem_mod_bond.new_value_dist_esd
MYRm1 delete C1 O2 single .
.
MYRm1 change C1 O1 double 1.203
0.0150
MYRm1 change C1 C2 single 1.503
0.0174
loop_
_chem_mod_angle.mod_id
_chem_mod_angle.function
_chem_mod_angle.atom_id_1
_chem_mod_angle.atom_id_2
_chem_mod_angle.atom_id_3
_chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
MYRm1 delete O1 C1 O2 . .
MYRm1 delete O2 C1 C2 . .
MYRm1 change O1 C1 C2 124.714 2.71
loop_
_chem_mod_plane.mod_id
_chem_mod_plane.function
_chem_mod_plane.plane_id
_chem_mod_plane.atom_id
_chem_mod_plane.dist_esd
MYRm1 delete plan-1 C1 0.020
MYRm1 delete plan-1 C2 0.020
MYRm1 delete plan-1 O1 0.020
MYRm1 delete plan-1 O2 0.020
data_link_FTT-MYR
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
FTT-MYR 1 O3 2 C1 SINGLE 1.342 0.0131
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
FTT-MYR 1 C3 1 O3 2 C1 117.944
1.50
FTT-MYR 2 O1 2 C1 1 O3 122.278
2.43
FTT-MYR 2 C2 2 C1 1 O3 113.008
3.00
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
FTT-MYR sp2_sp2_1 2 O1 2 C1 1 O3
1 C3 180.000 10.00 2
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
FTT-MYR plan-2 2 C1 0.020
FTT-MYR plan-2 2 C2 0.020
FTT-MYR plan-2 1 O3 0.020
FTT-MYR plan-2 2 O1 0.020
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