[phenixbb] Autobuild: problems with modified amino acids
Kendall Nettles
knettles at scripps.edu
Wed Jan 19 07:52:00 PST 2011
I'm running autobuild from a molecular replacement solution and having two problems:
1. methionines are converted to MSE
2. I'd like to include a .cif file for b-mercapto-ethanol adducted cysteines: CME. The .cif file is one that works for phenix.refine (listed below). I suspect I am not writing the .eff file correctly:
refinement.pdb_interpretation.apply_cif_modification
{
data_mod = cme
residue_selection = chain A and resid 530
residue_selection = chain B and resid 381
}
Thanks!
Kendall Nettles
# electronic Ligand Builder and Optimisation Workbench (eLBOW)
# - a module of PHENIX version 1.6-289 (Mon Jan 21 12:43:00 2010)
# - file written: Sat May 22 10:41:08 2010
#
# Input file: /AutoBuild_run_1_/TEMP0/LIGANDS.pdb
# Residue: CME
#
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
CME CME 'Unknown ' ligand 21 10 .
#
data_comp_CME
#
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
CME N N NH2 .
CME C C C1 .
CME O O O .
CME CA C CH1 .
CME CB C CH2 .
CME SG S S2 .
CME SD S S2 .
CME CE C CH2 .
CME CZ C CH2 .
CME OH O OH1 .
CME H H HNH2 .
CME H2 H HNH2 .
CME HC1 H H .
CME HA H HCH1 .
CME HB2 H HCH2 .
CME HB3 H HCH2 .
CME HE2 H HCH2 .
CME HE3 H HCH2 .
CME HZ2 H HCH2 .
CME HZ3 H HCH2 .
CME HH1 H HOH1 .
#
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
CME N CA single 1.450 0.02
CME C O double 1.224 0.02
CME C CA single 1.492 0.02
CME CA CB single 1.497 0.02
CME CB SG single 1.780 0.02
CME SG SD single 2.018 0.02
CME SD CE single 1.783 0.02
CME CE CZ single 1.485 0.02
CME CZ OH single 1.374 0.02
CME H N single 0.913 0.02
CME H2 N single 0.914 0.02
CME HC1 C single 0.965 0.02
CME HA CA single 0.975 0.02
CME HB2 CB single 0.966 0.02
CME HB3 CB single 0.973 0.02
CME HE2 CE single 0.972 0.02
CME HE3 CE single 0.973 0.02
CME HZ2 CZ single 0.976 0.02
CME HZ3 CZ single 0.968 0.02
CME HH1 OH single 0.880 0.02
#
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
CME C CA N 109.05 3.0
CME CB CA N 110.14 3.0
CME CB CA C 110.73 3.0
CME CA C O 119.98 3.0
CME SG CB CA 117.67 3.0
CME SD SG CB 109.52 3.0
CME CE SD SG 109.45 3.0
CME CZ CE SD 117.64 3.0
CME OH CZ CE 117.63 3.0
CME HA CA N 109.56 3.0
CME HA CA C 109.15 3.0
CME HC1 C O 120.00 3.0
CME H N CA 109.48 3.0
CME H2 N CA 109.47 3.0
CME HC1 C CA 120.00 3.0
CME HB2 CB CA 107.69 3.0
CME HB3 CB CA 107.72 3.0
CME HA CA CB 108.19 3.0
CME HB2 CB SG 107.73 3.0
CME HB3 CB SG 107.72 3.0
CME HE2 CE SD 107.78 3.0
CME HE3 CE SD 107.74 3.0
CME HZ2 CZ CE 107.71 3.0
CME HZ3 CZ CE 107.80 3.0
CME HE2 CE CZ 107.71 3.0
CME HE3 CE CZ 107.70 3.0
CME HH1 OH CZ 109.49 3.0
CME HZ2 CZ OH 107.74 3.0
CME HZ3 CZ OH 107.69 3.0
CME H2 N H 109.47 3.0
CME HB3 CB HB2 107.97 3.0
CME HE3 CE HE2 107.93 3.0
CME HZ3 CZ HZ2 107.94 3.0
#
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
CME Var_01 O C CA N 133.07 30.0 2
CME Var_02 SG CB CA N 179.49 30.0 3
CME Var_03 SG CB CA C 58.80 30.0 3
CME Var_04 CB CA C O -105.59 30.0 3
CME Var_05 SD SG CB CA 161.56 30.0 3
CME Var_06 CE SD SG CB -172.66 30.0 3
CME Var_07 CZ CE SD SG 177.33 30.0 3
CME Var_08 OH CZ CE SD 45.37 30.0 3
CME Var_09 HC1 C CA N -45.35 30.0 2
CME Var_10 HB2 CB CA N -58.63 30.0 3
CME Var_11 HB3 CB CA N 57.60 30.0 3
CME Var_12 H N CA C -165.67 30.0 3
CME Var_13 H2 N CA C -45.66 30.0 3
CME Var_14 HB2 CB CA C -179.32 30.0 3
CME Var_15 HB3 CB CA C -63.09 30.0 3
CME Var_16 HA CA C O 13.41 30.0 3
CME Var_17 H N CA CB 72.63 30.0 3
CME Var_18 H2 N CA CB -167.36 30.0 3
CME Var_19 HC1 C CA CB 75.99 30.0 2
CME Var_20 HA CA CB SG -60.78 30.0 2
CME Var_21 HE2 CE SD SG 55.43 30.0 3
CME Var_22 HE3 CE SD SG -60.81 30.0 3
CME Var_23 HB2 CB SG SD 39.69 30.0 1
CME Var_24 HB3 CB SG SD -76.55 30.0 1
CME Var_25 HZ2 CZ CE SD 167.25 30.0 3
CME Var_26 HZ3 CZ CE SD -76.51 30.0 3
CME Var_27 HH1 OH CZ CE 173.81 30.0 3
CME Var_28 HE2 CE CZ OH 167.31 30.0 3
CME Var_29 HE3 CE CZ OH -76.51 30.0 3
CME Var_30 HA CA N H -46.26 30.0 3
CME Var_31 HA CA N H2 73.74 30.0 3
CME Var_32 HA CA C HC1 -165.01 30.0 3
CME Var_33 HB2 CB CA HA 61.10 30.0 3
CME Var_34 HB3 CB CA HA 177.33 30.0 3
CME Var_35 HZ2 CZ CE HE2 -70.81 30.0 3
CME Var_36 HZ3 CZ CE HE2 45.43 30.0 3
CME Var_37 HZ2 CZ CE HE3 45.37 30.0 3
CME Var_38 HZ3 CZ CE HE3 161.61 30.0 3
CME Var_39 HH1 OH CZ HZ2 51.95 30.0 3
CME Var_40 HH1 OH CZ HZ3 -64.25 30.0 3
#
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
CME chir_01 CA N C CB both
#
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