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<TITLE>Autobuild: problems with modified amino acids</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>I’m running autobuild from a molecular replacement solution and having two problems:<BR>
</SPAN></FONT><OL><LI><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>methionines are converted to MSE
</SPAN></FONT><LI><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>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:<BR>
</SPAN></FONT></OL><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'><BR>
refinement.pdb_interpretation.apply_cif_modification<BR>
{<BR>
data_mod = cme<BR>
residue_selection = chain A and resid 530<BR>
residue_selection = chain B and resid 381<BR>
}<BR>
<BR>
<BR>
Thanks!<BR>
Kendall Nettles<BR>
<BR>
<BR>
<BR>
# electronic Ligand Builder and Optimisation Workbench (eLBOW)<BR>
# - a module of PHENIX version 1.6-289 (Mon Jan 21 12:43:00 2010)<BR>
# - file written: Sat May 22 10:41:08 2010<BR>
#<BR>
# Input file: /AutoBuild_run_1_/TEMP0/LIGANDS.pdb<BR>
# Residue: CME<BR>
#<BR>
data_comp_list<BR>
loop_<BR>
_chem_comp.id<BR>
_chem_comp.three_letter_code<BR>
_chem_comp.name<BR>
_chem_comp.group<BR>
_chem_comp.number_atoms_all<BR>
_chem_comp.number_atoms_nh<BR>
_chem_comp.desc_level<BR>
CME CME 'Unknown ' ligand 21 10 .<BR>
#<BR>
data_comp_CME<BR>
#<BR>
loop_<BR>
_chem_comp_atom.comp_id<BR>
_chem_comp_atom.atom_id<BR>
_chem_comp_atom.type_symbol<BR>
_chem_comp_atom.type_energy<BR>
_chem_comp_atom.partial_charge<BR>
<BR>
CME N N NH2 . <BR>
CME C C C1 . <BR>
CME O O O . <BR>
CME CA C CH1 . <BR>
CME CB C CH2 . <BR>
CME SG S S2 . <BR>
CME SD S S2 . <BR>
CME CE C CH2 . <BR>
CME CZ C CH2 . <BR>
CME OH O OH1 . <BR>
CME H H HNH2 . <BR>
CME H2 H HNH2 . <BR>
CME HC1 H H . <BR>
CME HA H HCH1 . <BR>
CME HB2 H HCH2 . <BR>
CME HB3 H HCH2 . <BR>
CME HE2 H HCH2 . <BR>
CME HE3 H HCH2 . <BR>
CME HZ2 H HCH2 . <BR>
CME HZ3 H HCH2 . <BR>
CME HH1 H HOH1 . <BR>
#<BR>
loop_<BR>
_chem_comp_bond.comp_id<BR>
_chem_comp_bond.atom_id_1<BR>
_chem_comp_bond.atom_id_2<BR>
_chem_comp_bond.type<BR>
_chem_comp_bond.value_dist<BR>
_chem_comp_bond.value_dist_esd<BR>
CME N CA single 1.450 0.02<BR>
CME C O double 1.224 0.02<BR>
CME C CA single 1.492 0.02<BR>
CME CA CB single 1.497 0.02<BR>
CME CB SG single 1.780 0.02<BR>
CME SG SD single 2.018 0.02<BR>
CME SD CE single 1.783 0.02<BR>
CME CE CZ single 1.485 0.02<BR>
CME CZ OH single 1.374 0.02<BR>
CME H N single 0.913 0.02<BR>
CME H2 N single 0.914 0.02<BR>
CME HC1 C single 0.965 0.02<BR>
CME HA CA single 0.975 0.02<BR>
CME HB2 CB single 0.966 0.02<BR>
CME HB3 CB single 0.973 0.02<BR>
CME HE2 CE single 0.972 0.02<BR>
CME HE3 CE single 0.973 0.02<BR>
CME HZ2 CZ single 0.976 0.02<BR>
CME HZ3 CZ single 0.968 0.02<BR>
CME HH1 OH single 0.880 0.02<BR>
#<BR>
loop_<BR>
_chem_comp_angle.comp_id<BR>
_chem_comp_angle.atom_id_1<BR>
_chem_comp_angle.atom_id_2<BR>
_chem_comp_angle.atom_id_3<BR>
_chem_comp_angle.value_angle<BR>
_chem_comp_angle.value_angle_esd<BR>
CME C CA N 109.05 3.0<BR>
CME CB CA N 110.14 3.0<BR>
CME CB CA C 110.73 3.0<BR>
CME CA C O 119.98 3.0<BR>
CME SG CB CA 117.67 3.0<BR>
CME SD SG CB 109.52 3.0<BR>
CME CE SD SG 109.45 3.0<BR>
CME CZ CE SD 117.64 3.0<BR>
CME OH CZ CE 117.63 3.0<BR>
CME HA CA N 109.56 3.0<BR>
CME HA CA C 109.15 3.0<BR>
CME HC1 C O 120.00 3.0<BR>
CME H N CA 109.48 3.0<BR>
CME H2 N CA 109.47 3.0<BR>
CME HC1 C CA 120.00 3.0<BR>
CME HB2 CB CA 107.69 3.0<BR>
CME HB3 CB CA 107.72 3.0<BR>
CME HA CA CB 108.19 3.0<BR>
CME HB2 CB SG 107.73 3.0<BR>
CME HB3 CB SG 107.72 3.0<BR>
CME HE2 CE SD 107.78 3.0<BR>
CME HE3 CE SD 107.74 3.0<BR>
CME HZ2 CZ CE 107.71 3.0<BR>
CME HZ3 CZ CE 107.80 3.0<BR>
CME HE2 CE CZ 107.71 3.0<BR>
CME HE3 CE CZ 107.70 3.0<BR>
CME HH1 OH CZ 109.49 3.0<BR>
CME HZ2 CZ OH 107.74 3.0<BR>
CME HZ3 CZ OH 107.69 3.0<BR>
CME H2 N H 109.47 3.0<BR>
CME HB3 CB HB2 107.97 3.0<BR>
CME HE3 CE HE2 107.93 3.0<BR>
CME HZ3 CZ HZ2 107.94 3.0<BR>
#<BR>
loop_<BR>
_chem_comp_tor.comp_id<BR>
_chem_comp_tor.id<BR>
_chem_comp_tor.atom_id_1<BR>
_chem_comp_tor.atom_id_2<BR>
_chem_comp_tor.atom_id_3<BR>
_chem_comp_tor.atom_id_4<BR>
_chem_comp_tor.value_angle<BR>
_chem_comp_tor.value_angle_esd<BR>
_chem_comp_tor.period<BR>
CME Var_01 O C CA N 133.07 30.0 2<BR>
CME Var_02 SG CB CA N 179.49 30.0 3<BR>
CME Var_03 SG CB CA C 58.80 30.0 3<BR>
CME Var_04 CB CA C O -105.59 30.0 3<BR>
CME Var_05 SD SG CB CA 161.56 30.0 3<BR>
CME Var_06 CE SD SG CB -172.66 30.0 3<BR>
CME Var_07 CZ CE SD SG 177.33 30.0 3<BR>
CME Var_08 OH CZ CE SD 45.37 30.0 3<BR>
CME Var_09 HC1 C CA N -45.35 30.0 2<BR>
CME Var_10 HB2 CB CA N -58.63 30.0 3<BR>
CME Var_11 HB3 CB CA N 57.60 30.0 3<BR>
CME Var_12 H N CA C -165.67 30.0 3<BR>
CME Var_13 H2 N CA C -45.66 30.0 3<BR>
CME Var_14 HB2 CB CA C -179.32 30.0 3<BR>
CME Var_15 HB3 CB CA C -63.09 30.0 3<BR>
CME Var_16 HA CA C O 13.41 30.0 3<BR>
CME Var_17 H N CA CB 72.63 30.0 3<BR>
CME Var_18 H2 N CA CB -167.36 30.0 3<BR>
CME Var_19 HC1 C CA CB 75.99 30.0 2<BR>
CME Var_20 HA CA CB SG -60.78 30.0 2<BR>
CME Var_21 HE2 CE SD SG 55.43 30.0 3<BR>
CME Var_22 HE3 CE SD SG -60.81 30.0 3<BR>
CME Var_23 HB2 CB SG SD 39.69 30.0 1<BR>
CME Var_24 HB3 CB SG SD -76.55 30.0 1<BR>
CME Var_25 HZ2 CZ CE SD 167.25 30.0 3<BR>
CME Var_26 HZ3 CZ CE SD -76.51 30.0 3<BR>
CME Var_27 HH1 OH CZ CE 173.81 30.0 3<BR>
CME Var_28 HE2 CE CZ OH 167.31 30.0 3<BR>
CME Var_29 HE3 CE CZ OH -76.51 30.0 3<BR>
CME Var_30 HA CA N H -46.26 30.0 3<BR>
CME Var_31 HA CA N H2 73.74 30.0 3<BR>
CME Var_32 HA CA C HC1 -165.01 30.0 3<BR>
CME Var_33 HB2 CB CA HA 61.10 30.0 3<BR>
CME Var_34 HB3 CB CA HA 177.33 30.0 3<BR>
CME Var_35 HZ2 CZ CE HE2 -70.81 30.0 3<BR>
CME Var_36 HZ3 CZ CE HE2 45.43 30.0 3<BR>
CME Var_37 HZ2 CZ CE HE3 45.37 30.0 3<BR>
CME Var_38 HZ3 CZ CE HE3 161.61 30.0 3<BR>
CME Var_39 HH1 OH CZ HZ2 51.95 30.0 3<BR>
CME Var_40 HH1 OH CZ HZ3 -64.25 30.0 3<BR>
#<BR>
loop_<BR>
_chem_comp_chir.comp_id<BR>
_chem_comp_chir.id<BR>
_chem_comp_chir.atom_id_centre<BR>
_chem_comp_chir.atom_id_1<BR>
_chem_comp_chir.atom_id_2<BR>
_chem_comp_chir.atom_id_3<BR>
_chem_comp_chir.volume_sign<BR>
CME chir_01 CA N C CB both<BR>
#<BR>
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