[phenixbb] Autobuild: problems with modified amino acids

Kendall Nettles knettles at scripps.edu
Wed Jan 19 09:06:41 PST 2011


The output of autobuild lacks the CME residues that were in the input. I was hoping to have the CME stay in the pdb file so I don't have to manually add it back in to a couple dozen structures of the same protein with different ligands. I don't care as much if it is refined or rebuilt.
Best,
Kendall


On 1/19/11 12:02 PM, "Nigel Moriarty" <nwmoriarty at lbl.gov> wrote:

Kendall

The CIF file you attached is a restraints file. It contains the
restraints for any residues in your model with the resid CME. To use
it, you just need to supply it to phenix.refine i.e. the
refinement.pdb_interpretation.apply_cif_modification shouldn't do
anything.

Do you wish to use the restraints in AutoBuild?

Nigel

On Wed, Jan 19, 2011 at 7:52 AM, Kendall Nettles <knettles at scripps.edu> wrote:
> I'm running autobuild from a molecular replacement solution and having two
> problems:
>
> methionines are converted to MSE
> 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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>



--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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