[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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