Re: [phenixbb] Autobuild: problems with modified amino acids

19 Jan 2011

      Hi Tom,
Thanks for the quick reply. It would be nice to be able to use the modified amino acids in the future. We have a couple dozen structures of the same protein with different ligands, so it adds up to quite a bit of editing.

I tried your suggestion and got this:

Last login: Fri Jan 14 13:26:20 on ttys000
knettles$  source /usr/local/phenix-1.6.4-486/phenix_env.sh
knettles$ phenix.autobuild show_facts | grep semet
Sorry    semet = False
: No current run to carry on with...cannot use carry_on

I didn't input a parameters file, and there is no semet in the structure. The autobuild.eff file says:

model_building {
    build_type = *RESOLVE RESOLVE_AND_BUCCANEER
    allow_negative_residues = False
    highest_resno = "697"
    semet = False
    use_met_in_align = Auto True *False

Any other ideas about where it could be coming from?
Best regards,
Kendall

On 1/19/11 11:26 AM, "Thomas C. Terwilliger"  wrote:

Hi Kendall,

I can help with the first problem at least...

Can you try this:

     phenix.autobuild show_facts | grep semet

That should yield (if everything is normal):

phenix.autobuild show_facts | grep semet
    semet = False
default_semet 0
semet  "False"

If it says semet True ...then we need to figure out where the True is
coming from.  Possibilities: (1) somewhere in your parameters file, (2)
any MSE in your input PDB file.

To just override semet=True, you can just specify "semet=False" and that
may take care of the problem.

I hope that helps for that problem!

On the second problem:  AutoBuild won't build models with modified
residues, but you should be able to pass your cif file to phenix.refine
through autobuild with

  refine_eff_file_list=my_refine_parameters.eff

where this parameters file has the commands for phenix.refine that you
list below.

In this particular case I don't think this is going to do exactly what you
want, however, as AutoBuild is going to remove the modified residues and
call them "ligands" and treat them separately from the rest of the model.
So refinement may not work quite optimally.  Down the road I intend to
make AutoBuild take care of this sort of situation in a better way. For
now you might do best to run AutoBuild with a dummy unmodified residue,
then when you are all done, edit to put in your modified residue.

All the best,
Tom T
...
...
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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