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" <[email protected]> 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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>>
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