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<TITLE>Re: [phenixbb] Autobuild: problems with modified amino acids</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi Tom, <BR>
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. <BR>
<BR>
I tried your suggestion and got this: <BR>
<BR>
Last login: Fri Jan 14 13:26:20 on ttys000<BR>
knettles$ source /usr/local/phenix-1.6.4-486/phenix_env.sh<BR>
knettles$ phenix.autobuild show_facts | grep semet<BR>
Sorry semet = False<BR>
: No current run to carry on with...cannot use carry_on<BR>
<BR>
<BR>
I didn’t input a parameters file, and there is no semet in the structure. The autobuild.eff file says:<BR>
<BR>
model_building {<BR>
build_type = *RESOLVE RESOLVE_AND_BUCCANEER<BR>
allow_negative_residues = False<BR>
highest_resno = "697"<BR>
semet = False<BR>
use_met_in_align = Auto True *False<BR>
<BR>
Any other ideas about where it could be coming from? <BR>
Best regards, <BR>
Kendall<BR>
<BR>
On 1/19/11 11:26 AM, "Thomas C. Terwilliger" <<a href="terwilliger@lanl.gov">terwilliger@lanl.gov</a>> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi Kendall,<BR>
<BR>
I can help with the first problem at least...<BR>
<BR>
Can you try this:<BR>
<BR>
phenix.autobuild show_facts | grep semet<BR>
<BR>
That should yield (if everything is normal):<BR>
<BR>
phenix.autobuild show_facts | grep semet<BR>
semet = False<BR>
default_semet 0<BR>
semet "False"<BR>
<BR>
If it says semet True ...then we need to figure out where the True is<BR>
coming from. Possibilities: (1) somewhere in your parameters file, (2)<BR>
any MSE in your input PDB file.<BR>
<BR>
To just override semet=True, you can just specify "semet=False" and that<BR>
may take care of the problem.<BR>
<BR>
I hope that helps for that problem!<BR>
<BR>
On the second problem: AutoBuild won't build models with modified<BR>
residues, but you should be able to pass your cif file to phenix.refine<BR>
through autobuild with<BR>
<BR>
refine_eff_file_list=my_refine_parameters.eff<BR>
<BR>
where this parameters file has the commands for phenix.refine that you<BR>
list below.<BR>
<BR>
In this particular case I don't think this is going to do exactly what you<BR>
want, however, as AutoBuild is going to remove the modified residues and<BR>
call them "ligands" and treat them separately from the rest of the model.<BR>
So refinement may not work quite optimally. Down the road I intend to<BR>
make AutoBuild take care of this sort of situation in a better way. For<BR>
now you might do best to run AutoBuild with a dummy unmodified residue,<BR>
then when you are all done, edit to put in your modified residue.<BR>
<BR>
All the best,<BR>
Tom T<BR>
<BR>
>> I'm running autobuild from a molecular replacement solution and having two<BR>
>> problems:<BR>
>><BR>
>> 1. methionines are converted to MSE<BR>
>> 2. I'd like to include a .cif file for b-mercapto-ethanol adducted<BR>
>> cysteines: CME. The .cif file is one that works for phenix.refine (listed<BR>
>> below). I suspect I am not writing the .eff file correctly:<BR>
>><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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>><BR>
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