[phenixbb] Autobuild: problems with modified amino acids
Pavel Afonine
pafonine at lbl.gov
Wed Jan 19 08:38:47 PST 2011
Hi Kendall,
>
> 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
> }
If the above set of parameters works with phenix.refine, then it should
work in AutoBuild too. Just save
refinement.pdb_interpretation.apply_cif_modification
{
data_mod = cme
residue_selection = chain A and resid 530
residue_selection = chain B and resid 381
}
in a file refinement_params.eff and run AutoBuild for example like this:
phenix.autobuild data=w1.sca seq_file=seq.dat model=coords.pdb
rebuild_in_place=True refine_eff_file=refinement_params.eff
Why you think it doesn't work correctly from within phenix.autobuild ?
Pavel.
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