Hi Kendall,
Autobuild: problems with modified amino ac
- 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
}
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.