[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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