Hello all,
suppose I would like to remove one alternate conformation B from residue 1 in chain A and set the occupancy of remaining atoms in that residue to 1.

phenix.pdbtools alts_minim.pdb occupancies.set=1 \
  occupancies.atom_selection=”chain A and resid 1” \
  keep=”not (chain A and altid B and resid 1)” \
  output.file_name=alts.out.pdb

There are better methods to achieve that, but I eventually would like to expand this command to do other “things” to my coordinates.
Well, so far I have failed to have the atom_selection to work the way I expect. stdout reveals that the program fails to apply a common scope to the command switches, and proceeds to reset occupancies of all atoms. Can this be done on the command line? A minimal (not) working example is attached, and your feedback appreciated.
Best regards.
Wolfram Tempel