Dear Wolfram,

I'm afraid you will have to use file with parameters to do this:

modify {

occupancies

{

atom_selection = chain A and resid 1

randomize = False

set = 1

normalize = False

}

keep = not (chain A and altid B and resid 1)

# or use: remove = chain A and altid B and resid 1

}

The scope "occupancies" is "multiple" which means you can have several of them. This kind of scopes cannot be populated correctly from command-line parameters. As you can see in the beginning of your set.out (in "Complete set of parameters"), you ended up with two "occupancies" scopes. The selection you provided ended up in the second scope with nothing to change, and set=1 ended up in the first scope with atom_selection=None, therefore set=1 was applied to the whole model.

Best regards,

Oleg Sobolev.

On Tue, Feb 7, 2017 at 12:19 PM, wtempel <wtempel@gmail.com> wrote:

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
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