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Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb "within(3, chain L and resseq 9 and name CA)" --write-pdb-file=cut.pdb which in the above example selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. Pavel On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer <[log in to unmask]>wrote: > I would like to specify a target atom in a pdb file and then isolate all > atoms within a given distance of the target. The selected atoms are then to > be placed in a new pdb file. > Any suggestions please. > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com >