Phenix? phenix.pdb_atom_selection model.pdb "within(5, (resid 4 and name CA))" where 5 - 5 Angstrom radius, (resid 4 and name CA) - selection of an atom. Don't have to be a single atom. More docs on selection syntax is here: https://www.phenix-online.org/documentation/reference/atom_selections.html
Expanding to include whole residues: phenix.pdb_atom_selection model.pdb "residues_within(5, (resid 4 and name CA))" Dumping result to a .pdb file: phenix.pdb_atom_selection model.pdb "residues_within(5, (resid 4 and name CA))" --write-pdb-file selected.pdb Best regards, Oleg Sobolev. On Wed, Apr 3, 2019 at 7:19 AM Stephen Cusack <cus...@embl.fr> wrote: > Dear All, > > I am looking for an accessible programme that allows selection of > atoms from a PDB file > > within a sphere of inputted radius from a central atom. > > Thanks for any help, > > Stephen Cusack > > -- > > ********************************************************************** > Dr. Stephen Cusack, FRS > Head of Grenoble Outstation of the European Molecular Biology Laboratory > (EMBL) > Group leader in structural biology of protein-RNA complexes and viral > proteins > ********************************************************************** > > Email: cus...@embl.fr > Website: http://www.embl.fr > Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 > > Fax: (33) 4 76 20 7199 > Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS > 90181, 38042 Grenoble Cedex 9, France > Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 > Avenue des Martyrs, 38000 Grenoble, France > ********************************************************************** > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
