[phenixbb] Extract coordinates from PDB file

Pavel Afonine pafonine at lbl.gov
Wed Jul 29 13:15:36 PDT 2015


Hi,

> I wish to extract xyz coordinates of Calpha atoms from the PDB file of 
> my interest.
> Is there a program in Phenix or CCP4 for the same?

some examples:

- this will select all CA atoms:

phenix.pdb_atom_selection model.pdb "name CA"

- this will select CA atoms in chain A and chain B:

phenix.pdb_atom_selection model.pdb "name CA and (chain A or chain B)"

- this will select all Carbon atoms:

phenix.pdb_atom_selection model.pdb "element C"

- this will select all atoms with alternative conformation id A:

phenix.pdb_atom_selection model.pdb "altloc A"

etc etc etc - this can be very detailed and flexible.

Pavel


More information about the phenixbb mailing list