[phenixbb] Extract coordinates from PDB file

[Tanner, John J.]

grep " CA " file.pdb > ca.pdb

Sent from Jack's iPhone

> On Jul 29, 2015, at 4:15 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> 
> 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
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