[phenixbb] Extract coordinates from PDB file
pafonine at lbl.gov
Wed Jul 29 14:59:47 PDT 2015
that may include Calcium or similarly called atoms in ligands -;)
But if you know there are none in your structure then your solution
would do the job and much faster!
On 7/29/15 14:53, Tanner, John J. wrote:
> 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:
>>> 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.
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