With a little modification it can be more specific ;) : grep -e '.\{12\} CA .\{61\}C' 1PRW.pdb But not so ideal for multi-model NMR structures: grep -e '.\{12\} CA .\{61\}C' 1cff.pdb Zhijie -----Original Message----- From: Pavel Afonine Sent: Wednesday, July 29, 2015 5:59 PM To: Tanner, John J. ; [email protected] ; Ashok Nayak Subject: Re: [phenixbb] Extract coordinates from PDB file John, 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! Pavel 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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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