[phenixbb] Extract coordinates from PDB file

[Zhijie Li]

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. ; phenixbb at phenix-online.org ; 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 <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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