Phenix?
phenix.pdb_atom_selection model.pdb "within(5, (resid 4 and name CA))"
where 5 - 5 Angstrom radius, (resid 4 and name CA) - selection of an atom.
Don't have to be a single atom. More docs on selection syntax is here:
In ChimeraX, you can promote a selection to whole residues with:
select up
Repeating the command will expand to whole secondary structure elements,
then whole chains, then whole models. You can reverse this with:
select down
On 2019-04-03 16:13, Gianluca Santoni wrote:
I could be useful
This is easy to do in Pymol again. If you have atoms in selection "nameX", the
command is "select nameX, br. nameX". Very simple.
Best regards,
Petr
From: CCP4 bulletin board on behalf of Gianluca Santoni
Sent: Wednesday, April 3, 2019 5:13:59 PM
To:
I could be useful to then expand the selection to include the full
residues and not just the atoms within the sphere:
byres S1
On 4/3/19 4:21 PM, Steiner, Roberto wrote:
pymol?
example
S1 around 12.3 a. Atoms with centers within 12.3 Angstroms of the center
of any atom in S1
Best
Dear Stephen,
PyMOL can do it. You have to choose your atom and then use following command:
select your-name, (sele) expand 10; where (sele) is your selection - atom or a
group of atoms and 10 is the radius in AA.
Best regards,
Petr
From: CCP4 bulletin
In ChimeraX:
ctrl-click to select your atom, then in the command line below:
select zone sel
Best regards,
Tristan
On 2019-04-03 15:18, Stephen Cusack wrote:
Dear All,
I am looking for an accessible programme that allows selection of
atoms from a PDB file
within a sphere of inputted
pymol?
example
S1 around 12.3 a. Atoms with centers within 12.3 Angstroms of the center
of any atom in S1
Best wishes
Roberto
On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>>
wrote:
Dear All,
I am looking for an accessible programme that allows selection of atoms from a
Dear All,
I am looking for an accessible programme that allows selection of
atoms from a PDB file
within a sphere of inputted radius from a central atom.
Thanks for any help,
Stephen Cusack
--
**
Dr. Stephen Cusack, FRS
