RE: [PyMOL] What's in a selection

[DeLano, W. <wa...@su...>]

Atom selections aren't directly exposed to Python, but you can have =
PyMOL build a Python list containing whatever information you need:

Using PyMOL commands:

list=3D[]
iterate (name ca),list.append((resi,resn))
print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), =
('LEU',
 '6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', =
'11'),=20
('CYS', '12'), ('THR', '13')]

or using a Python script (in PyMOL):

from pymol import cmd,stored
stored.list=3D[]
cmd.iterate("(name ca)","stored.list.append((resi,resn))")
print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), =
('6', '
LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', =
'TRP'),=20
('12', 'CYS'), ('13', 'THR')]

Cheers,
Warren

> -----Original Message-----
> From: ml...@um... [mailto:ml...@um...]
> Sent: Thursday, October 17, 2002 12:03 PM
> To: pym...@li...
> Subject: [PyMOL] What's in a selection
>=20
>=20
>=20
>=20
> Hi,
>=20
> How can I tell which atoms are in a selection?  For example,=20
> I've opened up a
> pdb file and selected all non-backbone atoms within five=20
> angstroms of the active
> site.  Now I want to get a list of the atoms in that=20
> selection.  My selection
> was called "nearby" and I tried "print nearby" but got a NameError.
>=20
> Sorry if the answer's obvious and I've just missed it.
>=20
> thanks,
>=20
> -michael
>=20
>=20
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>=20