Editing Selection Algebra (section)

== Examples ==
Logical selections can be combined. For example, you might select atoms that are part of chain a, but not residue number 125:
<source lang="python">
# selects atoms that are part of chain A, but not residue number 125.
select chain A and (not resi 125)

# The following two selections are equivalent, 
select (name CB or name CG1 or name CG2) and chain A

# select c-beta's, c-gamma-1's and c-gamma-2's 
# that are in chain A.
select name CB+CG1+CG2 and chain A

# select all residues within 5 Ang. or any organic small molecules
select br. all within 5 of organic

# select helices
select ss 'H'

# select anything shown as a line
select rep lines

# select all residues with a b-factor less than 20, within 3 angstroms of any water
select br. b<20 & (all within 3 of resn HOH)

# select anything colored blue
select color blue

# select the 1st arginine
select first resn ARG

# select 1foo's segment G's chain X's residue 444's alpha carbon
select 1foo/G/X/444/CA
# same thing
select 1foo and segi G and c. X and i. 444 and n. CA

# select the entire object that residue 23's beta caron is in:
select bo. i. 23 and n. CA

# select the molecule that chain C is in
select bm. c. C
</source>

Like the results of groups of arithmetic operations, the results of groups of logical operations depend on which operation is performed first. They have an order of precedence. To ensure that the operations are performed in the order you have in mind, use parentheses:

<source lang="python">byres ((chain A or (chain B and (not resi 125))) around 5)</source>

PyMOL will expand its logical selection out from the innermost parentheses.