Many molecular modelling applications have an atom selection language. This page summarizes and compares languages from different tools.
Selection Operators
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PyMOL
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Phenix
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BALL
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VMD
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CNS
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RasMol
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OpenStructure
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ProDy
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Maestro
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| Segment
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segi A
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segid A
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segname A
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segid A
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segment A
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| Chain
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chain A
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chain A
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chain(A)
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chain A
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*A
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cname=A
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chain A
|
chain.name A
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| Residue ID
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resi 3-8
|
resseq 3:8
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residueID(3)
|
resid 3 to 8
|
residue 3:8
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3-8
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rnum=3:8
|
resnum 3 to 8
|
res. 3 - 8
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| Residue Name
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resn HIS
|
resname HIS
|
residue(HIS)
|
resname HIS
|
resname HIS
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HIS
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rname=HIS
|
resname HIS
|
res.pt HIS
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| Atom Name
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name ND1
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name ND1
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name(ND1)
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name ND1
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name ND1
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*.ND1
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aname=ND1
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name ND1
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atom.pt ND1
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| Logical And
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and
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and
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AND
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and
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and
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and
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and
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and
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and
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| Logical Or
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or
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or
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OR
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or
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or
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or
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or
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or
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or
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| Logical Not
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not
|
not
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!
|
not
|
not
|
not
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|
not
|
not
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| Implicit operator
|
or
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|
and
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| Atom Symbol
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elem H
|
element H
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element(H)
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|
chemical H
|
elemno == 1
|
ele=H
|
element H
|
atom.ele H
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| Hydrogens
|
hydro
|
|
element(H)
|
hydrogen
|
hydrogen
|
hydrogen
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|
hydrogen
|
atom.ato 1
|
| Secondary Structure
|
ss H
|
|
secondaryStruct(...)
|
structure H
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|
helix or sheet
|
rtype=H
|
secondary H
|
res.sec h
|
| Solvent
|
solvent
|
water
|
solvent()
|
water
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|
solvent
|
water
|
water
|
water
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| Backbone
|
backbone (since 1.7)
|
backbone
|
backbone()
|
backbone
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|
backbone
|
|
backbone
|
backbone
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| Sidechain
|
sidechain (since 1.7)
|
sidechain
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|
sidechain
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|
sidechain
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|
sidechain
|
sidechain
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| Within Radius
|
within 6.0 of (chain A)
|
within(6.0, chain A)
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|
within 6.0 of (chain A)
|
(chain A) around 6.0
|
within(6.0, *A)
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6.0 <> [cname=A]
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|
within 6.0 (chain. A)
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| Protein+Nucleic
|
polymer
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| Protein
|
polymer.protein
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|
|
protein
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|
protein
|
peptide
|
protein
|
protein
|
| Peptide Sequence
|
pepseq ACDEF
|
|
|
protein sequence ACDEF
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| DNA
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|
dna
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| RNA
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|
rna
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| Nucleic Acids
|
polymer.nucleic
|
nucleotide
|
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nucleic
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|
nucleic
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|
nucleic
|
nucleic_acids
|
| B-factor
|
b < 50
|
|
|
|
|
temperature < 50
|
abfac<50
|
beta < 50
|
|
Selection Macros
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|
chain A and resi 32 and name CA
|
Comment
|
| PyMOL
|
A/32/CA
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|
| Modeller
|
mdl.atoms['CA:32:A']
|
mdl is model instance
|
| RasMol
|
*32A.CA
|
full macro example: SER32A.CA;B/2 (Serine, ..., Alt B, Model 2))
|
| Chimera
|
:32.A@CA
|
not tested
|
See Also
