Selection Language Comparison
Jump to navigation
Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
Many molecular modelling applications have an atom selection language. This page summarizes and compares languages from different tools.
Selection Operators
PyMOL | Phenix | BALL | VMD | CNS | RasMol | OpenStructure | ProDy | Maestro | |
---|---|---|---|---|---|---|---|---|---|
Segment | segi A | segid A | segname A | segid A | segment A | ||||
Chain | chain A | chain A | chain(A) | chain A | *A | cname=A | chain A | chain.name A | |
Residue ID | resi 3-8 | resseq 3:8 | residueID(3) | resid 3 to 8 | residue 3:8 | 3-8 | rnum=3:8 | resnum 3 to 8 | res. 3 - 8 |
Residue Name | resn HIS | resname HIS | residue(HIS) | resname HIS | resname HIS | HIS | rname=HIS | resname HIS | res.pt HIS |
Atom Name | name ND1 | name ND1 | name(ND1) | name ND1 | name ND1 | *.ND1 | aname=ND1 | name ND1 | atom.pt ND1 |
Logical And | and | and | AND | and | and | and | and | and | and |
Logical Or | or | or | OR | or | or | or | or | or | or |
Logical Not | not | not | ! | not | not | not | not | not | |
Implicit operator | or | and | |||||||
Atom Symbol | elem H | element H | element(H) | chemical H | elemno == 1 | ele=H | element H | atom.ele H | |
Hydrogens | hydro | element(H) | hydrogen | hydrogen | hydrogen | hydrogen | atom.ato 1 | ||
Secondary Structure | ss H | secondaryStruct(...) | structure H | helix or sheet | rtype=H | secondary H | res.sec h | ||
Solvent | solvent | water | solvent() | water | solvent | water | water | water | |
Backbone | backbone (since 1.7) | backbone | backbone() | backbone | backbone | backbone | backbone | ||
Sidechain | sidechain (since 1.7) | sidechain | sidechain | sidechain | sidechain | sidechain | |||
Within Radius | within 6.0 of (chain A) | within(6.0, chain A) | within 6.0 of (chain A) | (chain A) around 6.0 | within(6.0, *A) | 6.0 <> [cname=A] | within 6.0 (chain. A) | ||
Protein+Nucleic | polymer | ||||||||
Protein | polymer.protein | protein | protein | peptide | protein | protein | |||
Peptide Sequence | pepseq ACDEF | protein sequence ACDEF | |||||||
DNA | dna | ||||||||
RNA | rna | ||||||||
Nucleic Acids | polymer.nucleic | nucleotide | nucleic | nucleic | nucleic | nucleic_acids | |||
B-factor | b < 50 | temperature < 50 | abfac<50 | beta < 50 |
Selection Macros
chain A and resi 32 and name CA | Comment | |
---|---|---|
PyMOL | A/32/CA | |
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 |