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Revision as of 04:03, 8 January 2018
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 | protein | protein | peptide | protein | protein | ||||
| Peptide Sequence | pepseq ACDEF | protein sequence ACDEF | |||||||
| DNA | dna | ||||||||
| RNA | rna | ||||||||
| Nucleic Acids | 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 |