Selection Language Comparison: Difference between revisions
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! [http://www.openstructure.org/docs/dev/mol/base/query/ OpenStructure] | ! [http://www.openstructure.org/docs/dev/mol/base/query/ OpenStructure] | ||
! [http://prody.csb.pitt.edu/manual/reference/atomic/select.html ProDy] | ! [http://prody.csb.pitt.edu/manual/reference/atomic/select.html ProDy] | ||
! [http://gohom.win/ManualHom/Schrodinger/Schrodinger_2015-2_docs/maestro/help_Maestro/misc/asl.html Maestro] | |||
|- | |- | ||
! Segment | ! Segment | ||
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| | | | ||
| segment A | | segment A | ||
| | |||
|- | |- | ||
! Chain | ! Chain | ||
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| cname=A | | cname=A | ||
| chain A | | chain A | ||
| chain.name A | |||
|- | |- | ||
! Residue ID | ! Residue ID | ||
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| rnum=3:8 | | rnum=3:8 | ||
| resnum 3 to 8 | | resnum 3 to 8 | ||
| res. 3 - 8 | |||
|- | |- | ||
! Residue Name | ! Residue Name | ||
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| rname=HIS | | rname=HIS | ||
| resname HIS | | resname HIS | ||
| res.pt HIS | |||
|- | |- | ||
! Atom Name | ! Atom Name | ||
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| aname=ND1 | | aname=ND1 | ||
| name ND1 | | name ND1 | ||
| atom.pt ND1 | |||
|- | |- | ||
! Logical And | ! Logical And | ||
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| and | | and | ||
| AND | | AND | ||
| and | |||
| and | | and | ||
| and | | and | ||
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| or | | or | ||
| OR | | OR | ||
| or | |||
| or | | or | ||
| or | | or | ||
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| not | | not | ||
| | | | ||
| not | |||
| not | | not | ||
|- | |- | ||
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| | | | ||
| and | | and | ||
| | |||
| | | | ||
| | | | ||
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| ele=H | | ele=H | ||
| element H | | element H | ||
| atom.ele H | |||
|- | |- | ||
! Hydrogens | ! Hydrogens | ||
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| | | | ||
| hydrogen | | hydrogen | ||
| atom.ato 1 | |||
|- | |- | ||
! Secondary Structure | ! Secondary Structure | ||
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| rtype=H | | rtype=H | ||
| secondary H | | secondary H | ||
| res.sec h | |||
|- | |- | ||
! Solvent | ! Solvent | ||
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| | | | ||
| solvent | | solvent | ||
| water | |||
| water | | water | ||
| water | | water | ||
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| backbone | | backbone | ||
| | | | ||
| backbone | |||
| backbone | | backbone | ||
|- | |- | ||
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| sidechain | | sidechain | ||
| | | | ||
| sidechain | |||
| sidechain | | sidechain | ||
|- | |- | ||
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| 6.0 <> [cname=A] | | 6.0 <> [cname=A] | ||
| | | | ||
| within 6.0 (chain. A) | |||
|- | |- | ||
! Protein+Nucleic | ! Protein+Nucleic | ||
| polymer | | polymer | ||
| | |||
| | | | ||
| | | | ||
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| protein | | protein | ||
| peptide | | peptide | ||
| protein | |||
| protein | | protein | ||
|- | |- | ||
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| | | | ||
| protein sequence ACDEF | | protein sequence ACDEF | ||
| | |||
| | | | ||
| | | | ||
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| | | | ||
| dna | | dna | ||
| | |||
| | | | ||
| | | | ||
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| | | | ||
| rna | | rna | ||
| | |||
| | | | ||
| | | | ||
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| | | | ||
| nucleic | | nucleic | ||
| nucleic_acids | |||
|- | |- | ||
! B-factor | ! B-factor | ||
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| abfac<50 | | abfac<50 | ||
| beta < 50 | | beta < 50 | ||
| | |||
|} | |} | ||
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| full macro example: SER32A.CA;B/2 (Serine, ..., Alt B, Model 2)) | | full macro example: SER32A.CA;B/2 (Serine, ..., Alt B, Model 2)) | ||
|- | |- | ||
! Chimera | ! [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html Chimera] | ||
| :32.A@CA | | :32.A@CA | ||
| not tested | | not tested | ||
Revision as of 15:11, 18 December 2017
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 |