Difference between revisions of "Selection Language Comparison"

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(polymer.protein)
 
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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
−
|  
+
| polymer.protein
 
|  
 
|  
 
|  
 
|  
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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 Acids
 
! Nucleic Acids
−
|  
+
| polymer.nucleic
 
| nucleotide
 
| nucleotide
 
|  
 
|  
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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

Latest revision as of 10:34, 3 April 2019

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

See Also

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