Difference between revisions of "Selection Language Comparison"

From PyMOLWiki
Jump to: navigation, search
(created)
 
(Maestro)
Line 13: Line 13:
 
! [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
Line 23: Line 24:
 
|  
 
|  
 
| segment A
 
| segment A
 +
|
 
|-
 
|-
 
! Chain
 
! Chain
Line 33: Line 35:
 
| cname=A
 
| cname=A
 
| chain A
 
| chain A
 +
| chain.name A
 
|-
 
|-
 
! Residue ID
 
! Residue ID
Line 43: Line 46:
 
| rnum=3:8
 
| rnum=3:8
 
| resnum 3 to 8
 
| resnum 3 to 8
 +
| res. 3 - 8
 
|-
 
|-
 
! Residue Name
 
! Residue Name
Line 53: Line 57:
 
| rname=HIS
 
| rname=HIS
 
| resname HIS
 
| resname HIS
 +
| res.pt HIS
 
|-
 
|-
 
! Atom Name
 
! Atom Name
Line 63: Line 68:
 
| aname=ND1
 
| aname=ND1
 
| name ND1
 
| name ND1
 +
| atom.pt ND1
 
|-
 
|-
 
! Logical And
 
! Logical And
Line 68: Line 74:
 
| and
 
| and
 
| AND
 
| AND
 +
| and
 
| and
 
| and
 
| and
 
| and
Line 78: Line 85:
 
| or
 
| or
 
| OR
 
| OR
 +
| or
 
| or
 
| or
 
| or
 
| or
Line 92: Line 100:
 
| not
 
| not
 
|  
 
|  
 +
| not
 
| not
 
| not
 
|-
 
|-
Line 99: Line 108:
 
|  
 
|  
 
| and
 
| and
 +
|
 
|  
 
|  
 
|  
 
|  
Line 113: Line 123:
 
| ele=H
 
| ele=H
 
| element H
 
| element H
 +
| atom.ele H
 
|-
 
|-
 
! Hydrogens
 
! Hydrogens
Line 123: Line 134:
 
|  
 
|  
 
| hydrogen
 
| hydrogen
 +
| atom.ato 1
 
|-
 
|-
 
! Secondary Structure
 
! Secondary Structure
Line 133: Line 145:
 
| rtype=H
 
| rtype=H
 
| secondary H
 
| secondary H
 +
| res.sec h
 
|-
 
|-
 
! Solvent
 
! Solvent
Line 141: Line 154:
 
|  
 
|  
 
| solvent
 
| solvent
 +
| water
 
| water
 
| water
 
| water
 
| water
Line 152: Line 166:
 
| backbone
 
| backbone
 
|  
 
|  
 +
| backbone
 
| backbone
 
| backbone
 
|-
 
|-
Line 162: Line 177:
 
| sidechain
 
| sidechain
 
|  
 
|  
 +
| sidechain
 
| sidechain
 
| sidechain
 
|-
 
|-
Line 173: Line 189:
 
| 6.0 <> [cname=A]
 
| 6.0 <> [cname=A]
 
|  
 
|  
 +
| within 6.0 (chain. A)
 
|-
 
|-
 
! Protein+Nucleic
 
! Protein+Nucleic
 
| polymer
 
| polymer
 +
|
 
|  
 
|  
 
|  
 
|  
Line 192: Line 210:
 
| protein
 
| protein
 
| peptide
 
| peptide
 +
| protein
 
| protein
 
| protein
 
|-
 
|-
Line 199: Line 218:
 
|  
 
|  
 
| protein sequence ACDEF
 
| protein sequence ACDEF
 +
|
 
|  
 
|  
 
|  
 
|  
Line 207: Line 227:
 
|  
 
|  
 
| dna
 
| dna
 +
|
 
|  
 
|  
 
|  
 
|  
Line 217: Line 238:
 
|  
 
|  
 
| rna
 
| rna
 +
|
 
|  
 
|  
 
|  
 
|  
Line 233: Line 255:
 
|  
 
|  
 
| nucleic
 
| nucleic
 +
| nucleic_acids
 
|-
 
|-
 
! B-factor
 
! B-factor
Line 243: Line 266:
 
| abfac<50
 
| abfac<50
 
| beta < 50
 
| beta < 50
 +
|
 
|}
 
|}
  
Line 264: Line 288:
 
| 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

See Also