Selection Language Comparison - Revision history

Cchem: 1 revision

2019-04-29T03:23:33Z

1 revision

Speleo3: polymer.protein

2019-04-03T14:34:34Z

polymer.protein

Cchem: 2 revisions

2018-01-08T04:03:35Z

2 revisions

Speleo3: Maestro

2017-12-18T20:11:24Z

Maestro

Speleo3: created

2017-12-18T19:30:18Z

created

New page

Many molecular modelling applications have an atom selection language. This page summarizes and compares languages from different tools.

== Selection Operators ==

{| class="wikitable"
!
! [[Selection Algebra|PyMOL]]
! [http://www.phenix-online.org/documentation/reference/atom_selections.html Phenix]
! [http://ball-docs.bioinf.uni-sb.de/BALLView/V1.4.0/molecularControl.html#regular_expressions BALL]
! [http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node89.html VMD]
! [http://cns-online.org/v1.3/tutorial/language/atom_sele_basic/text.html CNS]
! [http://rasmol.org/doc/rasmol.html#chexprs RasMol]
! [http://www.openstructure.org/docs/dev/mol/base/query/ OpenStructure]
! [http://prody.csb.pitt.edu/manual/reference/atomic/select.html ProDy]
|-
! 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
|-
! 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
|-
! Residue Name
| resn HIS
| resname HIS
| residue(HIS)
| resname HIS
| resname HIS
| HIS
| rname=HIS
| resname HIS
|-
! Atom Name
| name ND1
| name ND1
| name(ND1)
| name ND1
| name ND1
| *.ND1
| aname=ND1
| name ND1
|-
! Logical And
| and
| and
| AND
| and
| and
| and
| and
| and
|-
! Logical Or
| or
| or
| OR
| or
| or
| or
| or
| or
|-
! Logical 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
|-
! Hydrogens
| hydro
|
| element(H)
| hydrogen
| hydrogen
| hydrogen
|
| hydrogen
|-
! Secondary Structure
| ss H
|
| secondaryStruct(...)
| structure H
|
| helix or sheet
| rtype=H
| secondary H
|-
! Solvent
| solvent
| water
| solvent()
| water
|
| solvent
| water
| water
|-
! Backbone
| backbone (since 1.7)
| backbone
| backbone()
| backbone
|
| backbone
|
| backbone
|-
! Sidechain
| sidechain (since 1.7)
| 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]
|
|-
! Protein+Nucleic
| polymer
|
|
|
|
|
|
|
|-
! Protein
|
|
|
| protein
|
| protein
| peptide
| protein
|-
! Peptide Sequence
| pepseq ACDEF
|
|
| protein sequence ACDEF
|
|
|
|
|-
! DNA
|
| dna
|
|
|
|
|
|
|-
! RNA
|
| rna
|
|
|
|
|
|
|-
! Nucleic Acids
|
| nucleotide
|
| nucleic
|
| nucleic
|
| nucleic
|-
! B-factor
| b < 50
|
|
|
|
| temperature < 50
| abfac<50
| beta < 50
|}

== Selection Macros ==

{| class="wikitable"
!
! chain A and resi 32 and name CA
! Comment
|-
! [[Selection Macros|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 ==

* [[Selection Algebra]]
* [[Selection Macros]]

[[Category:Selecting]]

← Older revision	Revision as of 03:23, 29 April 2019
(No difference)

@@ Line 203: / Line 203: @@
 |-
 ! Protein
+| polymer.protein
+|
+|
@@ Line 247: / Line 247: @@
 |-
 ! Nucleic Acids
+| polymer.nucleic
 | nucleotide
+|

← Older revision	Revision as of 04:03, 8 January 2018
(No difference)

@@ Line 13: / Line 13: @@
 ! [http://www.openstructure.org/docs/dev/mol/base/query/ OpenStructure]
 ! [http://prody.csb.pitt.edu/manual/reference/atomic/select.html ProDy]
 |-
 ! Segment
@@ Line 23: / Line 24: @@
+|
 | segment A
 |-
 ! Chain
@@ Line 33: / Line 35: @@
 | cname=A
 | chain A
 |-
 ! Residue ID
@@ Line 43: / Line 46: @@
 | rnum=3:8
 | resnum 3 to 8
 |-
 ! Residue Name
@@ Line 53: / Line 57: @@
 | rname=HIS
 | resname HIS
 |-
 ! Atom Name
@@ Line 63: / Line 68: @@
 | aname=ND1
 | name ND1
 |-
 ! Logical And
@@ Line 68: / Line 74: @@
 | and
 | AND
 | and
 | and
@@ Line 78: / Line 85: @@
 | or
 | OR
 | or
 | or
@@ Line 92: / Line 100: @@
 | not
+|
 | not
 |-
@@ Line 99: / Line 108: @@
+|
 | and
+|
+|
@@ Line 113: / Line 123: @@
 | ele=H
 | element H
 |-
 ! Hydrogens
@@ Line 123: / Line 134: @@
+|
 | hydrogen
 |-
 ! Secondary Structure
@@ Line 133: / Line 145: @@
 | rtype=H
 | secondary H
 |-
 ! Solvent
@@ Line 141: / Line 154: @@
+|
 | solvent
 | water
 | water
@@ Line 152: / Line 166: @@
 | backbone
+|
 | backbone
 |-
@@ Line 162: / Line 177: @@
 | sidechain
+|
 | sidechain
 |-
@@ Line 173: / Line 189: @@
 | 6.0 <> [cname=A]
+|
 |-
 ! Protein+Nucleic
 | polymer
+|
+|
@@ Line 192: / Line 210: @@
 | protein
 | peptide
 | protein
 |-
@@ Line 199: / Line 218: @@
+|
 | protein sequence ACDEF
+|
+|
@@ Line 207: / Line 227: @@
+|
 | dna
+|
+|
@@ Line 217: / Line 238: @@
+|
 | rna
+|
+|
@@ Line 233: / Line 255: @@
+|
 | nucleic
 |-
 ! B-factor
@@ Line 243: / Line 266: @@
 | abfac<50
 | beta < 50
 |}
@@ Line 264: / Line 288: @@
 | 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
 | not tested