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CCP4i projects Experimental data Model data Atom selection Servers

Contents


Coordinate Ids
Selection operators
Examples of selection commands

Coordinate IDs

A coordinate ID is an text string that has the following format:

         /mdl/chn/seq(res).ic/atm[elm]:aloc

where

Item Description
mdl the number of the model (usually an NMR model)
chn chain ID
seq residue sequence number
res residue name
ic residue insertion code
atm atom name
elm chemical element ID
aloc alternative location indicator

The residue name and atom element type are usually redundant, that is they are not essential to uniquely identify an atom, and do not need to be included when entering a CID. But note that all spaces in the coordinate ID are ignored and this means that certain atom names will be interpreted correctly only if the chemical element name is supplied (compare Calcium CA[CA] and Carbon in alpha-position CA[C]).

Any item in the coordinate ID may be replaced by a wildcard "*", which means an indefinite value for that item. The wildcard value is automatically implied for any missing item except the chain ID, insertion code and alternative location indicator:

A coordinate ID may be incomplete. Below are the rules for interpretation of incomplete IDs. Curling brackets {..} denote parts of an ID string that may be omitted as a whole:

  1. If the ID starts with slash "/" then it is interpreted as /mdl { /chn { /seq(res).ic { /atm[elm]:aloc }}}
  2. If the ID starts with a letter: chn { /seq(res).ic { /atm[elm]:aloc }}
  3. If ID starts with a (possibly negative) number, bracket "(" or dot ".": seq(res).ic { /atm[elm]:aloc }
  4. If none of the previous cases apply but the ID string contains square bracket "[" or colon ":", it is interpreted as atm[elm]:aloc

Below are examples of valid coordinate IDs:

Coordinate ID Description
/1/A/33(SER).B/CA[C].A model 1, chain A, residue SER with sequence number 33 and insertion code B, C-alpha atom in alternative location A.
/1/A/*(SER).* any SER residue in chain A, model 1.
/1/A/(SER) any SER residue with no insertion code in chain A, model 1.
/1//(SER) any SER residue with no insertion code in chain without a chain ID, model 1.
/1/A/*.*/CA[C] any C-alpha atom with no alternative location indicator in chain A, model 1, in residues with any sequence number and insertion code.
/1/A/*/CA[C] any C-alpha atom with no alternative location indicator in chain A, model 1, in residues with any sequence number and no insertion code.
A/*/CA any C-alpha or Calcium atom with no alternative location indicator in chain A of any model, in residues with any sequence number and no insertion code.
CA[C] any C-alpha atom with no alternative location indicator in any chain, any model, in residues with any sequence number and no insertion code.
CA any atom of chain CA with no alternative location indicator, in any model, in residues with any sequence number and no insertion code.

The following coordinate IDs are incorrect:

  1.   /A/23/CA[C]      stating with a slash implies that the model number will be given
  2.   /1/CG[C]         the residue is not defined 
  3.   /-15             stating with a slash implies that the model number will be given
  4.   */*(*).*/*[*]:*

Selection Operators

Complex selection commands are built up from CIDs, aliases and commands connected by the operators

a or b select all atoms defined by a and b
a and b select only the atoms in both a and b
not a select atoms that are not in a
a xor b select all atoms that are in a or b but not in both
a excl b select the atoms that are in a but exclude those in b. This is equivalent to 'and not'.

The selection components can also be grouped by using curly brace. Note that curly brace are used to be distinct from the brackets used to denote residue types in the CID.

Examples of Selection Commands


(GLU,ASP)/(O) and neighb (HIS)/NE2,ND1 5
Select oxygen atoms in glutamic acid or aspartic acid residues within 5A of the ND1 or NE2 of a histidine residue
{ /CA,N,C,O and {A/10-25 or A/35-40} } or (MTX)
Select the main chain atoms for two given ranges of residues and any residue with residue name MTX