RESI Instruction

RESI class [ ] number [0] alias

Until the next RESI instruction, all atoms are considered to be in the specified 'residue', which may be defined by a class (up to four characters, beginning with a letter) or number (up to four digits) or both. The same atom names may be employed in different residues, enabling them to be referenced globally or selectively. The residue number should be unique to a particular residue, but the class may be used to refer to a class of similar residues, e.g. a particular type of amino acid in a polypeptide.

Residues may be referenced by any instruction which allows atom names; the reference takes the form of the character '_' followed by either the residue class or number without intervening spaces. If an instruction codeword is followed immediately by a residue number, all atom names referred to in the instruction are assumed to belong to that residue unless they are themselves immediately followed by '_' and a residue number, which is then used instead. Thus: 


 RTAB_4 Ang N H0 O_11
would cause the calculation of an angle N_4 - H0_4 - O_11, where the first two atoms are in residue 4 and the third is in residue 11.

If the instruction codeword is followed immediately by a residue class, the instruction is effectively duplicated for all residues of that class. '_*' may be used to match all residue classes; this includes the default class ' ' (residue number 0) which applies until the first RESI instruction is encountered. Thus: 


 MPLA_phe CB > CZ
would calculate least-squares planes through atoms CB to CZ inclusive of all residues of class 'phe' (phenylalanine). In the special case of HFIX, only the FIRST instruction which applies to a given atom is applied. Thus:


 HFIX_1 33 N
 HFIX_* 43 N
would add hydrogens to the N-terminal nitrogen (residue 1) of a polypeptide to generate a -NH3+ group, but all other (amide) nitrogens would become -NH-.

Individual atom names in an instruction may be followed by '_' and a residue number, but not by '_*' or '_' and a residue class. If an atom name is not followed by a residue number, the current residue is assumed (unless overridden by a global residue number or class appended to the instruction codeword). The symbols '_+' meaning 'the next residue' and '_-' meaning 'the preceding residue' (i.e. residues number n+1 and n-1 if the current residue number is n) may be appended to atom names but not to instruction codenames. Thus the instruction:


 RTAB_* Omeg CA_- C_- N CA
could be used to calculate all the peptide (omega) torsion angles in a protein or polypeptide. If (as at the N-terminus in this example) some or all of the named atoms cannot be found for a particular residue, the instruction is simply ignored for that residue.

'_$n' does not refer to a residue; it uses the symmetry operation $n defined by a preceding 'EQIV $n' instruction to generate an equivalent of the named atom (see EQIV).

alias specifies an alternative value of the residue number so that cyclic chains of residues may be created; for a cyclic pentapeptide (residue numbers 2,3,..6) it could be set to 1 for residue 6 and to 7 for residue 2. If more than one RESI instruction refers to the same number, alias only needs to be specified once. alias is referenced only by the _+ and _- operations (see above), and a value used for alias may not be used as a residue number on a RESI instruction. Note that if there is more than one cyclic peptide in the asymmetric unit, it is a good idea to leave a gap of TWO residue numbers between them. E.g. a cyclic pentapeptide with two molecules in the asymmetric unit would be numbered 2 to 6 and 9 to 13, with aliases 7 on RESI 2, 1 on RESI 6, 14 on RESI 9 and 10 on RESI 13.

It will generally be found convenient for applying restraints etc. to use the same names for atoms in identical residues.