A complete example: The tRNA Anticodon stem loop Script

This section contains a complete MC-SYM III script for the modeling of the anticodon stem-loop of the tRNA. This example also acted as a bench mark for testing during development of MC-SYM III.

//                             -*- Mode: Mcsym -*- 
// anticodon.mcc
// Copyright © 2000 Laboratoire de Biologie Informatique et Théorique.
// Author           : 
// Created On       : 
// Last Modified By : Martin Larose
// Last Modified On : Mon Mar 27 16:52:08 2000
// Update Count     : 1
// Status           : Ok.
// 

// Script MC-Sym 3 pour la boucle anticodon du trna

//             3
//             123456789

sequence (r 31 ACUGAAGAU)

// Conformations -------------------------------------------

residue
(
      31  { helix }   1
      39  { helix }   1
  32  38  { type_A } 15
)

// Relations -----------------------------------------------

connect
(
  31  33  { stack }    20
  33  34  { ! stack }  20
  34  39  { stack }    20
)

pair (31  39  { wct } 1)

// Building ------------------------------------------------

anticodon = backtrack
            (
              (31 39)
              (39 38 37 36 35 34)
              (31 32 33)
            )

// Constraint ----------------------------------------------

adjacency (anticodon 1.0 2.5)

res_clash
(
  anticodon
  fixed_distance 1.0
  all
  no_hydrogen
)

// Exploration ---------------------------------------------

explore
(
  anticodon
  rmsd (1.0 base_only no_hydrogen)
  file_pdb ("ANTI/anti-%04d.pdb" zipped)
)