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)
)