1) Use moleman to generate short helix -> helix_moleman.pdb
2) Manually fit three copies of short helices into characteristic density in t-trimer.
   Use DLPdbl_14_b350_r7_cut.ccp4 density -> helix_1.pdb, helix_2.pdb, helix_3.pdb
3) Prune helices according to density feature (remove atoms in PDB file) and combine -> helix_boundle.pdb
3) Use rot_pdb to mutiply helix bundle 3-fold and rotate -> helix_boundle_t.pdb
4) Put three bundels into the 4 other equivalent density features
   -> helix_boundle_p.pdb, helix_boundle_q.pdb, helix_boundle_r.pdb, helix_boundle_s.pdb
5) Use get_matrix_lsqMan.scp to get initial rotation/translation matrices
   -> rt_p_to_t.mat, rt_q_to_t.mat, rt_r_to_t.mat, rt_s_to_t.mat
6) Generate mask using gen_VP6tTrimer_mask_manual.scp and helix_boundle_t3.pdb
   (shifted version of 3-fold helix bundle) -> VP6_tTrimer_modelAtoms_r15.mask
7) Use imp_iniMatrice_manual.scp to refine matrices
   -> rt_p_to_t.mat_20, rt_q_to_t.mat_20, rt_r_to_t.mat_20, rt_s_to_t.mat_20
8) Use multiply_Mats_indi.scp to generate 12 matrices out of the 4 previously determined transformations.
   Use rt_icos_3f_1.mat and rt_icos_3f_2.mat for rotation operations.
   -> rt_p_to_t.mat_20_1-3, rt_q_to_t.mat_20_1-3, rt_r_to_t.mat_20_1-3, rt_s_to_t.mat_20_1-3
9) Repeat setp 7 to refine 12 new matrices.
   -> rt_p_to_t.mat_47_1-3, rt_q_to_t.mat_47_1-3, rt_r_to_t.mat_47_1-3, rt_s_to_t.mat_47_1-3
10) Merge matices into one file for later use -> matrices_13fold_dbl_manual47_r15.mat
