#============================================================# # test visulaization of peptide planes. # #============================================================# system echo = off system verbose = false # set units #---------- #units #units scale name = mass uname = reducedMass value = 10000.0 units scale name = mass uname = reducedMass value = 100.0 # open pdb file #-------------- database open name = db1 format = pdb file = ../data/neck_xform.pdb # read molecule #-------------- molecule read name = m1 database = db1 # create helix domain #-------------------- domain create helix = C #domain helix backbone color = [ 1 1 1 ] width = 3 show domain create d = C[783-786] #domain d backbone color = [ 0 1 0 ] planes = true width = 2 show #domain d bonds atoms = true atom_color = element \ render = line bond_color = [ 1 0 0 ] show # peptide/sidechain 1 #-------------------- domain create d1 = C[783-784] peptide = true domain d1 bonds atoms = true atom_color = element \ bond_color = [ 1 0 0 ] render = line show domain d1 backbone color = [ 1 0.61 0 ] planes = true width = 2 show #----- domain create d2 = C[784] sidechain_group = true domain d2 bonds atoms = true atom_color = [ 1 0 0 ] bond_color = [ 0.5 0 0 ] show # peptide/sidechain 2 #-------------------- domain create d3 = C[784-785] peptide = true domain d3 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d3 backbone color = [ 0 1 0 ] planes = true #----- domain create d4 = C[785] sidechain_group = true domain d4 bonds atoms = true atom_color = [ 0 1 0 ] bond_color = [ 0 0.5 0 ] show # peptide/sidechain 3 #-------------------- domain create d5 = C[785-786] peptide = true domain d5 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d5 backbone color = [ 0 1 0 ] planes = true #----- domain create d6 = C[786] sidechain_group = true domain d6 bonds atoms = true atom_color = [ 1 1 0 ] bond_color = [ 0.5 0.5 0 ] show # peptide/sidechain 4 #-------------------- domain create d7 = C[786-787] peptide = true domain d7 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d7 backbone color = [ 0 1 0 ] planes = true #----- domain create d8 = C[787] sidechain_group = true domain d8 bonds atoms = true atom_color = [ 1 0 1 ] bond_color = [ 0.5 0 0.5 ] show # peptide/sidechain 5 #-------------------- domain create d9 = C[787-788] peptide = true domain d9 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d9 backbone color = [ 0 1 0 ] planes = true domain create d10 = C[788] sidechain_group = true domain d10 bonds atoms = true atom_color = [ 0 0 1 ] bond_color = [ 0.0 0 0.5 ] show # peptide/sidechain 6 #-------------------- domain create d11 = C[788-789] peptide = true domain d11 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d11 backbone color = [ 0 1 0 ] planes = true domain create d12 = C[789] sidechain_group = true domain d12 bonds atoms = true atom_color = [ 1 0.8 0 ] bond_color = [ 0.5 0.3 0 ] show # peptide/sidechain 7 #-------------------- domain create d13 = C[789-790] peptide = true domain d13 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d13 backbone color = [ 0 1 0 ] planes = true domain create d14 = C[790] sidechain_group = true domain d14 bonds atoms = true atom_color = [ 0 1 1 ] bond_color = [ 0 0.5 0.5 ] show # peptide/sidechain 8 #-------------------- domain create d15 = C[790-791] peptide = true domain d15 bonds atoms = true atom_color = element bond_color = element \ render = line show domain d15 backbone color = [ 0 1 0 ] planes = true domain create d16 = C[791] sidechain_group = true domain d16 bonds atoms = true atom_color = [ 0.6 1 0 ] bond_color = [ 0.3 0.5 0 ] show #--------------------------------------------------------------# # add rigid bodies # #--------------------------------------------------------------# body create name = ground type = ground body create name = d1b type = rigid domain = d1 body create name = d2b type = rigid domain = d2 body create name = d3b type = rigid domain = d3 body create name = d4b type = rigid domain = d4 body create name = d5b type = rigid domain = d5 body create name = d6b type = rigid domain = d6 body create name = d7b type = rigid domain = d7 body create name = d8b type = rigid domain = d8 body create name = d9b type = rigid domain = d9 body create name = d10b type = rigid domain = d10 body create name = d11b type = rigid domain = d11 body create name = d12b type = rigid domain = d12 body create name = d13b type = rigid domain = d13 body create name = d14b type = rigid domain = d14 body create name = d15b type = rigid domain = d15 body create name = d16b type = rigid domain = d16 #--------------------------------------------------------------# # add joints # #--------------------------------------------------------------# #----------- jnt 1 --------------- #joint create name = jnt1 type = weld domain = d1 res = C[783] use = C joint create name = jnt1 type = ball domain = d1 res = C[783] use = C joint jnt1 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt1 bodies = { ground d1b } #----------- jnt 2&3 --------------- joint create name = jnt2 type = hinge position = d2:C[784]:N \ use_bond = true bond = { d2:C[784]:CA d1:C[784]:N } #joint create name = jnt2 type = weld position = d2:C[784]:N joint jnt2 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt2 bodies = { d1b d2b } joint create name = jnt3 type = hinge position = d3:C[784]:C \ use_bond = true bond = { d2:C[784]:CA d3:C[784]:C } #joint create name = jnt3 type = ball position = d2:C[784]:C joint jnt3 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt3 bodies = { d2b d3b } #----------- jnt 4 & 5 --------------- joint create name = jnt4 type = hinge position = d4:C[785]:N \ use_bond = true bond = { d3:C[785]:N d4:C[785]:CA } joint jnt4 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt4 bodies = { d3b d4b } joint create name = jnt5 type = hinge position = d5:C[785]:C \ use_bond = true bond = { d4:C[785]:CA d5:C[785]:C } joint jnt5 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt5 bodies = { d4b d5b } #----------- jnt 6 & 7 --------------- joint create name = jnt6 type = hinge position = d6:C[786]:N \ use_bond = true bond = { d5:C[786]:N d6:C[786]:CA } joint jnt6 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt6 bodies = { d5b d6b } joint create name = jnt7 type = hinge position = d7:C[786]:C \ use_bond = true bond = { d6:C[786]:CA d7:C[786]:C } joint jnt7 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt7 bodies = { d6b d7b } #----------- jnt 8 & 9 --------------- joint create name = jnt8 type = hinge position = d8:C[787]:N \ use_bond = true bond = { d7:C[787]:N d8:C[787]:CA } joint jnt8 color = [ 0 1 0 ] msize = 0.01 shading = flat show = true joint jnt8 bodies = { d7b d8b } joint create name = jnt9 type = hinge position = d9:C[787]:C \ use_bond = true bond = { d8:C[787]:CA d9:C[787]:C } joint jnt9 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt9 bodies = { d8b d9b } #----------- jnt 10 & 11 --------------- joint create name = jnt10 type = hinge position = d10:C[788]:N \ use_bond = true bond = { d9:C[788]:N d10:C[788]:CA } joint jnt10 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt10 bodies = { d9b d10b } joint create name = jnt11 type = hinge position = d11:C[788]:C \ use_bond = true bond = { d10:C[788]:CA d11:C[788]:C } joint jnt11 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt11 bodies = { d10b d11b } #----------- jnt 12 & 13 --------------- joint create name = jnt12 type = hinge position = d12:C[789]:N \ use_bond = true bond = { d11:C[789]:N d12:C[789]:CA } joint jnt12 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt12 bodies = { d11b d12b } joint create name = jnt13 type = hinge position = d13:C[789]:C \ use_bond = true bond = { d12:C[789]:CA d13:C[789]:C } joint jnt13 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt13 bodies = { d12b d13b } #----------- jnt 14 & 15 --------------- joint create name = jnt14 type = hinge position = d14:C[790]:N \ use_bond = true bond = { d13:C[790]:N d14:C[790]:CA } joint jnt14 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt14 bodies = { d13b d14b } joint create name = jnt15 type = hinge position = d15:C[790]:C \ use_bond = true bond = { d14:C[790]:CA d15:C[790]:C } joint jnt15 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt15 bodies = { d14b d15b } #----------- jnt 16 --------------- joint create name = jnt16 type = hinge position = d16:C[791]:N \ use_bond = true bond = { d15:C[791]:N d16:C[791]:CA } joint jnt16 color = [ 1 1 1 ] msize = 0.01 shading = flat show = true joint jnt16 bodies = { d15b d16b } #--------------------------------------------------------------# # create a rigid simulation # #--------------------------------------------------------------# simulation create name = rsim type = rigid simulation rsim add bodies = all simulation rsim add joints = all # set solver #----------- simulation rsim solver = ode simulation rsim solver finite_rotation = on # add forces #----------- force create name = force1 \ type = explicit \ point = d16:C[791] \ global_frame = true \ direction = [ 0 1 0 ] \ scale = 1.0 simulation rsim add force = force1 \ body = d16b \ time = { 0 1000 } # initialize simulation #---------------------- simulation rsim initialize simulation rsim time step = 0.01 graphics center point = [ 1.32939 2.57201 2.19204 ]