# PyMOL script for SRP assembly movie
# -----------------------------------
# Luca Jovine, MSSM NY, 23.10.02
#
# Run this script with: @/Users/luca/srp_assembly/srp_assembly_movie.pml
#
#
#
# flush frame cache:
mclear
# delete previous stuff:
delete *
# go to PDB frame directory:
cd /Users/luca/srp_assembly/pdb_frames/
#
# load simulation trajectories 1/6 = 1->2 :
load srp_assembly_12_00.pdb,srp,1
load srp_assembly_12_01.pdb,srp,2
load srp_assembly_12_02.pdb,srp,3
load srp_assembly_12_03.pdb,srp,4
load srp_assembly_12_04.pdb,srp,5
load srp_assembly_12_05.pdb,srp,6
load srp_assembly_12_06.pdb,srp,7
load srp_assembly_12_07.pdb,srp,8
load srp_assembly_12_08.pdb,srp,9
load srp_assembly_12_09.pdb,srp,10
load srp_assembly_12_10.pdb,srp,11
load srp_assembly_12_11.pdb,srp,12
load srp_assembly_12_12.pdb,srp,13
load srp_assembly_12_13.pdb,srp,14
load srp_assembly_12_14.pdb,srp,15
load srp_assembly_12_15.pdb,srp,16
load srp_assembly_12_16.pdb,srp,17
load srp_assembly_12_17.pdb,srp,18
load srp_assembly_12_18.pdb,srp,19
load srp_assembly_12_19.pdb,srp,20
load srp_assembly_12_20.pdb,srp,21
load srp_assembly_12_21.pdb,srp,22
load srp_assembly_12_22.pdb,srp,23
load srp_assembly_12_23.pdb,srp,24
load srp_assembly_12_24.pdb,srp,25
load srp_assembly_12_25.pdb,srp,26
load srp_assembly_12_26.pdb,srp,27
load srp_assembly_12_27.pdb,srp,28
load srp_assembly_12_28.pdb,srp,29
load srp_assembly_12_29.pdb,srp,30
load srp_assembly_12_30.pdb,srp,31
load srp_assembly_12_31.pdb,srp,32
#
# load simulation trajectories 2/6 = 2->3 :
load srp_assembly_23_00.pdb,srp,33
load srp_assembly_23_01.pdb,srp,34
load srp_assembly_23_02.pdb,srp,35
load srp_assembly_23_03.pdb,srp,36
load srp_assembly_23_04.pdb,srp,37
load srp_assembly_23_05.pdb,srp,38
load srp_assembly_23_06.pdb,srp,39
load srp_assembly_23_07.pdb,srp,40
load srp_assembly_23_08.pdb,srp,41
load srp_assembly_23_09.pdb,srp,42
load srp_assembly_23_10.pdb,srp,43
load srp_assembly_23_11.pdb,srp,44
load srp_assembly_23_12.pdb,srp,45
load srp_assembly_23_13.pdb,srp,46
load srp_assembly_23_14.pdb,srp,47
load srp_assembly_23_15.pdb,srp,48
load srp_assembly_23_16.pdb,srp,49
load srp_assembly_23_17.pdb,srp,50
load srp_assembly_23_18.pdb,srp,51
load srp_assembly_23_19.pdb,srp,52
load srp_assembly_23_20.pdb,srp,53
load srp_assembly_23_21.pdb,srp,54
load srp_assembly_23_22.pdb,srp,55
load srp_assembly_23_23.pdb,srp,56
load srp_assembly_23_24.pdb,srp,57
load srp_assembly_23_25.pdb,srp,58
load srp_assembly_23_26.pdb,srp,59
load srp_assembly_23_27.pdb,srp,60
load srp_assembly_23_28.pdb,srp,61
load srp_assembly_23_29.pdb,srp,62
load srp_assembly_23_30.pdb,srp,63
load srp_assembly_23_31.pdb,srp,64
#
# load simulation trajectories 3/6 = 3->4 :
load srp_assembly_34_00.pdb,srp,65
load srp_assembly_34_01.pdb,srp,66
load srp_assembly_34_02.pdb,srp,67
load srp_assembly_34_03.pdb,srp,68
load srp_assembly_34_04.pdb,srp,69
load srp_assembly_34_05.pdb,srp,70
load srp_assembly_34_06.pdb,srp,71
load srp_assembly_34_07.pdb,srp,72
load srp_assembly_34_08.pdb,srp,73
load srp_assembly_34_09.pdb,srp,74
load srp_assembly_34_10.pdb,srp,75
load srp_assembly_34_11.pdb,srp,76
load srp_assembly_34_12.pdb,srp,77
load srp_assembly_34_13.pdb,srp,78
load srp_assembly_34_14.pdb,srp,79
load srp_assembly_34_15.pdb,srp,80
load srp_assembly_34_16.pdb,srp,81
load srp_assembly_34_17.pdb,srp,82
load srp_assembly_34_18.pdb,srp,83
load srp_assembly_34_19.pdb,srp,84
load srp_assembly_34_20.pdb,srp,85
load srp_assembly_34_21.pdb,srp,86
load srp_assembly_34_22.pdb,srp,87
load srp_assembly_34_23.pdb,srp,88
load srp_assembly_34_24.pdb,srp,89
load srp_assembly_34_25.pdb,srp,90
load srp_assembly_34_26.pdb,srp,91
load srp_assembly_34_27.pdb,srp,92
load srp_assembly_34_28.pdb,srp,93
load srp_assembly_34_29.pdb,srp,94
load srp_assembly_34_30.pdb,srp,95
load srp_assembly_34_31.pdb,srp,96
#
# load simulation trajectories 4/6 = 4->3 :
# skip first frame as it's the same as the last one from 3/6:
#    load srp_assembly_34_31.pdb,srp,97
load srp_assembly_34_30.pdb,srp,97
load srp_assembly_34_29.pdb,srp,98
load srp_assembly_34_28.pdb,srp,99
load srp_assembly_34_27.pdb,srp,100
load srp_assembly_34_26.pdb,srp,101
load srp_assembly_34_25.pdb,srp,102
load srp_assembly_34_24.pdb,srp,103
load srp_assembly_34_23.pdb,srp,104
load srp_assembly_34_22.pdb,srp,105
load srp_assembly_34_21.pdb,srp,106
load srp_assembly_34_20.pdb,srp,107
load srp_assembly_34_19.pdb,srp,108
load srp_assembly_34_18.pdb,srp,109
load srp_assembly_34_17.pdb,srp,110
load srp_assembly_34_16.pdb,srp,111
load srp_assembly_34_15.pdb,srp,112
load srp_assembly_34_14.pdb,srp,113
load srp_assembly_34_13.pdb,srp,114
load srp_assembly_34_12.pdb,srp,115
load srp_assembly_34_11.pdb,srp,116
load srp_assembly_34_10.pdb,srp,117
load srp_assembly_34_09.pdb,srp,118
load srp_assembly_34_08.pdb,srp,119
load srp_assembly_34_07.pdb,srp,120
load srp_assembly_34_06.pdb,srp,121
load srp_assembly_34_05.pdb,srp,122
load srp_assembly_34_04.pdb,srp,123
load srp_assembly_34_03.pdb,srp,124
load srp_assembly_34_02.pdb,srp,125
load srp_assembly_34_01.pdb,srp,126
load srp_assembly_34_00.pdb,srp,127
#
# load simulation trajectories 5/6 = 3->2 :
load srp_assembly_23_31.pdb,srp,128
load srp_assembly_23_30.pdb,srp,129
load srp_assembly_23_29.pdb,srp,130
load srp_assembly_23_28.pdb,srp,131
load srp_assembly_23_27.pdb,srp,132
load srp_assembly_23_26.pdb,srp,133
load srp_assembly_23_25.pdb,srp,134
load srp_assembly_23_24.pdb,srp,135
load srp_assembly_23_23.pdb,srp,136
load srp_assembly_23_22.pdb,srp,137
load srp_assembly_23_21.pdb,srp,138
load srp_assembly_23_20.pdb,srp,139
load srp_assembly_23_19.pdb,srp,140
load srp_assembly_23_18.pdb,srp,141
load srp_assembly_23_17.pdb,srp,142
load srp_assembly_23_16.pdb,srp,143
load srp_assembly_23_15.pdb,srp,144
load srp_assembly_23_14.pdb,srp,145
load srp_assembly_23_13.pdb,srp,146
load srp_assembly_23_12.pdb,srp,147
load srp_assembly_23_11.pdb,srp,148
load srp_assembly_23_10.pdb,srp,149
load srp_assembly_23_09.pdb,srp,150
load srp_assembly_23_08.pdb,srp,151
load srp_assembly_23_07.pdb,srp,152
load srp_assembly_23_06.pdb,srp,153
load srp_assembly_23_05.pdb,srp,154
load srp_assembly_23_04.pdb,srp,155
load srp_assembly_23_03.pdb,srp,156
load srp_assembly_23_02.pdb,srp,157
load srp_assembly_23_01.pdb,srp,158
load srp_assembly_23_00.pdb,srp,159
#
# load simulation trajectories (6/6 = 2->1):
load srp_assembly_12_31.pdb,srp,160
load srp_assembly_12_30.pdb,srp,161
load srp_assembly_12_29.pdb,srp,162
load srp_assembly_12_28.pdb,srp,163
load srp_assembly_12_27.pdb,srp,164
load srp_assembly_12_26.pdb,srp,165
load srp_assembly_12_25.pdb,srp,166
load srp_assembly_12_24.pdb,srp,167
load srp_assembly_12_23.pdb,srp,168
load srp_assembly_12_22.pdb,srp,169
load srp_assembly_12_21.pdb,srp,170
load srp_assembly_12_20.pdb,srp,171
load srp_assembly_12_19.pdb,srp,172
load srp_assembly_12_18.pdb,srp,173
load srp_assembly_12_17.pdb,srp,174
load srp_assembly_12_16.pdb,srp,175
load srp_assembly_12_15.pdb,srp,176
load srp_assembly_12_14.pdb,srp,177
load srp_assembly_12_13.pdb,srp,178
load srp_assembly_12_12.pdb,srp,179
load srp_assembly_12_11.pdb,srp,180
load srp_assembly_12_10.pdb,srp,181
load srp_assembly_12_09.pdb,srp,182
load srp_assembly_12_08.pdb,srp,183
load srp_assembly_12_07.pdb,srp,184
load srp_assembly_12_06.pdb,srp,185
load srp_assembly_12_05.pdb,srp,186
load srp_assembly_12_04.pdb,srp,187
load srp_assembly_12_03.pdb,srp,188
load srp_assembly_12_02.pdb,srp,189
load srp_assembly_12_01.pdb,srp,190
# skip last frame as it's the same as the first one from 1/6:
#    load srp_assembly_12_00.pdb,srp,191
#
# define 249 frame movie:
mset 1 1 x8 1 -32   32 32 x8 32 -64   64 64 x8 64 -96   96 96 x8 96 -127   127 127 x8 127 -159   159 159 x8 159 -190 
#
# set proper orientation:
set_view (\
    -0.307021171,    0.115307309,    0.944758773,\
     0.111839555,    0.990128100,   -0.084512204,\
    -0.945174038,    0.079682365,   -0.316885203,\
     0.000000000,   10.000000000, -422.311248779,\
    96.711807251,  108.405914307,   43.255210876,\
   133.480957031,  733.480957031,    0.000000000 )
# set slab:
clip slab, 300
# specify representation features:
cartoon tube, (chain a)
cartoon automatic, (chain b or chain c)
set cartoon_fancy_helices = 1
set cartoon_flat_sheets = 1
set cartoon_smooth_loops = 1
show cartoon
# NOTE: all residue numbers below are -111 compared to real ones! (1 = 112 etc.)
# color SRP19 in blue:
color marine, chain b
# color SRP54 in dark green:
color forest, chain c
# first, homogeneously color the whole SRP RNA:
color yellow, chain a
# color SRP RNA helix 5:
#color yellow, (chain a and (resi 1:17 or resi 111:128))
color cyan, (chain a and (resi 1:17 or resi 111:128))
# color SRP RNA helix 6:
#color yellow, (chain a and (resi 18:57))
color green, (chain a and (resi 18:57))
# color nt 172,173:
color blue, (chain a and (resi 61:62))
# color nt 183-186 and 213,214:
color red, (chain a and (resi 72:75 or resi 102,103))
# color nt 191-194 and 205-208:
color orange, (chain a and (resi 80:83 or resi 94:97))
# hide all atoms:
hide lines
# now show "hot" nucleotides in stick representation:
show stick, (chain a and (resi 61:62 or resi 72:75 or resi 102:103 or resi 80:83 or resi 94:97))
# and also show helix 6 and helix 5 nt involved in A-minor interactions:
# (helix 6 nt 135-136, nt 161-162)
show stick, (chain a and (resi 24:25 or resi 50:51))
# (helix 5 nt 126-127, nt 223-224)
show stick, (chain a and (resi 15:16 or resi 112:113))
# hide atoms that stick out of the backbone tube for simplifying the view:
hide stick, (chain a and (name o1p or name o2p or name o3* or name o2*))
# crank-up the glossyness of rendered atoms:
set spec_power = 200
set spec_refl = 2.0
#
# go to the first frame of the first sweep:
frame 1
# go to correct directory for movie frame output:
cd /Users/luca/srp_assembly/png_frames/
# set screen/output PNG file size:
viewport 1024,768
# turn ray tracing on:
set ray_trace_frame = 1
# turn antialias on:
set antialias = 1
# turn off caching:
set cache_frames = 0
# output rendered movie frames in PNG format:
mpng srp_assembly, 1
# tell me when you're done!
system echo " *** FINISHED ***"