| 1 | UCSF ChimeraX version: 1.0 (2020-06-04)
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| 2 | © 2016-2020 Regents of the University of California. All rights reserved.
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| 3 | open /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs format session
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| 4 | Log from Mon Jul 6 18:47:44 2020opened ChimeraX session
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| 5 | show #10 models
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| 6 | hide #10 models
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| 7 | close #10
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| 8 | hide #12 models
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| 9 | open /Users/fbsrfr/process/20200214_newfigure1/microtubule_smooth1.8_scalesh4k_thr3k_zone15.mrcOpened microtubule_smooth1.8_scalesh4k_thr3k_zone15.mrc, grid size 823,411,157, pixel 1, shown at level 1.85e+03, step 2, values float32
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| 10 | volume #10 level 1317
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| 11 | volume #10 level 2215
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| 12 | volume #10 color #ffff0a
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| 13 | show #12 models
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| 14 | hide #12 models
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| 15 | close #12
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| 16 | hide #!6 models
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| 17 | open /Users/fbsrfr/process/20200214_newfigure1/test_actin2_PA_more_PA_more_PA_more_PA_more_PtsAdded_smooth1.8_scalesh4k_th3k_zone5.mrcOpened test_actin2_PA_more_PA_more_PA_more_PA_more_PtsAdded_smooth1.8_scalesh4k_th3k_zone5.mrc, grid size 805,431,289, pixel 1, shown at level 5.37e+03, step 2, values float32
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| 18 | volume #12 level 4073
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| 19 | volume #12 level 3929
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| 20 | volume #12 color #fd8008
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| 21 | volume #12 color #fecc66
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| 22 | volume #12 color #fecc66fb
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| 23 | volume #12 color #fecc66ef
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| 24 | volume #12 color #fecc66db
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| 25 | volume #12 color #fecc66d7
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| 26 | volume #12 color #fecc66cb
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| 27 | volume #12 color #fecc66c0
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| 28 | volume #12 color #fecc66ab
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| 29 | volume #12 color #fecc66a8
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| 30 | volume #12 color #fecc668e
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| 31 | volume #12 color #fecc6680
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| 32 | volume #12 color #fecc6689
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| 33 | volume #12 color #fecc668a
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| 34 | volume #12 color #fecc668c
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| 35 | volume #12 color #fecc668e
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| 36 | volume #12 color #fecc668f
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| 37 | volume #12 color #fecc6698
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| 38 | volume #12 color #fecc6699
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| 39 | volume #12 color #fecc669a
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| 40 | volume #12 color #fecc669b
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| 41 | volume #12 color #fecc669f
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| 42 | volume #12 color #fecc66a2
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| 43 | volume #12 color #fecc66af
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| 44 | volume #12 color #fecc66c3
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| 45 | volume #12 color #fecc66c9
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| 46 | volume #12 color #fecc66d8
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| 47 | volume #12 color #fecc66d9
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| 48 | volume #12 color #fecc66e0
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| 49 | volume #12 color #fecc66e1
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| 50 | volume #12 color #fecc66de
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| 51 | volume #12 color #fecc66dd
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| 52 | volume #12 color #fecc66db
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| 53 | volume #12 color #fecc66d7
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| 54 | volume #12 color #fecc66cb
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| 55 | volume #12 color #fecc66ca
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| 56 | volume #12 color #fecc66c8
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| 57 | volume #12 color #fecc66c5
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| 58 | volume #12 color #fecc66c4
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| 59 | volume #12 color #fecc66b8
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| 60 | volume #12 color #fecc66b6
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| 61 | volume #12 color #fecc66b7
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| 62 | volume #12 color #fecc66b9
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| 63 | volume #12 color #fecc66c4
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| 64 | volume #12 color #fecc66c5
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| 65 | open /Users/fbsrfr/process/20200214_newfigure1/jnk/cleft_cleftmatrix_sc4k_zone.mrcOpened cleft_cleftmatrix_sc4k_zone.mrc, grid size 283,41,84, pixel 1, shown at level 4.19e+03, step 1, values float32
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| 66 | volume #15 level 2329
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| 67 | volume #15 level 1877
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| 68 | volume #15 color #fd6fcf
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| 69 | volume #15 color #66ccff
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| 70 | volume #15 color #21ff80
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| 71 | volume #15 color #808003
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| 72 | volume #15 color #fd6666
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| 73 | volume #15 color #fc0107
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| 74 | volume #15 color #804002
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| 75 | volume #15 color #808003
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| 76 | volume #15 color #108001
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| 77 | volume #15 color #108080
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| 78 | volume #15 color #074080
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| 79 | volume #15 color #0f80ff
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| 80 | undo
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| 81 | redo
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| 82 | hide #!12 models
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| 83 | show #!12 models
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| 84 | hide #!6 models
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| 85 | show #!6 models
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| 86 | hide #!6 models
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| 87 | show #!6 models
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| 88 | hide #!6 models
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| 89 | save /Users/fbsrfr/Desktop/image3.png supersample 3
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| 90 | ui tool show "Side View"
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| 91 | save /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs includeMaps false
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| 92 | save /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs includeMaps true
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| 93 | movie record
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| 94 | turn y 2 180
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| 95 | wait 180
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| 96 | movie encode /Users/fbsrfr/Desktop/movie3.mp4Movie saved to /Users/fbsrfr/Desktop/movie3.mp4
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| 97 |
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| 98 | Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000299aee0> contents scale of 2 - updating layer to match.
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| 99 | Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000299aee0> contents scale of 2 - updating layer to match.
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| 100 | set bgColor white
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| 101 | save /Users/fbsrfr/Desktop/image3.png supersample 3
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| 102 | lighting full
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| 103 | save /Users/fbsrfr/Desktop/image4.png supersample 3
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| 104 | lighting shadows false
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| 105 | lighting shadows true
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| 106 | lighting full
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| 107 | lighting full
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| 108 | lighting direction -1,-1,-1
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| 109 | lighting direction 1,1,1
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| 110 | lighting direction 1,1,-1
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| 111 | lighting direction 1,-1,1
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| 112 | lighting direction -1,-1,1
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| 113 | lighting direction -1,1,1
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| 114 | lighting direction -1,1,-1
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| 115 | lighting direction -1,1,-.5
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| 116 | lighting direction -1,.5,-.5
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| 117 | lighting direction -1,-.5,-.5
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| 118 | lighting direction 1,-.5,-.5
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| 119 | lighting direction -1,-.5,-.5
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| 120 | lighting direction -1,-.5,0
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| 121 | lighting direction -1,-.5,-0.5
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| 122 | lighting direction -1,0,-0.5
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| 123 | lighting direction -1,-.5,1
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| 124 | lighting direction -1,-.5,-1
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| 125 | lighting direction -.5,-.5,-1
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| 126 | lighting direction .5,-.5,-1
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| 127 | lighting direction .5,.5,-1
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| 128 | lighting direction -.5,.5,-1
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| 129 | lighting direction .5,-.5,-1
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| 130 | lighting direction -1,-.5,-1
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| 131 | lighting direction -.,-.5,-1
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| 132 | Invalid "direction" argument: Expected a number
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| 133 | lighting direction -.9,-.5,-1
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| 134 | lighting direction -.7,-.5,-1
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| 135 | lighting direction -.7,-.2,-1
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| 136 | lighting direction -.7,-.9,-1
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| 137 | lighting direction -.7,.9,-1
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| 138 | lighting direction -.7,0.3,-1
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| 139 | lighting direction -.7,-0.3,-1
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| 140 | lighting direction -.7,-0.5,-1
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| 141 | lighting direction -.5,-0.5,-1
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| 142 | lighting direction -.5,-0.6,-1
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| 143 | lighting direction -.5,-0.8,-1
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| 144 | lighting direction -.5,-0.2,-1
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| 145 | lighting full
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| 146 | lighting shadows false
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| 147 | save /Users/fbsrfr/Desktop/image5.png supersample 3
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| 148 | lighting soft
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| 149 | lighting full
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| 150 | lighting soft
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| 151 | save /Users/fbsrfr/Desktop/image6.png supersample 3
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| 152 | lighting soft
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| 153 | lighting soft
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| 154 | lighting full
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| 155 | lighting soft
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| 156 | lighting soft
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| 157 | save /Users/fbsrfr/Desktop/image7.png supersample 3
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| 158 | lighting soft direction -.5,-0.2,-1
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| 159 | lighting full
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| 160 | lighting soft
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| 161 | lighting full
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| 162 | lighting soft
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| 163 | lighting direction -.5,-0.2,-1
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| 164 | lighting full
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| 165 | lighting direction 1,-1,-1
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| 166 | lighting soft
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| 167 | lighting soft
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| 168 | lighting full
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| 169 | lighting direction -.5,-0.2,-1
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| 170 | lighting soft
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| 171 | lighting full
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| 172 | lighting soft
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| 173 | lighting direction -.5,-0.2,-1
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| 174 | lighting direction -.5,0.2,-1
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| 175 | lighting direction -.5,-0.8,-1
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| 176 | lighting light direction -.5,-0.8,-1
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| 177 | Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword
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| 178 | lighting soft direction -.5,-0.8,-1
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| 179 | lighting soft direction -.5,-0.2,-1
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| 180 | lighting full
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| 181 | lighting soft
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| 182 | lighting soft direction -.1,-0.2,-1
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| 183 | lighting soft direction -.15-0.2,-1
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| 184 | Invalid "direction" argument: Expected a number
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| 185 | lighting soft direction -.5-0.2,-1
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| 186 | Invalid "direction" argument: Expected a number
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| 187 | lighting soft direction -.5,-0.2,-1
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| 188 | lighting full
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| 189 | save /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs includeMaps true
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| 190 | save /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs includeMaps false
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| 191 | close session
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| 192 | open /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_aligned_bin4_sirt5_inv.recOpened D04_TS_10_aligned_bin4_sirt5_inv.rec, grid size 960,928,187, pixel 11.9,11.9,11.9, shown at level 2.15e+03, step 4, values float32
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| 193 | set bgColor black
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| 194 | volume scale shift 4000
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| 195 | Missing or invalid "volumes" argument: invalid density maps specifier
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| 196 | volume #1 scale shift 4000
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| 197 | Expected a keyword
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| 198 | volume scale #1 shift 4000
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| 199 | volume #2 level 4696
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| 200 | ui mousemode right "mark point"
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| 201 | marker #3 position 4705,5969,2556 color yellow radius 1
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| 202 | marker change #3 radius 20
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| 203 | ui mousemode right "move markers"
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| 204 | marker change #3:1 position 4609,5951,2527
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| 205 | ui tool show "Side View"
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| 206 | hide #!2 models
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| 207 | show #!2 models
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| 208 | cofr sel
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| 209 | lighting simple
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| 210 | marker change #3:1 position 4602,5944,2521
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| 211 | marker change #3:1 position 4608,5950,2523
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| 212 | ui mousemode right "mark point"
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| 213 | marker #3 position 3915,6787,2677 color yellow radius 20
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| 215 | ui mousemode right "move markers"
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| 216 | marker change #3:3 position 4641,6297,2117
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| 222 | ui mousemode right "mark point"
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| 223 | marker #3 position 4677,6106,1458 color yellow radius 20
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| 224 | ui mousemode right "move markers"
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| 225 | marker change #3:4 position 4505,5999,1928
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| 226 | marker change #3:4 position 4764,5902,2197
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| 227 | marker change #3:4 position 4774,5897,2019
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| 228 | volume #1 color #ffff0a
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| 230 | volume #2 color #ffff0a
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| 231 | volume #2 color #ffff66
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| 232 | volume #2 color #f5ffbf
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| 233 | volume #2 color #aeffa5
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| 234 | volume #2 color #caffc1
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| 235 | ui mousemode right "mark point"
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| 236 | marker #3 position 4800,5789,2406 color yellow radius 20
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| 291 | marker #3 position 4379,6222,1862 color yellow radius 20
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| 292 | marker #3 position 4401,6165,1760 color yellow radius 20
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| 293 | volume #2 color #caffc1fe
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| 294 | volume #2 color #caffc1fa
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| 295 | volume #2 color #caffc1f8
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| 296 | volume #2 color #caffc1f2
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| 297 | volume #2 color #caffc1ef
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| 298 | volume #2 color #caffc1eb
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| 299 | volume #2 color #caffc1e9
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| 300 | volume #2 color #caffc1e7
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| 301 | volume #2 color #caffc1e5
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| 302 | volume #2 color #caffc1e4
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| 303 | volume #2 color #caffc1e0
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| 304 | volume #2 color #caffc1df
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| 306 | volume #2 color #caffc1da
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| 310 | volume #2 color #caffc1d0
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| 311 | volume #2 color #caffc1cd
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| 312 | volume #2 color #caffc1ca
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| 313 | volume #2 color #caffc1c9
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| 314 | volume #2 color #caffc1c6
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| 315 | volume #2 color #caffc1c3
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| 316 | volume #2 color #caffc1c2
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| 317 | volume #2 color #caffc1c0
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| 318 | volume #2 color #caffc1bf
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| 319 | volume #2 color #caffc1bd
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| 320 | volume #2 color #caffc1b9
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| 321 | volume #2 color #caffc1af
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| 322 | volume #2 color #caffc1a8
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| 323 | volume #2 color #caffc1a3
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| 324 | volume #2 color #caffc19e
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| 325 | volume #2 color #caffc19a
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| 326 | volume #2 color #caffc194
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| 327 | volume #2 color #caffc190
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| 328 | volume #2 color #caffc18b
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| 329 | volume #2 color #caffc182
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| 330 | volume #2 color #caffc17d
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| 331 | volume #2 color #caffc178
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| 332 | volume #2 color #caffc174
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| 333 | volume #2 color #caffc171
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| 334 | volume #2 color #caffc16c
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| 335 | volume #2 color #caffc16a
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| 336 | volume #2 color #caffc168
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| 337 | volume #2 color #caffc165
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| 338 | volume #2 color #caffc164
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| 339 | volume #2 color #caffc165
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| 340 | volume #2 color #caffc167
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| 341 | volume #2 color #caffc168
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|---|
| 342 | volume #2 color #caffc16c
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| 343 | volume #2 color #caffc16e
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| 344 | volume #2 color #caffc172
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| 345 | volume #2 color #caffc175
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| 346 | volume #2 color #caffc178
|
|---|
| 347 | volume #2 color #caffc17c
|
|---|
| 348 | volume #2 color #caffc17d
|
|---|
| 349 | marker #3 position 4701,5475,2131 color yellow radius 20
|
|---|
| 350 | marker #3 position 4549,5412,2391 color yellow radius 20
|
|---|
| 351 | marker #3 position 4777,5380,2608 color yellow radius 20
|
|---|
| 352 | marker #3 position 5021,5658,2721 color yellow radius 20
|
|---|
| 353 | marker #3 position 4566,6248,2296 color yellow radius 20
|
|---|
| 354 | marker #3 position 4723,6057,1683 color yellow radius 20
|
|---|
| 355 | marker #3 position 4696,6084,1642 color yellow radius 20
|
|---|
| 356 | marker #3 position 4832,5941,1649 color yellow radius 20
|
|---|
| 357 | marker #3 position 4663,6122,1686 color yellow radius 20
|
|---|
| 358 | marker #3 position 4967,5620,2373 color yellow radius 20
|
|---|
| 359 | marker #3 position 5027,5525,2321 color yellow radius 20
|
|---|
| 360 | marker #3 position 5092,5613,2434 color yellow radius 20
|
|---|
| 361 | marker #3 position 5043,5488,2476 color yellow radius 20
|
|---|
| 362 | marker #3 position 4846,5355,2351 color yellow radius 20
|
|---|
| 363 | marker #3 position 5067,5481,2258 color yellow radius 20
|
|---|
| 364 | marker #3 position 5024,5723,1955 color yellow radius 20
|
|---|
| 365 | marker #3 position 5070,5741,2087 color yellow radius 20
|
|---|
| 366 | marker #3 position 4356,6176,2304 color yellow radius 20
|
|---|
| 367 | marker #3 position 4354,6230,2301 color yellow radius 20
|
|---|
| 368 | marker #3 position 4506,6197,2166 color yellow radius 20
|
|---|
| 369 | marker #3 position 4589,6237,1887 color yellow radius 20
|
|---|
| 370 | marker #3 position 4645,6239,1795 color yellow radius 20
|
|---|
| 371 | marker #3 position 4848,5961,2815 color yellow radius 20
|
|---|
| 372 | marker #3 position 4766,6158,2672 color yellow radius 20
|
|---|
| 373 | marker #3 position 4905,6219,2359 color yellow radius 20
|
|---|
| 374 | marker #3 position 4966,6158,2052 color yellow radius 20
|
|---|
| 375 | marker #3 position 4654,6124,1918 color yellow radius 20
|
|---|
| 376 | marker #3 position 4751,6302,2285 color yellow radius 20
|
|---|
| 377 | marker #3 position 4741,5827,1950 color yellow radius 20
|
|---|
| 378 | marker #3 position 4764,5904,1945 color yellow radius 20
|
|---|
| 379 | marker #3 position 4710,5969,1945 color yellow radius 20
|
|---|
| 380 | marker #3 position 4675,5958,1941 color yellow radius 20
|
|---|
| 381 | marker #3 position 4649,5889,1920 color yellow radius 20
|
|---|
| 382 | marker #3 position 4738,5995,2413 color yellow radius 20
|
|---|
| 383 | hide #3 models
|
|---|
| 384 | show #3 models
|
|---|
| 385 | hide #!2 modelsDrag select of 87 atoms
|
|---|
| 386 | show #!2 models
|
|---|
| 387 | volume zone #3 nearAtoms #50 range 10 newMap trueno atoms specified for zone
|
|---|
| 388 | volume zone #2 nearAtoms #3 range 10 newMap true
|
|---|
| 389 | volume #4 level 1648
|
|---|
| 390 | volume #4 level 816
|
|---|
| 391 | select #395 atoms, 1 model selected
|
|---|
| 392 | close #4
|
|---|
| 393 | volume zone #2 nearAtoms #3 range 10 newMap true
|
|---|
| 394 | volume #4 level 1762
|
|---|
| 395 | hide #3 models
|
|---|
| 396 | show #3 models
|
|---|
| 397 | close #4
|
|---|
| 398 | show #!2 models
|
|---|
| 399 | volume zone #2 nearAtoms #3 range 100 newMap true
|
|---|
| 400 | close #4
|
|---|
| 401 | volume zone #2 nearAtoms #3 range 160 newMap true
|
|---|
| 402 | volume #4 step 1
|
|---|
| 403 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrin_vesicle.cmm format markers models #13Wrote 0 marker sets containing 0 markers
|
|---|
| 404 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrin_vesicle.cmm format markers models #3Wrote 1 marker sets containing 95 markers
|
|---|
| 405 | volume #4 level 3815
|
|---|
| 406 | volume #4 level 4558
|
|---|
| 407 | ~select #3Nothing selected
|
|---|
| 408 | select #395 atoms, 1 model selected
|
|---|
| 409 | hide #3 models
|
|---|
| 410 | volume #4 level 4109
|
|---|
| 411 | volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
|
|---|
| 412 | volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
|
|---|
| 413 | show #3 models
|
|---|
| 414 | select /M:5@M1 atom, 1 model selected
|
|---|
| 415 | color radiall #4 centre sel rainbow
|
|---|
| 416 | Expected a keyword
|
|---|
| 417 | color radiall #4 centre sel
|
|---|
| 418 | Expected a keyword
|
|---|
| 419 | color radiall #4 center sel
|
|---|
| 420 | color radiall #4 center sel rainbow
|
|---|
| 421 | Expected a keyword
|
|---|
| 422 | hide #!4 models
|
|---|
| 423 | show #!4 models
|
|---|
| 424 | hide #!4 models
|
|---|
| 425 | show #!4 models
|
|---|
| 426 | color radiall #4 center sel
|
|---|
| 427 | volume #4 level 3071
|
|---|
| 428 | volume zone #2 nearAtoms #3 range 250 newMap true
|
|---|
| 429 | select #395 atoms, 1 model selected
|
|---|
| 430 | ~select #3Nothing selected
|
|---|
| 431 | close #5
|
|---|
| 432 | select upNothing selected
|
|---|
| 433 | select downNothing selected
|
|---|
| 434 | select upNothing selected
|
|---|
| 435 | select upNothing selected
|
|---|
| 436 | select downNothing selected
|
|---|
| 437 | select downNothing selected
|
|---|
| 438 | select downNothing selected
|
|---|
| 439 | select downNothing selected
|
|---|
| 440 | select downNothing selected
|
|---|
| 441 | select downNothing selected
|
|---|
| 442 | volume zone #2 nearAtoms #3 range 250 newMap true
|
|---|
| 443 | hide #!4 models
|
|---|
| 444 | volume #4 level 3213
|
|---|
| 445 | volume #4 level 2983
|
|---|
| 446 | volume #4 level 3726
|
|---|
| 447 | volume #5 level 2991
|
|---|
| 448 | volume #2 step 1
|
|---|
| 449 | hide #!2 modelsDrag select of
|
|---|
| 450 | Drag select of 95 atoms
|
|---|
| 451 | show #!2 models
|
|---|
| 452 | volume zone #2 nearAtoms #3 range 350 newMap false
|
|---|
| 453 | volume #2 color #caffc1b3
|
|---|
| 454 | volume #2 color #caffc1d7
|
|---|
| 455 | volume #2 color #caffc1e7
|
|---|
| 456 | volume #2 color #caffc1ed
|
|---|
| 457 | volume #2 color #caffc1f9
|
|---|
| 458 | volume #2 color #caffc1
|
|---|
| 459 | volume #2 color #4eff48
|
|---|
| 460 | volume #2 color #8484fc
|
|---|
| 461 | volume #2 color #9fb2fc
|
|---|
| 462 | volume #2 color #a5bbfd
|
|---|
| 463 | select /M:5@M1 atom, 1 model selected
|
|---|
| 464 | color radiall #2 center sel rainbow
|
|---|
| 465 | Expected a keyword
|
|---|
| 466 | color radiall #2 center sel
|
|---|
| 467 | volume zone #2 nearAtoms #3 range 350 newMap true
|
|---|
| 468 | color radiall #6 center sel
|
|---|
| 469 | volume #6 level 3621
|
|---|
| 470 | open /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_aligned_bin4_sirt5_smth1.3_inv.recOpened D04_TS_10_aligned_bin4_sirt5_smth1.3_inv.rec, grid size 960,928,187, pixel 11.9,11.9,11.9, shown at level 1.83e+03, step 4, values float32
|
|---|
| 471 | close #4
|
|---|
| 472 | close #5
|
|---|
| 473 | close #6
|
|---|
| 474 | volume scale #7 shift 4000
|
|---|
| 475 | volume #4 step 1
|
|---|
| 476 | volume #4 level 2654
|
|---|
| 477 | volume #4 level 3000
|
|---|
| 478 | volume #4 level 4000
|
|---|
| 479 | select up95 atoms, 1 model selected
|
|---|
| 480 | select up95 atoms, 9 models selected
|
|---|
| 481 | select down95 atoms, 1 model selected
|
|---|
| 482 | select down1 atom, 1 model selected
|
|---|
| 483 | volume zone #2 nearAtoms #3 range 350 newMap true
|
|---|
| 484 | volume zone #7 nearAtoms #3 range 350 newMap true
|
|---|
| 485 | show #!7 models
|
|---|
| 486 | hide #!6 models
|
|---|
| 487 | hide #!5 models
|
|---|
| 488 | hide #!4 models
|
|---|
| 489 | show #!4 models
|
|---|
| 490 | hide #!4 models
|
|---|
| 491 | hide #!7 models
|
|---|
| 492 | show #!7 models
|
|---|
| 493 | show #!6 models
|
|---|
| 494 | close #6
|
|---|
| 495 | show #!2 models
|
|---|
| 496 | hide #!2 models
|
|---|
| 497 | show #!2 models
|
|---|
| 498 | hide #!2 models
|
|---|
| 499 | show #!1 models
|
|---|
| 500 | hide #!1 models
|
|---|
| 501 | show #!4 models
|
|---|
| 502 | hide #!4 models
|
|---|
| 503 | show #!4 models
|
|---|
| 504 | hide #!4 models
|
|---|
| 505 | show #!4 models
|
|---|
| 506 | hide #!4 models
|
|---|
| 507 | show #!5 models
|
|---|
| 508 | hide #!7 models
|
|---|
| 509 | show #!7 models
|
|---|
| 510 | hide #!7 models
|
|---|
| 511 | close #7
|
|---|
| 512 | show #!4 models
|
|---|
| 513 | hide #3 models
|
|---|
| 514 | show #3 models
|
|---|
| 515 | hide #!4 models
|
|---|
| 516 | hide #!5 models
|
|---|
| 517 | show #!5 models
|
|---|
| 518 | volume #5 level 4326
|
|---|
| 519 | color radiall #5 center sel
|
|---|
| 520 | marker #3 position 4579,5911,2589 color yellow radius 20
|
|---|
| 521 | ui mousemode right "move markers"
|
|---|
| 522 | marker change #3:96 position 4489,6001,2463
|
|---|
| 523 | color radiall #5 center sel
|
|---|
| 524 | volume #5 level 3825
|
|---|
| 525 | select up96 atoms, 1 model selected
|
|---|
| 526 | select down2 atoms, 1 model selected
|
|---|
| 527 | volume zone #2 nearAtoms #3 range 300 newMap true
|
|---|
| 528 | hide #!5 models
|
|---|
| 529 | close #6
|
|---|
| 530 | volume zone #2 nearAtoms #3 range 270 newMap true
|
|---|
| 531 | close #6
|
|---|
| 532 | volume zone #2 nearAtoms #3 range 240 newMap true
|
|---|
| 533 | ui mousemode right "mark point"
|
|---|
| 534 | marker #3 position 5135,5931,2381 color yellow radius 20
|
|---|
| 535 | marker #3 position 5079,5876,2221 color yellow radius 20
|
|---|
| 536 | marker #3 position 5153,6011,2287 color yellow radius 20
|
|---|
| 537 | ui mousemode right "move markers"
|
|---|
| 538 | marker change #3:99 position 5159,5944,2222
|
|---|
| 539 | marker change #3:99 position 5140,5953,2185
|
|---|
| 540 | ui mousemode right "mark point"
|
|---|
| 541 | marker #3 position 5196,5770,2404 color yellow radius 20
|
|---|
| 542 | marker #3 position 5221,5786,2466 color yellow radius 20
|
|---|
| 543 | ui mousemode right "move markers"
|
|---|
| 544 | marker change #3:101 position 5231,5732,2463
|
|---|
| 545 | marker change #3:100 position 5217,5732,2422
|
|---|
| 546 | marker change #3:101 position 5262,5774,2337
|
|---|
| 547 | marker change #3:101 position 5231,5754,2343
|
|---|
| 548 | close #6
|
|---|
| 549 | volume zone #2 nearAtoms #3 range 240 newMap true
|
|---|
| 550 | volume #6 level 3992
|
|---|
| 551 | surface dust #6 size 120
|
|---|
| 552 | hide #3 models
|
|---|
| 553 | surface dust #6 size 220
|
|---|
| 554 | show #3 models
|
|---|
| 555 | marker delete selDeleted 2 markers
|
|---|
| 556 | marker delete selDeleted 4 markers
|
|---|
| 557 | volume zone #2 nearAtoms #3 range 200 newMap true
|
|---|
| 558 | hide #!6 models
|
|---|
| 559 | show #!6 models
|
|---|
| 560 | volume #7 level 4214
|
|---|
| 561 | volume #7 level 4010
|
|---|
| 562 | hide #!6 models
|
|---|
| 563 | show #!6 models
|
|---|
| 564 | hide #!6 models
|
|---|
| 565 | show #!6 models
|
|---|
| 566 | hide #!6 models
|
|---|
| 567 | select upNothing selected
|
|---|
| 568 | select upNothing selected
|
|---|
| 569 | select downNothing selected
|
|---|
| 570 | select downNothing selected
|
|---|
| 571 | select downNothing selected
|
|---|
| 572 | surface dust #7 size 220
|
|---|
| 573 | color radiall #7 center sel Drag select of
|
|---|
| 574 | color radiall #7 center sel
|
|---|
| 575 | volume #7 level 3825
|
|---|
| 576 | hide #3 models
|
|---|
| 577 | color cylinder radial #7 center sel
|
|---|
| 578 | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
|
|---|
| 579 | color cylinder radius #7 center sel
|
|---|
| 580 | Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
|
|---|
| 581 | scolor cylinder radius #7 center sel
|
|---|
| 582 | Unknown command: scolor cylinder radius #7 center sel
|
|---|
| 583 | color radiall #7 center sel goldred
|
|---|
| 584 | Expected a keyword
|
|---|
| 585 | color radiall #7 center sel gold,red
|
|---|
| 586 | Expected a keyword
|
|---|
| 587 | color radiall #7 center sel yelow,red
|
|---|
| 588 | Expected a keyword
|
|---|
| 589 | color radiall #7 center sel yelow, red
|
|---|
| 590 | Expected a keyword
|
|---|
| 591 | color radiall #7 center sel yelow-red
|
|---|
| 592 | Expected a keyword
|
|---|
| 593 | Fetching compressed palette yelow-red from http://www.colourlovers.com/api/palettes?keywords=yelow-red&format=json&numResults=100
|
|---|
| 594 | Could not find palette yelow-red at COLOURlovers.com using keyword search
|
|---|
| 595 | color radiall #7 center sel palette yelow:red
|
|---|
| 596 | Invalid "palette" argument: Invalid color name or specifier
|
|---|
| 597 | Fetching compressed palette goldred from http://www.colourlovers.com/api/palettes?keywords=goldred&format=json&numResults=100
|
|---|
| 598 | Could not find palette goldred at COLOURlovers.com using keyword search
|
|---|
| 599 | color radiall #7 center sel palette gold:red
|
|---|
| 600 | color radiall #7 center sel palette gold:0.7,red
|
|---|
| 601 | Invalid "palette" argument: Number of values and color must match in colormap
|
|---|
| 602 | color radiall #7 center sel palette gold:red,05
|
|---|
| 603 | Invalid "palette" argument: could not convert string to float: 'red'
|
|---|
| 604 | color radiall #7 center sel palette gold:0.5,red
|
|---|
| 605 | Invalid "palette" argument: Number of values and color must match in colormap
|
|---|
| 606 | color radiall #7 center sel palette 1,gold:0.5,red
|
|---|
| 607 | color radiall #7 center sel palette 0.5,gold:0.5,red
|
|---|
| 608 | color radiall #7 center sel palette 5,gold:0.5,red
|
|---|
| 609 | color radiall #7 center sel palette 5,gold:,red
|
|---|
| 610 | Invalid "palette" argument: could not convert string to float:
|
|---|
| 611 | color radiall #7 center sel palette 5,gold:0.1,red
|
|---|
| 612 | color radiall #7 center sel palette .2,gold:0.1,red
|
|---|
| 613 | color radiall #7 center sel palette 0.2,gold:0.1,red
|
|---|
| 614 | color radiall #7 center sel palette 0.2,gold:0.5,red
|
|---|
| 615 | color radiall #7 center sel palette 0.2,gold:0.2,red
|
|---|
| 616 | color radiall #7 center sel palette 0.2,gold:0.3,red
|
|---|
| 617 | color radiall #7 center sel palette 10,gold:5,red
|
|---|
| 618 | color radiall #7 center sel palette 10,gold:50,red
|
|---|
| 619 | color radiall #7 center sel palette 40,gold:50,red
|
|---|
| 620 | color radiall #7 center sel palette 50,gold:40,red
|
|---|
| 621 | color radiall #7 center sel palette 50,gold:45,red
|
|---|
| 622 | palette listNo custom palettes.
|
|---|
| 623 | 310 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8.
|
|---|
| 624 | color radiall #7 center sel palette accent
|
|---|
| 625 | close #3
|
|---|
| 626 | close #2
|
|---|
| 627 | close #1
|
|---|
| 628 | close #5
|
|---|
| 629 | close #6
|
|---|
| 630 | close #7
|
|---|
| 631 | open /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrinvesicle_mem_imod.cmmOpened 1 marker sets containing 71 markers
|
|---|
| 632 | volume #4 originIndex 0
|
|---|
| 633 | volume #4 voxelSize 1
|
|---|
| 634 | show #!4 models
|
|---|
| 635 | cofr #1
|
|---|
| 636 | hide #1 models
|
|---|
| 637 | show #1 models
|
|---|
| 638 | hide #!4 models
|
|---|
| 639 | show #!4 models
|
|---|
| 640 | volume #4 step 4
|
|---|
| 641 | open /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrinvesicle_clathrin_imod.cmmOpened 1 marker sets containing 140 markers
|
|---|
| 642 | hide #1 models
|
|---|
| 643 | show #1 models
|
|---|
| 644 | hide #2 models
|
|---|
| 645 | hide #!4 modelsDrag select of 71 atoms
|
|---|
| 646 | volume zone #2 nearAtoms sel range 50 newMap true
|
|---|
| 647 | volume zone #4 nearAtoms sel range 50 newMap true
|
|---|
| 648 | show #2 models
|
|---|
| 649 | close #3Drag select of 211 atoms
|
|---|
| 650 | volume zone #4 nearAtoms sel range 20 newMap true
|
|---|
| 651 | hide #1 models
|
|---|
| 652 | hide #2 models
|
|---|
| 653 | hide #!3 models
|
|---|
| 654 | show #2 models
|
|---|
| 655 | hide #2 models
|
|---|
| 656 | show #1 modelsDrag select of
|
|---|
| 657 | Drag select of 71 atoms
|
|---|
| 658 | show #!4 models
|
|---|
| 659 | hide #!4 models
|
|---|
| 660 | show #!3 models
|
|---|
| 661 | hide #1 models
|
|---|
| 662 | select up211 atoms, 6 models selected
|
|---|
| 663 | select up211 atoms, 6 models selected
|
|---|
| 664 | select down71 atoms, 1 model selected
|
|---|
| 665 | select down71 atoms, 1 model selected
|
|---|
| 666 | color radiall sel center sel palette accent
|
|---|
| 667 | show #2 models
|
|---|
| 668 | hide #2 models
|
|---|
| 669 | show #1 models
|
|---|
| 670 | hide #1 models
|
|---|
| 671 | show #1 models
|
|---|
| 672 | hide #1 models
|
|---|
| 673 | color radiall #3 center sel palette accent
|
|---|
| 674 | scolor #3 zone sel range 80 autoUpdate true
|
|---|
| 675 | Unknown command: scolor #3 zone sel range 80 autoUpdate true
|
|---|
| 676 | color zone #3 near sel distance 15 update true
|
|---|
| 677 | ~select #1Nothing selected
|
|---|
| 678 | select #2140 atoms, 1 model selected
|
|---|
| 679 | color zone #3 near sel distance 15 update true
|
|---|
| 680 | color zone #3 near sel distance 15 update true
|
|---|
| 681 | color zone #3 near sel distance 10 update true
|
|---|
| 682 | color zone #3 near sel distance 10 update true palette blue:red
|
|---|
| 683 | Expected a keyword
|
|---|
| 684 | volume #3 level 3660
|
|---|
| 685 | color zone #3 near sel distance 10 update true palette blue:red
|
|---|
| 686 | Expected a keyword
|
|---|
| 687 | color zone #3 near sel distance 10 update true
|
|---|
| 688 | surface dust #3 size 220
|
|---|
| 689 | surface dust #3 size 20
|
|---|
| 690 | color zone #3 near sel distance 10 update true palette rainbow
|
|---|
| 691 | Expected a keyword
|
|---|
| 692 | color zone #3 near sel distance 10 update true palette Accent
|
|---|
| 693 | Expected a keyword
|
|---|
| 694 | hide #!3 models
|
|---|
| 695 | show #2 models
|
|---|
| 696 | hide #2 models
|
|---|
| 697 | show #1 models
|
|---|
| 698 | select up211 atoms, 2 models selected
|
|---|
| 699 | select up211 atoms, 6 models selected
|
|---|
| 700 | select down211 atoms, 2 models selected
|
|---|
| 701 | select down141 atoms, 2 models selected
|
|---|
| 702 | color radiall #3 center sel palette gold:red
|
|---|
| 703 | show #!3 models
|
|---|
| 704 | hide #1 models
|
|---|
| 705 | hide #!3 models
|
|---|
| 706 | show #1 models
|
|---|
| 707 | show #!3 models
|
|---|
| 708 | hide #1 models
|
|---|
| 709 | color radiall #3 center sel palette gold:red
|
|---|
| 710 | color radiall #3 center sel palette gold:red
|
|---|
| 711 | color radiall #3 center sel palette 0.3,gold:0.7,red
|
|---|
| 712 | color radiall #3 center sel palette 0.3,gold:0.07,red
|
|---|
| 713 | color radiall #3 center sel palette 0.3,gold:0.1,red
|
|---|
| 714 | color radiall #3 center sel palette 0.3,gold:0.3,red
|
|---|
| 715 | color radiall #3 center sel palette 0.3,gold:0.29,red
|
|---|
| 716 | color radiall #3 center sel palette 0.3,gold:0.29,red:pink
|
|---|
| 717 | Invalid "palette" argument: Number of values and color must match in colormap
|
|---|
| 718 | color radiall #3 center sel palette 0.3,gold:red:0.29,pink
|
|---|
| 719 | Invalid "palette" argument: Number of values and color must match in colormap
|
|---|
| 720 | color radiall #3 center sel palette 0,gold:0.7,red:0.29,pink
|
|---|
| 721 | color radiall #3 center sel palette 0.5,gold:0.7,red:0.29,pink
|
|---|
| 722 | color radiall #3 center sel palette 0.5,gold:0.6,red:0.29,pink
|
|---|
| 723 | color radiall #3 center sel palette 10,gold:10,red:10,pink
|
|---|
| 724 | color radiall #3 center sel palette 30,gold:20,red:10,pink
|
|---|
| 725 | color radiall #3 center sel palette 50,pink:45,red:10,yellow
|
|---|
| 726 | show #1 models
|
|---|
| 727 | hide #1 models
|
|---|
| 728 | color cylindrical #3 centre sel palette 50,pink:45,red:10,yellow
|
|---|
| 729 | Expected a keyword
|
|---|
| 730 | hide #1 models
|
|---|
| 731 | hide #!3 models
|
|---|
| 732 | show #1 models
|
|---|
| 733 | select #1/M:62@M1 atom, 1 model selected
|
|---|
| 734 | select #1/M:48@M1 atom, 1 model selected
|
|---|
| 735 | hide #1 models
|
|---|
| 736 | show #2 models
|
|---|
| 737 | hide #2 models
|
|---|
| 738 | show #!3 models
|
|---|
| 739 | color cylindrical #3 axis sel palette 50,pink:45,red:10,yellow
|
|---|
| 740 | Invalid "axis" argument: Axis argument requires 2 atoms, got 3 atoms
|
|---|
| 741 | show #1 models
|
|---|
| 742 | hide #!3 models
|
|---|
| 743 | select #1/M:4@M1 atom, 1 model selected
|
|---|
| 744 | show #!3 models
|
|---|
| 745 | hide #1 models
|
|---|
| 746 | color cylindrical #3 axis sel palette 50,pink:45,red:10,yellow
|
|---|
| 747 | color cylindrical #3 axis sel palette 50,pink:45,red:30,yellow
|
|---|
| 748 | color cylindrical #3 axis sel palette 50,pink:45,red:20,yellow
|
|---|
| 749 | show #1 models
|
|---|
| 750 | hide #!3 models
|
|---|
| 751 | select #1/M:66@M1 atom, 1 model selected
|
|---|
| 752 | show #!3 models
|
|---|
| 753 | hide #1 models
|
|---|
| 754 | color cylindrical #3 axis sel palette 50,pink:45,red:20,yellow
|
|---|
| 755 | color cylindrical #3 axis sel palette 50,pink:48,red:20,yellow
|
|---|
| 756 | color cylindrical #3 axis sel palette 52,pink:48,red:20,yellow
|
|---|
| 757 | color cylindrical #3 axis sel palette 52,magenta:48,red:20,yellow
|
|---|
| 758 | color cylindrical #3 axis sel palette 55,magenta:48,red:20,yellow
|
|---|
| 759 | show #1 models
|
|---|
| 760 | hide #!3 models
|
|---|
| 761 | show #!3 models
|
|---|
| 762 | hide #1 models
|
|---|
| 763 | color cylindrical #3 axis sel palette 55,magenta:48,red:20,yellow
|
|---|
| 764 | volume #3 step 1
|
|---|
| 765 | volume #3 level 4009
|
|---|
| 766 | color cylindrical #3 axis sel palette 60,magenta:48,red:20,yellow
|
|---|
| 767 | color cylindrical #3 axis sel palette 70,magenta:48,red:20,yellow
|
|---|
| 768 | color cylindrical #3 axis sel palette 70,magenta:48,red:40,yellow
|
|---|
| 769 | color cylindrical #3 axis sel palette 70,magenta:48,red:40,yellow
|
|---|
| 770 | color cylindrical #3 axis sel palette 70,magenta:48,red:30,yellow
|
|---|
| 771 | color cylindrical #3 axis sel palette 70,magenta:48,red:25,yellow
|
|---|
| 772 | volume #1 surfaceSmoothing true smoothingIterations 3 smoothingFactor 0.3No volumes specified
|
|---|
| 773 | volume #4 surfaceSmoothing true smoothingIterations 3 smoothingFactor 0.3
|
|---|
| 774 | volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
|
|---|
| 775 | volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
|
|---|
| 776 | volume #3 level 3708
|
|---|
| 777 | volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
|
|---|
| 778 | surface dust #3 size 20
|
|---|
| 779 | surface dust #3 size 50
|
|---|
| 780 | surface dust #3 size 40
|
|---|
| 781 | surface dust #3 size 100
|
|---|
| 782 | surface dust #3 size 200
|
|---|
| 783 | surface dust #3 size 100
|
|---|
| 784 | volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.4
|
|---|
| 785 | volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.6
|
|---|
| 786 | ui mousemode right "map eraser"
|
|---|
| 787 | ui mousemode right "mark point"
|
|---|
| 788 | marker #1 position 349.9,542.7,125.1 color yellow radius 20
|
|---|
| 789 | show #2 models
|
|---|
| 790 | show #1 models
|
|---|
| 791 | marker change #1:102 radius 5
|
|---|
| 792 | ui mousemode right "move markers"
|
|---|
| 793 | marker change #1:102 position 340.5,536.7,125.1
|
|---|
| 794 | marker change #1:102 position 342.1,536.8,133.1
|
|---|
| 795 | ui mousemode right "mark point"
|
|---|
| 796 | marker #1 position 342.1,536.6,123.4 color yellow radius 5
|
|---|
| 797 | marker #1 position 342.4,536.7,127 color yellow radius 5
|
|---|
| 798 | marker #1 position 340.2,537.7,119.9 color yellow radius 5
|
|---|
| 799 | marker #1 position 337.5,539.3,114.7 color yellow radius 5
|
|---|
| 800 | marker #1 position 336.3,538.7,108.2 color yellow radius 5
|
|---|
| 801 | marker #1 position 345.8,535.6,138.4 color yellow radius 5
|
|---|
| 802 | marker #1 position 337.1,528.6,133.9 color yellow radius 5
|
|---|
| 803 | ui mousemode right "move markers"
|
|---|
| 804 | marker change #1:109 position 339.5,534.5,132.1
|
|---|
| 805 | marker change #1:109 position 338.6,535.4,127.1
|
|---|
| 806 | marker change #1:109 position 340.4,536.7,129
|
|---|
| 807 | marker change #1:109 position 340.6,536.5,125.1
|
|---|
| 808 | ui mousemode right "mark point"
|
|---|
| 809 | marker #1 position 335.1,527.2,129.6 color yellow radius 5
|
|---|
| 810 | ui mousemode right "move markers"
|
|---|
| 811 | marker change #1:110 position 340.9,537,129.6
|
|---|
| 812 | select #1/M:108@M1 atom, 1 model selected
|
|---|
| 813 | marker change #1:108 position 344.9,536.5,136.9
|
|---|
| 814 | select #1/M:110@M1 atom, 1 model selected
|
|---|
| 815 | marker change #1:110 position 340.1,536.5,129.3
|
|---|
| 816 | cofr sel
|
|---|
| 817 | ui mousemode right "map eraser"
|
|---|
| 818 | hide #1 models
|
|---|
| 819 | hide #2 models
|
|---|
| 820 | hide #!3 models
|
|---|
| 821 | show #!3 models
|
|---|
| 822 | select clear
|
|---|
| 823 | select clear
|
|---|
| 824 | select #33 models selected
|
|---|
| 825 | select clear
|
|---|
| 826 | select clear
|
|---|
| 827 | select clear
|
|---|
| 828 | select clear
|
|---|
| 829 | hide #!3 modelsDrag select of eraser sphere, 6 of 1000 triangles
|
|---|
| 830 | show #!3 models
|
|---|
| 831 | volume erase #3 center 332.43,552.34,106.68 radius 16.8
|
|---|
| 832 | volume erase #3 center 331.6,541.54,125.62 radius 16.8
|
|---|
| 833 | ui mousemode right "map eraser"
|
|---|
| 834 | ui mousemode right translate
|
|---|
| 835 | ui mousemode right translate
|
|---|
| 836 | ui mousemode right "mark point"
|
|---|
| 837 | ui mousemode right "mark point"
|
|---|
| 838 | marker #1 position 355.1,503.1,172.2 color yellow radius 5
|
|---|
| 839 | show #1 models
|
|---|
| 840 | marker #1 position 392.5,509.8,34.16 color yellow radius 5
|
|---|
| 841 | ui mousemode right "move markers"
|
|---|
| 842 | select #1/M:111@M1 atom, 1 model selected
|
|---|
| 843 | marker change #1:111 position 350.8,509.3,171.9
|
|---|
| 844 | select #1/M:112@M1 atom, 1 model selected
|
|---|
| 845 | hide #1 models
|
|---|
| 846 | color cylindrical #3 axis sel palette 70,magenta:48,red:25,yellow
|
|---|
| 847 | volume #3 level 3708
|
|---|
| 848 | color cylindrical #3 axis sel palette 70,magenta:55,red:25,yellow
|
|---|
| 849 | color cylindrical #3 axis sel palette 70,magenta:53,red:25,yellow
|
|---|
| 850 | color cylindrical #3 axis sel palette 70,magenta:50,red:25,yellow
|
|---|
| 851 | ui mousemode right "map eraser"
|
|---|
| 852 | hide #!3 models
|
|---|
| 853 | show #2 models
|
|---|
| 854 | hide #2 models
|
|---|
| 855 | show #!3 models
|
|---|
| 856 | volume erase #3 center 343.34,466.19,90.744 radius 15.36
|
|---|
| 857 | color cylindrical #3 axis sel palette 70,magenta:50,red:23,yellow
|
|---|
| 858 | color cylindrical #3 axis sel palette 70,magenta:50,red:20,yellow
|
|---|
| 859 | set bgColor white
|
|---|
| 860 | lighting full
|
|---|
| 861 | lighting soft
|
|---|
| 862 | lighting shadows true intensity 0.5
|
|---|
| 863 | lighting simple
|
|---|
| 864 | ui mousemode right "map eraser"
|
|---|
| 865 | hide #!3 models
|
|---|
| 866 | show #!3 models
|
|---|
| 867 | volume erase #3 center 341.7,493.34,145.53 radius 15.36
|
|---|
| 868 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_vesicleclathrin_scale_zoned.mrc models #3
|
|---|
| 869 | close #4
|
|---|
| 870 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs includeMaps trueTraceback (most recent call last):
|
|---|
| 871 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 872 | self.processed[key] = self.process(obj, parents)
|
|---|
| 873 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 874 | return copy_state(data, convert=convert)
|
|---|
| 875 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 876 | return _copy(data)
|
|---|
| 877 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 878 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 879 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 880 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 881 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 882 | return convert(data)
|
|---|
| 883 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 884 | return add_obj(obj, parents)
|
|---|
| 885 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 886 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 887 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 888 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 889 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 890 |
|
|---|
| 891 | During handling of the above exception, another exception occurred:
|
|---|
| 892 |
|
|---|
| 893 | Traceback (most recent call last):
|
|---|
| 894 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 895 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 896 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 897 | mgr.discovery(self._state_containers)
|
|---|
| 898 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 899 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 900 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 901 |
|
|---|
| 902 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 903 |
|
|---|
| 904 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 905 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 906 |
|
|---|
| 907 | See log for complete Python traceback.
|
|---|
| 908 |
|
|---|
| 909 | Traceback (most recent call last):
|
|---|
| 910 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 911 | self.processed[key] = self.process(obj, parents)
|
|---|
| 912 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 913 | return copy_state(data, convert=convert)
|
|---|
| 914 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 915 | return _copy(data)
|
|---|
| 916 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 917 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 918 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 919 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 920 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 921 | return convert(data)
|
|---|
| 922 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 923 | return add_obj(obj, parents)
|
|---|
| 924 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 925 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 926 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 927 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 928 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 929 |
|
|---|
| 930 | During handling of the above exception, another exception occurred:
|
|---|
| 931 |
|
|---|
| 932 | Traceback (most recent call last):
|
|---|
| 933 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute
|
|---|
| 934 | cmd.run(cmd_text)
|
|---|
| 935 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 936 | result = ci.function(session, **kw_args)
|
|---|
| 937 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 66, in cmd_save
|
|---|
| 938 | Command(session, registry=registry).run(provider_cmd_text, log=log)
|
|---|
| 939 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 940 | result = ci.function(session, **kw_args)
|
|---|
| 941 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 79, in provider_save
|
|---|
| 942 | mgr).save(session, path, **provider_kw)
|
|---|
| 943 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core_formats/__init__.py", line 79, in save
|
|---|
| 944 | return cxs_save(session, path, **kw)
|
|---|
| 945 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 946 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 947 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 948 | mgr.discovery(self._state_containers)
|
|---|
| 949 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 950 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 951 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 952 |
|
|---|
| 953 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 954 |
|
|---|
| 955 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 956 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 957 |
|
|---|
| 958 | See log for complete Python traceback.
|
|---|
| 959 |
|
|---|
| 960 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs includeMaps falseTraceback (most recent call last):
|
|---|
| 961 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 962 | self.processed[key] = self.process(obj, parents)
|
|---|
| 963 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 964 | return copy_state(data, convert=convert)
|
|---|
| 965 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 966 | return _copy(data)
|
|---|
| 967 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 968 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 969 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 970 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 971 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 972 | return convert(data)
|
|---|
| 973 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 974 | return add_obj(obj, parents)
|
|---|
| 975 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 976 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 977 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 978 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 979 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 980 |
|
|---|
| 981 | During handling of the above exception, another exception occurred:
|
|---|
| 982 |
|
|---|
| 983 | Traceback (most recent call last):
|
|---|
| 984 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 985 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 986 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 987 | mgr.discovery(self._state_containers)
|
|---|
| 988 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 989 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 990 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 991 |
|
|---|
| 992 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 993 |
|
|---|
| 994 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 995 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 996 |
|
|---|
| 997 | See log for complete Python traceback.
|
|---|
| 998 |
|
|---|
| 999 | Traceback (most recent call last):
|
|---|
| 1000 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 1001 | self.processed[key] = self.process(obj, parents)
|
|---|
| 1002 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 1003 | return copy_state(data, convert=convert)
|
|---|
| 1004 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 1005 | return _copy(data)
|
|---|
| 1006 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 1007 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1008 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 1009 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1010 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 1011 | return convert(data)
|
|---|
| 1012 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 1013 | return add_obj(obj, parents)
|
|---|
| 1014 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 1015 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 1016 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 1017 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 1018 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 1019 |
|
|---|
| 1020 | During handling of the above exception, another exception occurred:
|
|---|
| 1021 |
|
|---|
| 1022 | Traceback (most recent call last):
|
|---|
| 1023 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute
|
|---|
| 1024 | cmd.run(cmd_text)
|
|---|
| 1025 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1026 | result = ci.function(session, **kw_args)
|
|---|
| 1027 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 66, in cmd_save
|
|---|
| 1028 | Command(session, registry=registry).run(provider_cmd_text, log=log)
|
|---|
| 1029 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1030 | result = ci.function(session, **kw_args)
|
|---|
| 1031 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 79, in provider_save
|
|---|
| 1032 | mgr).save(session, path, **provider_kw)
|
|---|
| 1033 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core_formats/__init__.py", line 79, in save
|
|---|
| 1034 | return cxs_save(session, path, **kw)
|
|---|
| 1035 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 1036 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 1037 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 1038 | mgr.discovery(self._state_containers)
|
|---|
| 1039 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1040 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1041 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 1042 |
|
|---|
| 1043 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 1044 |
|
|---|
| 1045 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1046 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1047 |
|
|---|
| 1048 | See log for complete Python traceback.
|
|---|
| 1049 |
|
|---|
| 1050 | select down2 atoms, 1 model selected
|
|---|
| 1051 | select up82 atoms, 1 model selected
|
|---|
| 1052 | select up222 atoms, 4 models selected
|
|---|
| 1053 | select up222 atoms, 4 models selected
|
|---|
| 1054 | select down82 atoms, 1 model selected
|
|---|
| 1055 | select down2 atoms, 1 model selected
|
|---|
| 1056 | select down2 atoms, 1 model selected
|
|---|
| 1057 | select down2 atoms, 1 model selected
|
|---|
| 1058 | show #1 models
|
|---|
| 1059 | hide #1 models
|
|---|
| 1060 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin_mem.cmm format markers models #1Wrote 1 marker sets containing 82 markers
|
|---|
| 1061 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin_clathrin.cmm format markers models #2Wrote 1 marker sets containing 140 markers
|
|---|
| 1062 | rename #1 mem
|
|---|
| 1063 | rename #2 clathrin
|
|---|
| 1064 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs includeMaps falseTraceback (most recent call last):
|
|---|
| 1065 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 1066 | self.processed[key] = self.process(obj, parents)
|
|---|
| 1067 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 1068 | return copy_state(data, convert=convert)
|
|---|
| 1069 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 1070 | return _copy(data)
|
|---|
| 1071 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 1072 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1073 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 1074 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1075 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 1076 | return convert(data)
|
|---|
| 1077 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 1078 | return add_obj(obj, parents)
|
|---|
| 1079 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 1080 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 1081 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 1082 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 1083 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 1084 |
|
|---|
| 1085 | During handling of the above exception, another exception occurred:
|
|---|
| 1086 |
|
|---|
| 1087 | Traceback (most recent call last):
|
|---|
| 1088 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 1089 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 1090 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 1091 | mgr.discovery(self._state_containers)
|
|---|
| 1092 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1093 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1094 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 1095 |
|
|---|
| 1096 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 1097 |
|
|---|
| 1098 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1099 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1100 |
|
|---|
| 1101 | See log for complete Python traceback.
|
|---|
| 1102 |
|
|---|
| 1103 | Traceback (most recent call last):
|
|---|
| 1104 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 1105 | self.processed[key] = self.process(obj, parents)
|
|---|
| 1106 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 1107 | return copy_state(data, convert=convert)
|
|---|
| 1108 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 1109 | return _copy(data)
|
|---|
| 1110 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 1111 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1112 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 1113 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1114 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 1115 | return convert(data)
|
|---|
| 1116 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 1117 | return add_obj(obj, parents)
|
|---|
| 1118 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 1119 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 1120 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 1121 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 1122 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 1123 |
|
|---|
| 1124 | During handling of the above exception, another exception occurred:
|
|---|
| 1125 |
|
|---|
| 1126 | Traceback (most recent call last):
|
|---|
| 1127 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute
|
|---|
| 1128 | cmd.run(cmd_text)
|
|---|
| 1129 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1130 | result = ci.function(session, **kw_args)
|
|---|
| 1131 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 66, in cmd_save
|
|---|
| 1132 | Command(session, registry=registry).run(provider_cmd_text, log=log)
|
|---|
| 1133 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1134 | result = ci.function(session, **kw_args)
|
|---|
| 1135 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 79, in provider_save
|
|---|
| 1136 | mgr).save(session, path, **provider_kw)
|
|---|
| 1137 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core_formats/__init__.py", line 79, in save
|
|---|
| 1138 | return cxs_save(session, path, **kw)
|
|---|
| 1139 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 1140 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 1141 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 1142 | mgr.discovery(self._state_containers)
|
|---|
| 1143 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1144 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1145 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 1146 |
|
|---|
| 1147 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 1148 |
|
|---|
| 1149 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1150 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1151 |
|
|---|
| 1152 | See log for complete Python traceback.
|
|---|
| 1153 |
|
|---|
| 1154 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/Vesicleclathrin_electrondensity.png width 1126 height 827 supersample 3
|
|---|
| 1155 | save /Users/fbsrfr/Desktop/image8.png supersample 3
|
|---|
| 1156 | save /Users/fbsrfr/Desktop/image8.png supersample 3
|
|---|
| 1157 | save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxsTraceback (most recent call last):
|
|---|
| 1158 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 1159 | self.processed[key] = self.process(obj, parents)
|
|---|
| 1160 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 1161 | return copy_state(data, convert=convert)
|
|---|
| 1162 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 1163 | return _copy(data)
|
|---|
| 1164 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 1165 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1166 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 1167 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1168 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 1169 | return convert(data)
|
|---|
| 1170 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 1171 | return add_obj(obj, parents)
|
|---|
| 1172 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 1173 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 1174 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 1175 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 1176 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 1177 |
|
|---|
| 1178 | During handling of the above exception, another exception occurred:
|
|---|
| 1179 |
|
|---|
| 1180 | Traceback (most recent call last):
|
|---|
| 1181 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 1182 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 1183 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 1184 | mgr.discovery(self._state_containers)
|
|---|
| 1185 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1186 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1187 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 1188 |
|
|---|
| 1189 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 1190 |
|
|---|
| 1191 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1192 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1193 |
|
|---|
| 1194 | See log for complete Python traceback.
|
|---|
| 1195 |
|
|---|
| 1196 | Traceback (most recent call last):
|
|---|
| 1197 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 259, in discovery
|
|---|
| 1198 | self.processed[key] = self.process(obj, parents)
|
|---|
| 1199 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 292, in process
|
|---|
| 1200 | return copy_state(data, convert=convert)
|
|---|
| 1201 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 208, in copy_state
|
|---|
| 1202 | return _copy(data)
|
|---|
| 1203 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in _copy
|
|---|
| 1204 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1205 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 193, in <listcomp>
|
|---|
| 1206 | items = [(_copy(k), _copy(v)) for k, v in data.items()]
|
|---|
| 1207 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/state.py", line 206, in _copy
|
|---|
| 1208 | return convert(data)
|
|---|
| 1209 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 291, in convert
|
|---|
| 1210 | return add_obj(obj, parents)
|
|---|
| 1211 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 265, in _add_obj
|
|---|
| 1212 | uid = _UniqueName.from_obj(self.session, obj)
|
|---|
| 1213 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 132, in from_obj
|
|---|
| 1214 | obj_cls.__module__, obj_cls.__name__))
|
|---|
| 1215 | RuntimeError: No bundle information for tinyarray.ndarray_float
|
|---|
| 1216 |
|
|---|
| 1217 | During handling of the above exception, another exception occurred:
|
|---|
| 1218 |
|
|---|
| 1219 | Traceback (most recent call last):
|
|---|
| 1220 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/gui.py", line 1541, in <lambda>
|
|---|
| 1221 | action.triggered.connect(lambda arg, cb = callback: cb())
|
|---|
| 1222 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/dialog.py", line 102, in <lambda>
|
|---|
| 1223 | lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file",
|
|---|
| 1224 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog
|
|---|
| 1225 | _dlg.display(session, **kw)
|
|---|
| 1226 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/dialog.py", line 48, in display
|
|---|
| 1227 | run(session, cmd)
|
|---|
| 1228 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run
|
|---|
| 1229 | results = command.run(text, log=log)
|
|---|
| 1230 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1231 | result = ci.function(session, **kw_args)
|
|---|
| 1232 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 66, in cmd_save
|
|---|
| 1233 | Command(session, registry=registry).run(provider_cmd_text, log=log)
|
|---|
| 1234 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run
|
|---|
| 1235 | result = ci.function(session, **kw_args)
|
|---|
| 1236 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 79, in provider_save
|
|---|
| 1237 | mgr).save(session, path, **provider_kw)
|
|---|
| 1238 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core_formats/__init__.py", line 79, in save
|
|---|
| 1239 | return cxs_save(session, path, **kw)
|
|---|
| 1240 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 839, in save
|
|---|
| 1241 | session.save(output, version=version, include_maps=include_maps)
|
|---|
| 1242 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 590, in save
|
|---|
| 1243 | mgr.discovery(self._state_containers)
|
|---|
| 1244 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1245 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1246 | ValueError: error processing: '_surface_updaters' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x17ce88590> -> <chimerax.surface.colorgeom.CylinderColor object at 0x122b97f10>: No bundle information for tinyarray.ndarray_float
|
|---|
| 1247 |
|
|---|
| 1248 | ValueError: error processing: '_surface_updaters' -> -> : No bundle information for tinyarray.ndarray_float
|
|---|
| 1249 |
|
|---|
| 1250 | File "/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 261, in discovery
|
|---|
| 1251 | raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
|
|---|
| 1252 |
|
|---|
| 1253 | See log for complete Python traceback.
|
|---|
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