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#3491 closed defect (fixed)
Cannot save session containing tinyarray.ndarray_float
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | major | Milestone: | 1.1 |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Could not save session from GUI or command line with or without maps included. I have included a copy of the log.
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> format session
Log from Mon Jul 6 18:47:44 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> format session
Log from Wed Jun 24 12:48:10 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/fbsrfr/process/20200214_newfigure1/dynamo/presm2_molmap.cmp
> format cmap
Opened presm2_molmap.cmp, grid size 91,123,73, pixel 3, shown at level 0.0185,
step 1, values float32
> open /Users/fbsrfr/process/20200214_newfigure1/imodvesicle_chxedit.cmm
Opened 1 marker sets containing 1983524 markers
> marker change #2 radius 2
> molmap sel 5 gridSpacing 3
No atoms specified
> molmap #2 5 gridSpacing 3
> hide #2 models
> volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #3,#1 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
Expected a density maps specifier or a keyword
> volume #3 #1 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #3 level 0.0015
> ui tool show "Side View"
> volume #3 level 0.0085
> volume #1 level 0.00328
> volume #3 level 0.00328
> open
> /Users/fbsrfr/process/20200214_newfigure1/dynamo/posm1c_dyntbl_imodedit_chxedit_molmap.cmp
> format cmap
Opened posm1c_dyntbl_imodedit_chxedit_molmap.cmp, grid size 269,144,92, pixel
3, shown at level 0.0163, step 1, values float32
> open
> /Users/fbsrfr/process/20200214_newfigure1/dynamo/presm1c_dyntbl_imodedit_chxedit_molmap.cmp
Opened presm1c_dyntbl_imodedit_chxedit_molmap.cmp, grid size 325,128,89, pixel
3, shown at level 0.0214, step 1, values float32
> open /Users/fbsrfr/process/20200214_newfigure1/dynamo/actin_molmap.cmp
Opened actin_molmap.cmp, grid size 261,145,93, pixel 3, shown at level 0.0558,
step 1, values float32
> open
> /Users/fbsrfr/process/20200214_newfigure1/dynamo/smoothERall_dyntbl_chxedit_molmap.cmp
Opened smoothERall_dyntbl_chxedit_molmap.cmp, grid size 150,50,60, pixel 3,
shown at level 0.0782, step 1, values float32
> open
> /Users/fbsrfr/process/20200214_newfigure1/dynamo/mitoall_dyntbl_imodedit_chxedit_molmap.cmp
Opened mitoall_dyntbl_imodedit_chxedit_molmap.cmp, grid size 324,263,77, pixel
3, shown at level 0.0213, step 1, values float32
> save /Users/fbsrfr/process/20200214_newfigure1/imodvesicle_molmap.cmp format
> cmap models #3
> close #2
> open /Users/fbsrfr/process/20200214_newfigure1/posm_vesicle.cmm
Opened 1 marker sets containing 4105 markers
> marker change #2 radius 2
> molmap #2 5 gridSpacing 3
> close #2
> volume #9 level 0.00328
> volume #3 #1 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #3 #1 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #9 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #1 #3 #4 #5 #6 #7 #8 #9 level 0.00328
> volume #1 #3 #4 #5 #7 #8 #9 level 0.00328
> volume #6 level 0.05562
> volume #1 #3 #4 #5 #6 #7 #8 #9 surfaceSmoothing true smoothingIterations 5
> smoothingFactor 0.8
> save /Users/fbsrfr/process/20200214_newfigure1/posmvesicle_molmap.cmp format
> cmap models #9
> volume #6 surfaceSmoothing true smoothingIterations 3 smoothingFactor 0.3
> volume #6level 0.0228
Expected a density maps specifier or a keyword
> volume #6 level 0.0328
> volume #6 level 0.00128
> open
> /Users/fbsrfr/process/20200214_newfigure1/D02_TS_09_aligned_bin4_ng_sirt5_filter_iGluR_inv.rec
Opened D02_TS_09_aligned_bin4_ng_sirt5_filter_iGluR_inv.rec, grid size
960,928,315, pixel 11.9,11.9,11.9, shown at step 1, values float32
> open /Users/fbsrfr/process/20200214_newfigure1/test_cleft.cmm
Opened 1 marker sets containing 4037 markers
> volume #2 region 0,0,0,959,927,314 step 4
> volume #2 region 0,0,0,959,927,314 step 4
> volume #2 level 2
> volume #2 change image level -4894,0 level 8583,0.8 level 2.256e+04,1
> volume #2 originIndex 0
> volume #2 voxelSize 1
> hide #!2 models
> volume #2 step 1
> volume zone #2 nearAtoms #10 radius 10
Expected a keyword
> volume zone #2 nearAtoms #10 range 10
> show #!2 models
> hide #10 models
> volume zone #2 nearAtoms #10 range 10 newMap true
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> includeMaps true
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs
> includeMaps false
> surface dust #11 size 10
> open /Users/fbsrfr/process/20200214_newfigure1/test_microtubles_PtsAdded.cmm
Opened 1 marker sets containing 1597 markers
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs
> includeMaps false
> volume #2 style image region 0,0,157,959,927,157 step 1 showOutlineBox true
> volume #2 transparency 0
> volume #2 transparency 0
> volume 2 transparency 1
Expected a density maps specifier or a keyword
> volume #2 transparency 0
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs
> includeMaps false
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> includeMaps true
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!11 models
> open /Users/fbsrfr/process/20200214_newfigure1/jnk/cleft_iglur_sc4k_zone.mrc
Opened cleft_iglur_sc4k_zone.mrc, grid size 716,177,221, pixel 1, shown at
level 0.817, step 2, values float32
> volume #13 color #fc0280
> open
> /Users/fbsrfr/process/20200214_newfigure1/jnk/cleft_transynaptic_sc4k_zone.mrc
Opened cleft_transynaptic_sc4k_zone.mrc, grid size 791,255,111, pixel 1, shown
at level 0.995, step 2, values float32
> ui tool show "Side View"
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> includeMaps true
opened ChimeraX session
> show #10 models
> hide #10 models
> close #10
> hide #12 models
> open
> /Users/fbsrfr/process/20200214_newfigure1/microtubule_smooth1.8_scalesh4k_thr3k_zone15.mrc
Opened microtubule_smooth1.8_scalesh4k_thr3k_zone15.mrc, grid size
823,411,157, pixel 1, shown at level 1.85e+03, step 2, values float32
> volume #10 level 1317
> volume #10 level 2215
> volume #10 color #ffff0a
> show #12 models
> hide #12 models
> close #12
> hide #!6 models
> open
> /Users/fbsrfr/process/20200214_newfigure1/test_actin2_PA_more_PA_more_PA_more_PA_more_PtsAdded_smooth1.8_scalesh4k_th3k_zone5.mrc
Opened
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
> volume #12 level 4073
> volume #12 level 3929
> volume #12 color #fd8008
> volume #12 color #fecc66
> volume #12 color #fecc66fb
> volume #12 color #fecc66ef
> volume #12 color #fecc66db
> volume #12 color #fecc66d7
> volume #12 color #fecc66cb
> volume #12 color #fecc66c0
> volume #12 color #fecc66ab
> volume #12 color #fecc66a8
> volume #12 color #fecc668e
> volume #12 color #fecc6680
> volume #12 color #fecc6689
> volume #12 color #fecc668a
> volume #12 color #fecc668c
> volume #12 color #fecc668e
> volume #12 color #fecc668f
> volume #12 color #fecc6698
> volume #12 color #fecc6699
> volume #12 color #fecc669a
> volume #12 color #fecc669b
> volume #12 color #fecc669f
> volume #12 color #fecc66a2
> volume #12 color #fecc66af
> volume #12 color #fecc66c3
> volume #12 color #fecc66c9
> volume #12 color #fecc66d8
> volume #12 color #fecc66d9
> volume #12 color #fecc66e0
> volume #12 color #fecc66e1
> volume #12 color #fecc66de
> volume #12 color #fecc66dd
> volume #12 color #fecc66db
> volume #12 color #fecc66d7
> volume #12 color #fecc66cb
> volume #12 color #fecc66ca
> volume #12 color #fecc66c8
> volume #12 color #fecc66c5
> volume #12 color #fecc66c4
> volume #12 color #fecc66b8
> volume #12 color #fecc66b6
> volume #12 color #fecc66b7
> volume #12 color #fecc66b9
> volume #12 color #fecc66c4
> volume #12 color #fecc66c5
> open
> /Users/fbsrfr/process/20200214_newfigure1/jnk/cleft_cleftmatrix_sc4k_zone.mrc
Opened cleft_cleftmatrix_sc4k_zone.mrc, grid size 283,41,84, pixel 1, shown at
level 4.19e+03, step 1, values float32
> volume #15 level 2329
> volume #15 level 1877
> volume #15 color #fd6fcf
> volume #15 color #66ccff
> volume #15 color #21ff80
> volume #15 color #808003
> volume #15 color #fd6666
> volume #15 color #fc0107
> volume #15 color #804002
> volume #15 color #808003
> volume #15 color #108001
> volume #15 color #108080
> volume #15 color #074080
> volume #15 color #0f80ff
> undo
> redo
> hide #!12 models
> show #!12 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save /Users/fbsrfr/Desktop/image3.png supersample 3
> ui tool show "Side View"
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs
> includeMaps false
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> includeMaps true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fbsrfr/Desktop/movie3.mp4
Movie saved to /Users/fbsrfr/Desktop/movie3.mp4
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000299aee0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000299aee0>
contents scale of 2 - updating layer to match.
> set bgColor white
> save /Users/fbsrfr/Desktop/image3.png supersample 3
> lighting full
> save /Users/fbsrfr/Desktop/image4.png supersample 3
> lighting shadows false
> lighting shadows true
> lighting full
> lighting full
> lighting direction -1,-1,-1
> lighting direction 1,1,1
> lighting direction 1,1,-1
> lighting direction 1,-1,1
> lighting direction -1,-1,1
> lighting direction -1,1,1
> lighting direction -1,1,-1
> lighting direction -1,1,-.5
> lighting direction -1,.5,-.5
> lighting direction -1,-.5,-.5
> lighting direction 1,-.5,-.5
> lighting direction -1,-.5,-.5
> lighting direction -1,-.5,0
> lighting direction -1,-.5,-0.5
> lighting direction -1,0,-0.5
> lighting direction -1,-.5,1
> lighting direction -1,-.5,-1
> lighting direction -.5,-.5,-1
> lighting direction .5,-.5,-1
> lighting direction .5,.5,-1
> lighting direction -.5,.5,-1
> lighting direction .5,-.5,-1
> lighting direction -1,-.5,-1
> lighting direction -.,-.5,-1
Invalid "direction" argument: Expected a number
> lighting direction -.9,-.5,-1
> lighting direction -.7,-.5,-1
> lighting direction -.7,-.2,-1
> lighting direction -.7,-.9,-1
> lighting direction -.7,.9,-1
> lighting direction -.7,0.3,-1
> lighting direction -.7,-0.3,-1
> lighting direction -.7,-0.5,-1
> lighting direction -.5,-0.5,-1
> lighting direction -.5,-0.6,-1
> lighting direction -.5,-0.8,-1
> lighting direction -.5,-0.2,-1
> lighting full
> lighting shadows false
> save /Users/fbsrfr/Desktop/image5.png supersample 3
> lighting soft
> lighting full
> lighting soft
> save /Users/fbsrfr/Desktop/image6.png supersample 3
> lighting soft
> lighting soft
> lighting full
> lighting soft
> lighting soft
> save /Users/fbsrfr/Desktop/image7.png supersample 3
> lighting soft direction -.5,-0.2,-1
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting direction -.5,-0.2,-1
> lighting full
> lighting direction 1,-1,-1
> lighting soft
> lighting soft
> lighting full
> lighting direction -.5,-0.2,-1
> lighting soft
> lighting full
> lighting soft
> lighting direction -.5,-0.2,-1
> lighting direction -.5,0.2,-1
> lighting direction -.5,-0.8,-1
> lighting light direction -.5,-0.8,-1
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting soft direction -.5,-0.8,-1
> lighting soft direction -.5,-0.2,-1
> lighting full
> lighting soft
> lighting soft direction -.1,-0.2,-1
> lighting soft direction -.15-0.2,-1
Invalid "direction" argument: Expected a number
> lighting soft direction -.5-0.2,-1
Invalid "direction" argument: Expected a number
> lighting soft direction -.5,-0.2,-1
> lighting full
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation.cxs
> includeMaps true
> save
> /Users/fbsrfr/process/20200214_newfigure1/chimera_composition/fig1_chimerax_compilation_nomaps.cxs
> includeMaps false
> close session
> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_aligned_bin4_sirt5_inv.rec
Opened 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
> set bgColor black
> volume scale shift 4000
Missing or invalid "volumes" argument: invalid density maps specifier
> volume #1 scale shift 4000
Expected a keyword
> volume scale #1 shift 4000
> volume #2 level 4696
> ui mousemode right "mark point"
> marker #3 position 4705,5969,2556 color yellow radius 1
> marker change #3 radius 20
> ui mousemode right "move markers"
> marker change #3:1 position 4609,5951,2527
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> cofr sel
> lighting simple
> marker change #3:1 position 4602,5944,2521
> marker change #3:1 position 4608,5950,2523
> ui mousemode right "mark point"
> marker #3 position 3915,6787,2677 color yellow radius 20
> marker #3 position 3910,6784,2698 color yellow radius 20
> ui mousemode right "move markers"
> marker change #3:3 position 4641,6297,2117
> marker change #3:2 position 4658,6274,2068
> marker change #3:3 position 4575,5998,2413
> marker change #3:2 position 4555,6006,2248
> marker change #3:2 position 4624,6004,2199
> marker change #3:2 position 4711,5936,2187
> ui mousemode right "mark point"
> marker #3 position 4677,6106,1458 color yellow radius 20
> ui mousemode right "move markers"
> marker change #3:4 position 4505,5999,1928
> marker change #3:4 position 4764,5902,2197
> marker change #3:4 position 4774,5897,2019
> volume #1 color #ffff0a
> volume #2 color #fd8008
> volume #2 color #ffff0a
> volume #2 color #ffff66
> volume #2 color #f5ffbf
> volume #2 color #aeffa5
> volume #2 color #caffc1
> ui mousemode right "mark point"
> marker #3 position 4800,5789,2406 color yellow radius 20
> marker #3 position 4384,6036,2462 color yellow radius 20
> marker #3 position 4553,5871,2333 color yellow radius 20
> marker #3 position 4650,5934,2254 color yellow radius 20
> marker #3 position 4610,5897,1878 color yellow radius 20
> marker #3 position 4643,5905,1717 color yellow radius 20
> marker #3 position 4739,5883,2275 color yellow radius 20
> marker #3 position 4522,5867,2366 color yellow radius 20
> marker #3 position 4499,5906,2372 color yellow radius 20
> marker #3 position 4726,6085,2291 color yellow radius 20
> marker #3 position 4707,6042,2252 color yellow radius 20
> marker #3 position 4784,5741,2483 color yellow radius 20
> marker #3 position 4770,5814,1813 color yellow radius 20
> marker #3 position 4766,5854,1811 color yellow radius 20
> marker #3 position 4751,5978,1748 color yellow radius 20
> marker #3 position 4751,6041,1845 color yellow radius 20
> marker #3 position 4755,6094,1994 color yellow radius 20
> marker #3 position 4765,6096,2157 color yellow radius 20
> marker #3 position 4790,6042,2501 color yellow radius 20
> marker #3 position 4591,5640,2296 color yellow radius 20
> marker #3 position 4708,5550,2392 color yellow radius 20
> marker #3 position 4879,5557,2522 color yellow radius 20
> marker #3 position 4971,5669,2586 color yellow radius 20
> marker #3 position 4984,5807,2586 color yellow radius 20
> marker #3 position 4925,5973,2529 color yellow radius 20
> marker #3 position 5006,6049,2586 color yellow radius 20
> marker #3 position 4994,6038,2681 color yellow radius 20
> marker #3 position 4928,5554,2673 color yellow radius 20
> marker #3 position 4887,5405,2560 color yellow radius 20
> marker #3 position 5053,5613,2282 color yellow radius 20
> marker #3 position 4849,5452,2229 color yellow radius 20
> marker #3 position 4894,5413,2411 color yellow radius 20
> marker #3 position 4902,5471,2504 color yellow radius 20
> marker #3 position 4936,5459,2659 color yellow radius 20
> marker #3 position 4612,6200,2673 color yellow radius 20
> marker #3 position 4606,6088,2746 color yellow radius 20
> marker #3 position 4659,6187,2632 color yellow radius 20
> marker #3 position 4775,6214,2493 color yellow radius 20
> marker #3 position 4599,5950,2835 color yellow radius 20
> marker #3 position 4480,6075,2717 color yellow radius 20
> marker #3 position 4486,6161,2694 color yellow radius 20
> marker #3 position 4392,6101,2616 color yellow radius 20
> marker #3 position 4380,6195,2575 color yellow radius 20
> marker #3 position 4439,6110,2626 color yellow radius 20
> marker #3 position 4431,6040,2651 color yellow radius 20
> marker #3 position 4472,6121,2631 color yellow radius 20
> marker #3 position 4415,5853,2494 color yellow radius 20
> marker #3 position 4387,5928,2412 color yellow radius 20
> marker #3 position 4338,6021,2259 color yellow radius 20
> marker #3 position 4331,6178,2297 color yellow radius 20
> marker #3 position 4378,6164,2481 color yellow radius 20
> marker #3 position 4409,6149,2596 color yellow radius 20
> marker #3 position 4392,6151,1980 color yellow radius 20
> marker #3 position 4411,6087,1947 color yellow radius 20
> marker #3 position 4375,6194,2052 color yellow radius 20
> marker #3 position 4379,6222,1862 color yellow radius 20
> marker #3 position 4401,6165,1760 color yellow radius 20
> volume #2 color #caffc1fe
> volume #2 color #caffc1fa
> volume #2 color #caffc1f8
> volume #2 color #caffc1f2
> volume #2 color #caffc1ef
> volume #2 color #caffc1eb
> volume #2 color #caffc1e9
> volume #2 color #caffc1e7
> volume #2 color #caffc1e5
> volume #2 color #caffc1e4
> volume #2 color #caffc1e0
> volume #2 color #caffc1df
> volume #2 color #caffc1db
> volume #2 color #caffc1da
> volume #2 color #caffc1d8
> volume #2 color #caffc1d5
> volume #2 color #caffc1d4
> volume #2 color #caffc1d0
> volume #2 color #caffc1cd
> volume #2 color #caffc1ca
> volume #2 color #caffc1c9
> volume #2 color #caffc1c6
> volume #2 color #caffc1c3
> volume #2 color #caffc1c2
> volume #2 color #caffc1c0
> volume #2 color #caffc1bf
> volume #2 color #caffc1bd
> volume #2 color #caffc1b9
> volume #2 color #caffc1af
> volume #2 color #caffc1a8
> volume #2 color #caffc1a3
> volume #2 color #caffc19e
> volume #2 color #caffc19a
> volume #2 color #caffc194
> volume #2 color #caffc190
> volume #2 color #caffc18b
> volume #2 color #caffc182
> volume #2 color #caffc17d
> volume #2 color #caffc178
> volume #2 color #caffc174
> volume #2 color #caffc171
> volume #2 color #caffc16c
> volume #2 color #caffc16a
> volume #2 color #caffc168
> volume #2 color #caffc165
> volume #2 color #caffc164
> volume #2 color #caffc165
> volume #2 color #caffc167
> volume #2 color #caffc168
> volume #2 color #caffc16c
> volume #2 color #caffc16e
> volume #2 color #caffc172
> volume #2 color #caffc175
> volume #2 color #caffc178
> volume #2 color #caffc17c
> volume #2 color #caffc17d
> marker #3 position 4701,5475,2131 color yellow radius 20
> marker #3 position 4549,5412,2391 color yellow radius 20
> marker #3 position 4777,5380,2608 color yellow radius 20
> marker #3 position 5021,5658,2721 color yellow radius 20
> marker #3 position 4566,6248,2296 color yellow radius 20
> marker #3 position 4723,6057,1683 color yellow radius 20
> marker #3 position 4696,6084,1642 color yellow radius 20
> marker #3 position 4832,5941,1649 color yellow radius 20
> marker #3 position 4663,6122,1686 color yellow radius 20
> marker #3 position 4967,5620,2373 color yellow radius 20
> marker #3 position 5027,5525,2321 color yellow radius 20
> marker #3 position 5092,5613,2434 color yellow radius 20
> marker #3 position 5043,5488,2476 color yellow radius 20
> marker #3 position 4846,5355,2351 color yellow radius 20
> marker #3 position 5067,5481,2258 color yellow radius 20
> marker #3 position 5024,5723,1955 color yellow radius 20
> marker #3 position 5070,5741,2087 color yellow radius 20
> marker #3 position 4356,6176,2304 color yellow radius 20
> marker #3 position 4354,6230,2301 color yellow radius 20
> marker #3 position 4506,6197,2166 color yellow radius 20
> marker #3 position 4589,6237,1887 color yellow radius 20
> marker #3 position 4645,6239,1795 color yellow radius 20
> marker #3 position 4848,5961,2815 color yellow radius 20
> marker #3 position 4766,6158,2672 color yellow radius 20
> marker #3 position 4905,6219,2359 color yellow radius 20
> marker #3 position 4966,6158,2052 color yellow radius 20
> marker #3 position 4654,6124,1918 color yellow radius 20
> marker #3 position 4751,6302,2285 color yellow radius 20
> marker #3 position 4741,5827,1950 color yellow radius 20
> marker #3 position 4764,5904,1945 color yellow radius 20
> marker #3 position 4710,5969,1945 color yellow radius 20
> marker #3 position 4675,5958,1941 color yellow radius 20
> marker #3 position 4649,5889,1920 color yellow radius 20
> marker #3 position 4738,5995,2413 color yellow radius 20
> hide #3 models
> show #3 models
> hide #!2 models
Drag select of 87 atoms
> show #!2 models
> volume zone #3 nearAtoms #50 range 10 newMap true
no atoms specified for zone
> volume zone #2 nearAtoms #3 range 10 newMap true
> volume #4 level 1648
> volume #4 level 816
> select #3
95 atoms, 1 model selected
> close #4
> volume zone #2 nearAtoms #3 range 10 newMap true
> volume #4 level 1762
> hide #3 models
> show #3 models
> close #4
> show #!2 models
> volume zone #2 nearAtoms #3 range 100 newMap true
> close #4
> volume zone #2 nearAtoms #3 range 160 newMap true
> volume #4 step 1
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrin_vesicle.cmm
> format markers models #13
Wrote 0 marker sets containing 0 markers
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrin_vesicle.cmm
> format markers models #3
Wrote 1 marker sets containing 95 markers
> volume #4 level 3815
> volume #4 level 4558
> ~select #3
Nothing selected
> select #3
95 atoms, 1 model selected
> hide #3 models
> volume #4 level 4109
> volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.8
> volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
> show #3 models
> select /M:5@M
1 atom, 1 model selected
> color radiall #4 centre sel rainbow
Expected a keyword
> color radiall #4 centre sel
Expected a keyword
> color radial #4 center sel
> color radiall #4 center sel rainbow
Expected a keyword
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color radial #4 center sel
> volume #4 level 3071
> volume zone #2 nearAtoms #3 range 250 newMap true
> select #3
95 atoms, 1 model selected
> ~select #3
Nothing selected
> close #5
> select up
Nothing selected
> select down
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> volume zone #2 nearAtoms #3 range 250 newMap true
> hide #!4 models
> volume #4 level 3213
> volume #4 level 2983
> volume #4 level 3726
> volume #5 level 2991
> volume #2 step 1
> hide #!2 models
Drag select of
Drag select of 95 atoms
> show #!2 models
> volume zone #2 nearAtoms #3 range 350 newMap false
> volume #2 color #caffc1b3
> volume #2 color #caffc1d7
> volume #2 color #caffc1e7
> volume #2 color #caffc1ed
> volume #2 color #caffc1f9
> volume #2 color #caffc1
> volume #2 color #4eff48
> volume #2 color #8484fc
> volume #2 color #9fb2fc
> volume #2 color #a5bbfd
> select /M:5@M
1 atom, 1 model selected
> color radiall #2 center sel rainbow
Expected a keyword
> color radial #2 center sel
> volume zone #2 nearAtoms #3 range 350 newMap true
> color radial #6 center sel
> volume #6 level 3621
> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_aligned_bin4_sirt5_smth1.3_inv.rec
Opened 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
> close #4
> close #5
> close #6
> volume scale #7 shift 4000
> volume #4 step 1
> volume #4 level 2654
> volume #4 level 3000
> volume #4 level 4000
> select up
95 atoms, 1 model selected
> select up
95 atoms, 9 models selected
> select down
95 atoms, 1 model selected
> select down
1 atom, 1 model selected
> volume zone #2 nearAtoms #3 range 350 newMap true
> volume zone #7 nearAtoms #3 range 350 newMap true
> show #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!7 models
> show #!7 models
> show #!6 models
> close #6
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7
> show #!4 models
> hide #3 models
> show #3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> volume #5 level 4326
> color radial #5 center sel
> marker #3 position 4579,5911,2589 color yellow radius 20
> ui mousemode right "move markers"
> marker change #3:96 position 4489,6001,2463
> color radial #5 center sel
> volume #5 level 3825
> select up
96 atoms, 1 model selected
> select down
2 atoms, 1 model selected
> volume zone #2 nearAtoms #3 range 300 newMap true
> hide #!5 models
> close #6
> volume zone #2 nearAtoms #3 range 270 newMap true
> close #6
> volume zone #2 nearAtoms #3 range 240 newMap true
> ui mousemode right "mark point"
> marker #3 position 5135,5931,2381 color yellow radius 20
> marker #3 position 5079,5876,2221 color yellow radius 20
> marker #3 position 5153,6011,2287 color yellow radius 20
> ui mousemode right "move markers"
> marker change #3:99 position 5159,5944,2222
> marker change #3:99 position 5140,5953,2185
> ui mousemode right "mark point"
> marker #3 position 5196,5770,2404 color yellow radius 20
> marker #3 position 5221,5786,2466 color yellow radius 20
> ui mousemode right "move markers"
> marker change #3:101 position 5231,5732,2463
> marker change #3:100 position 5217,5732,2422
> marker change #3:101 position 5262,5774,2337
> marker change #3:101 position 5231,5754,2343
> close #6
> volume zone #2 nearAtoms #3 range 240 newMap true
> volume #6 level 3992
> surface dust #6 size 120
> hide #3 models
> surface dust #6 size 220
> show #3 models
> marker delete sel
Deleted 2 markers
> marker delete sel
Deleted 4 markers
> volume zone #2 nearAtoms #3 range 200 newMap true
> hide #!6 models
> show #!6 models
> volume #7 level 4214
> volume #7 level 4010
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select up
Nothing selected
> select up
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> surface dust #7 size 220
> color radial #7 center sel
Drag select of
> color radial #7 center sel
> volume #7 level 3825
> hide #3 models
> color cylinder radial #7 center sel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color cylinder radius #7 center sel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> scolor cylinder radius #7 center sel
Unknown command: scolor cylinder radius #7 center sel
> color radiall #7 center sel goldred
Expected a keyword
> color radiall #7 center sel gold,red
Expected a keyword
> color radiall #7 center sel yelow,red
Expected a keyword
> color radiall #7 center sel yelow, red
Expected a keyword
> color radiall #7 center sel yelow-red
Expected a keyword
Fetching compressed palette yelow-red from
http://www.colourlovers.com/api/palettes?keywords=yelow-
red&format=json&numResults=100
Could not find palette yelow-red at COLOURlovers.com using keyword search
> color radiall #7 center sel palette yelow:red
Invalid "palette" argument: Invalid color name or specifier
Fetching compressed palette goldred from
http://www.colourlovers.com/api/palettes?keywords=goldred&format=json&numResults=100
Could not find palette goldred at COLOURlovers.com using keyword search
> color radial #7 center sel palette gold:red
> color radiall #7 center sel palette gold:0.7,red
Invalid "palette" argument: Number of values and color must match in colormap
> color radiall #7 center sel palette gold:red,05
Invalid "palette" argument: could not convert string to float: 'red'
> color radiall #7 center sel palette gold:0.5,red
Invalid "palette" argument: Number of values and color must match in colormap
> color radial #7 center sel palette 1,gold:0.5,red
> color radial #7 center sel palette 0.5,gold:0.5,red
> color radial #7 center sel palette 5,gold:0.5,red
> color radiall #7 center sel palette 5,gold:,red
Invalid "palette" argument: could not convert string to float:
> color radial #7 center sel palette 5,gold:0.1,red
> color radial #7 center sel palette .2,gold:0.1,red
> color radial #7 center sel palette 0.2,gold:0.1,red
> color radial #7 center sel palette 0.2,gold:0.5,red
> color radial #7 center sel palette 0.2,gold:0.2,red
> color radial #7 center sel palette 0.2,gold:0.3,red
> color radial #7 center sel palette 10,gold:5,red
> color radial #7 center sel palette 10,gold:50,red
> color radial #7 center sel palette 40,gold:50,red
> color radial #7 center sel palette 50,gold:40,red
> color radial #7 center sel palette 50,gold:45,red
> palette list
No custom palettes.
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.
> color radial #7 center sel palette accent
> close #3
> close #2
> close #1
> close #5
> close #6
> close #7
> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrinvesicle_mem_imod.cmm
Opened 1 marker sets containing 71 markers
> volume #4 originIndex 0
> volume #4 voxelSize 1
> show #!4 models
> cofr #1
> hide #1 models
> show #1 models
> hide #!4 models
> show #!4 models
> volume #4 step 4
> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/clathrinvesicle_clathrin_imod.cmm
Opened 1 marker sets containing 140 markers
> hide #1 models
> show #1 models
> hide #2 models
> hide #!4 models
Drag select of 71 atoms
> volume zone #2 nearAtoms sel range 50 newMap true
> volume zone #4 nearAtoms sel range 50 newMap true
> show #2 models
> close #3
Drag select of 211 atoms
> volume zone #4 nearAtoms sel range 20 newMap true
> hide #1 models
> hide #2 models
> hide #!3 models
> show #2 models
> hide #2 models
> show #1 models
Drag select of
Drag select of 71 atoms
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #1 models
> select up
211 atoms, 6 models selected
> select up
211 atoms, 6 models selected
> select down
71 atoms, 1 model selected
> select down
71 atoms, 1 model selected
> color radial sel center sel palette accent
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> color radial #3 center sel palette accent
> scolor #3 zone sel range 80 autoUpdate true
Unknown command: scolor #3 zone sel range 80 autoUpdate true
> color zone #3 near sel distance 15 update true
> ~select #1
Nothing selected
> select #2
140 atoms, 1 model selected
> color zone #3 near sel distance 15 update true
> color zone #3 near sel distance 15 update true
> color zone #3 near sel distance 10 update true
> color zone #3 near sel distance 10 update true palette blue:red
Expected a keyword
> volume #3 level 3660
> color zone #3 near sel distance 10 update true palette blue:red
Expected a keyword
> color zone #3 near sel distance 10 update true
> surface dust #3 size 220
> surface dust #3 size 20
> color zone #3 near sel distance 10 update true palette rainbow
Expected a keyword
> color zone #3 near sel distance 10 update true palette Accent
Expected a keyword
> hide #!3 models
> show #2 models
> hide #2 models
> show #1 models
> select up
211 atoms, 2 models selected
> select up
211 atoms, 6 models selected
> select down
211 atoms, 2 models selected
> select down
141 atoms, 2 models selected
> color radial #3 center sel palette gold:red
> show #!3 models
> hide #1 models
> hide #!3 models
> show #1 models
> show #!3 models
> hide #1 models
> color radial #3 center sel palette gold:red
> color radial #3 center sel palette gold:red
> color radial #3 center sel palette 0.3,gold:0.7,red
> color radial #3 center sel palette 0.3,gold:0.07,red
> color radial #3 center sel palette 0.3,gold:0.1,red
> color radial #3 center sel palette 0.3,gold:0.3,red
> color radial #3 center sel palette 0.3,gold:0.29,red
> color radiall #3 center sel palette 0.3,gold:0.29,red:pink
Invalid "palette" argument: Number of values and color must match in colormap
> color radiall #3 center sel palette 0.3,gold:red:0.29,pink
Invalid "palette" argument: Number of values and color must match in colormap
> color radial #3 center sel palette 0,gold:0.7,red:0.29,pink
> color radial #3 center sel palette 0.5,gold:0.7,red:0.29,pink
> color radial #3 center sel palette 0.5,gold:0.6,red:0.29,pink
> color radial #3 center sel palette 10,gold:10,red:10,pink
> color radial #3 center sel palette 30,gold:20,red:10,pink
> color radial #3 center sel palette 50,pink:45,red:10,yellow
> show #1 models
> hide #1 models
> color cylindrical #3 centre sel palette 50,pink:45,red:10,yellow
Expected a keyword
> hide #1 models
> hide #!3 models
> show #1 models
> select #1/M:62@M
1 atom, 1 model selected
> select #1/M:48@M
1 atom, 1 model selected
> hide #1 models
> show #2 models
> hide #2 models
> show #!3 models
> color cylindrical #3 axis sel palette 50,pink:45,red:10,yellow
Invalid "axis" argument: Axis argument requires 2 atoms, got 3 atoms
> show #1 models
> hide #!3 models
> select #1/M:4@M
1 atom, 1 model selected
> show #!3 models
> hide #1 models
> color cylindrical #3 axis sel palette 50,pink:45,red:10,yellow
> color cylindrical #3 axis sel palette 50,pink:45,red:30,yellow
> color cylindrical #3 axis sel palette 50,pink:45,red:20,yellow
> show #1 models
> hide #!3 models
> select #1/M:66@M
1 atom, 1 model selected
> show #!3 models
> hide #1 models
> color cylindrical #3 axis sel palette 50,pink:45,red:20,yellow
> color cylindrical #3 axis sel palette 50,pink:48,red:20,yellow
> color cylindrical #3 axis sel palette 52,pink:48,red:20,yellow
> color cylindrical #3 axis sel palette 52,magenta:48,red:20,yellow
> color cylindrical #3 axis sel palette 55,magenta:48,red:20,yellow
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> color cylindrical #3 axis sel palette 55,magenta:48,red:20,yellow
> volume #3 step 1
> volume #3 level 4009
> color cylindrical #3 axis sel palette 60,magenta:48,red:20,yellow
> color cylindrical #3 axis sel palette 70,magenta:48,red:20,yellow
> color cylindrical #3 axis sel palette 70,magenta:48,red:40,yellow
> color cylindrical #3 axis sel palette 70,magenta:48,red:40,yellow
> color cylindrical #3 axis sel palette 70,magenta:48,red:30,yellow
> color cylindrical #3 axis sel palette 70,magenta:48,red:25,yellow
> volume #1 surfaceSmoothing true smoothingIterations 3 smoothingFactor 0.3
No volumes specified
> volume #4 surfaceSmoothing true smoothingIterations 3 smoothingFactor 0.3
> volume #4 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
> volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
> volume #3 level 3708
> volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.3
> surface dust #3 size 20
> surface dust #3 size 50
> surface dust #3 size 40
> surface dust #3 size 100
> surface dust #3 size 200
> surface dust #3 size 100
> volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.4
> volume #3 surfaceSmoothing true smoothingIterations 5 smoothingFactor 0.6
> ui mousemode right "map eraser"
> ui mousemode right "mark point"
> marker #1 position 349.9,542.7,125.1 color yellow radius 20
> show #2 models
> show #1 models
> marker change #1:102 radius 5
> ui mousemode right "move markers"
> marker change #1:102 position 340.5,536.7,125.1
> marker change #1:102 position 342.1,536.8,133.1
> ui mousemode right "mark point"
> marker #1 position 342.1,536.6,123.4 color yellow radius 5
> marker #1 position 342.4,536.7,127 color yellow radius 5
> marker #1 position 340.2,537.7,119.9 color yellow radius 5
> marker #1 position 337.5,539.3,114.7 color yellow radius 5
> marker #1 position 336.3,538.7,108.2 color yellow radius 5
> marker #1 position 345.8,535.6,138.4 color yellow radius 5
> marker #1 position 337.1,528.6,133.9 color yellow radius 5
> ui mousemode right "move markers"
> marker change #1:109 position 339.5,534.5,132.1
> marker change #1:109 position 338.6,535.4,127.1
> marker change #1:109 position 340.4,536.7,129
> marker change #1:109 position 340.6,536.5,125.1
> ui mousemode right "mark point"
> marker #1 position 335.1,527.2,129.6 color yellow radius 5
> ui mousemode right "move markers"
> marker change #1:110 position 340.9,537,129.6
> select #1/M:108@M
1 atom, 1 model selected
> marker change #1:108 position 344.9,536.5,136.9
> select #1/M:110@M
1 atom, 1 model selected
> marker change #1:110 position 340.1,536.5,129.3
> cofr sel
> ui mousemode right "map eraser"
> hide #1 models
> hide #2 models
> hide #!3 models
> show #!3 models
> select clear
> select clear
> select #3
3 models selected
> select clear
> select clear
> select clear
> select clear
> hide #!3 models
Drag select of eraser sphere, 6 of 1000 triangles
> show #!3 models
> volume erase #3 center 332.43,552.34,106.68 radius 16.8
> volume erase #3 center 331.6,541.54,125.62 radius 16.8
> ui mousemode right "map eraser"
> ui mousemode right translate
> ui mousemode right translate
> ui mousemode right "mark point"
> ui mousemode right "mark point"
> marker #1 position 355.1,503.1,172.2 color yellow radius 5
> show #1 models
> marker #1 position 392.5,509.8,34.16 color yellow radius 5
> ui mousemode right "move markers"
> select #1/M:111@M
1 atom, 1 model selected
> marker change #1:111 position 350.8,509.3,171.9
> select #1/M:112@M
1 atom, 1 model selected
> hide #1 models
> color cylindrical #3 axis sel palette 70,magenta:48,red:25,yellow
> volume #3 level 3708
> color cylindrical #3 axis sel palette 70,magenta:55,red:25,yellow
> color cylindrical #3 axis sel palette 70,magenta:53,red:25,yellow
> color cylindrical #3 axis sel palette 70,magenta:50,red:25,yellow
> ui mousemode right "map eraser"
> hide #!3 models
> show #2 models
> hide #2 models
> show #!3 models
> volume erase #3 center 343.34,466.19,90.744 radius 15.36
> color cylindrical #3 axis sel palette 70,magenta:50,red:23,yellow
> color cylindrical #3 axis sel palette 70,magenta:50,red:20,yellow
> set bgColor white
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> ui mousemode right "map eraser"
> hide #!3 models
> show #!3 models
> volume erase #3 center 341.7,493.34,145.53 radius 15.36
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/D04_TS_10_vesicleclathrin_scale_zoned.mrc
> models #3
> close #4
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs
> includeMaps true
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
cmd.run(cmd_text)
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
result = ci.function(session, **kw_args)
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
Command(session, registry=registry).run(provider_cmd_text, log=log)
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
result = ci.function(session, **kw_args)
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
mgr).save(session, path, **provider_kw)
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
return cxs_save(session, path, **kw)
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs
> includeMaps false
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
cmd.run(cmd_text)
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
result = ci.function(session, **kw_args)
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
Command(session, registry=registry).run(provider_cmd_text, log=log)
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
result = ci.function(session, **kw_args)
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
mgr).save(session, path, **provider_kw)
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
return cxs_save(session, path, **kw)
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> select down
2 atoms, 1 model selected
> select up
82 atoms, 1 model selected
> select up
222 atoms, 4 models selected
> select up
222 atoms, 4 models selected
> select down
82 atoms, 1 model selected
> select down
2 atoms, 1 model selected
> select down
2 atoms, 1 model selected
> select down
2 atoms, 1 model selected
> show #1 models
> hide #1 models
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin_mem.cmm
> format markers models #1
Wrote 1 marker sets containing 82 markers
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin_clathrin.cmm
> format markers models #2
Wrote 1 marker sets containing 140 markers
> rename #1 mem
> rename #2 clathrin
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs
> includeMaps false
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
cmd.run(cmd_text)
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
result = ci.function(session, **kw_args)
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
Command(session, registry=registry).run(provider_cmd_text, log=log)
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
result = ci.function(session, **kw_args)
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
mgr).save(session, path, **provider_kw)
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
return cxs_save(session, path, **kw)
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/Vesicleclathrin_electrondensity.png
> width 1126 height 827 supersample 3
> save /Users/fbsrfr/Desktop/image8.png supersample 3
> save /Users/fbsrfr/Desktop/image8.png supersample 3
> save
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
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
self.processed[key] = self.process(obj, parents)
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
return copy_state(data, convert=convert)
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
return _copy(data)
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
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
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
return convert(data)
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
return add_obj(obj, parents)
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
uid = _UniqueName.from_obj(self.session, obj)
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
obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for tinyarray.ndarray_float
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
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>
action.triggered.connect(lambda arg, cb = callback: cb())
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>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
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
_dlg.display(session, **kw)
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
run(session, cmd)
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
results = command.run(text, log=log)
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
result = ci.function(session, **kw_args)
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
Command(session, registry=registry).run(provider_cmd_text, log=log)
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
result = ci.function(session, **kw_args)
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
mgr).save(session, path, **provider_kw)
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
return cxs_save(session, path, **kw)
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
session.save(output, version=version, include_maps=include_maps)
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
mgr.discovery(self._state_containers)
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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
ValueError: error processing: '_surface_updaters' -> -> : No bundle
information for tinyarray.ndarray_float
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
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.19
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 207.0.0.0.0
SMC Version (system): 2.43f6
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G5033)
Kernel Version: Darwin 18.7.0
Time since boot: 16 days 10:15
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
PL2483H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 1156292263699
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: chimerax_error.md
Attachments (1)
Change History (8)
by , 5 years ago
| Attachment: | chimerax_error.md added |
|---|
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Milestone: | → 1.1 |
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → major |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cannot save session containing tinyarray.ndarray_float |
I though sessions knew about tinyarray types already?
comment:2 by , 5 years ago
| Status: | assigned → accepted |
|---|
I see explicit support for tinyarray.ndarray_float, will investigate.
comment:3 by , 5 years ago
The session save failure was for surface_updaters which is probably from the preceeding cylindrical coloring command "color cylindrical #3 axis sel palette 70,magenta:50,red:20,yellow". This coloring updates when the surface shape changes and so the cylinder coloring details are put into the session file.
comment:4 by , 5 years ago
I tried the cylinder coloring followed by session save in ChimeraX 1.0 and 1.1 and it worked. But the surface_updaters are either handling coloring or zoning of surfaces and in the past tiny array was used for some colors. But the tiny array could also be a position used in a surface zone.
comment:5 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Fixed. Serialization code understood tinyarrays, but the layer above it didn't.
comment:6 by , 5 years ago
Reproduced with:
open 3rec select @c1' surf color cylindrical #1 axis sel save foo.cxs
comment:7 by , 5 years ago
Here is a recipe to reproduce it. It is the axis specification in the color cylinder command
open 1a0m
surface
color cyl #1.1 axis /A:7@CA,CB
save test.cxs
Apparently the axis is being saved as a tiny array vector.
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