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 2020opened 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.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 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.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 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.mrcOpened 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.mp4Movie 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.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 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 modelsDrag select of 87 atoms show #!2 models volume zone #3 nearAtoms #50 range 10 newMap trueno atoms specified for zone volume zone #2 nearAtoms #3 range 10 newMap true volume #4 level 1648 volume #4 level 816 select #395 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 #13Wrote 0 marker sets containing 0 markers 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 volume #4 level 3815 volume #4 level 4558 ~select #3Nothing selected select #395 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@M1 atom, 1 model selected color radiall #4 centre sel rainbow Expected a keyword color radiall #4 centre sel Expected a keyword color radiall #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 radiall #4 center sel volume #4 level 3071 volume zone #2 nearAtoms #3 range 250 newMap true select #395 atoms, 1 model selected ~select #3Nothing selected close #5 select upNothing selected select downNothing selected select upNothing selected select upNothing selected select downNothing selected select downNothing selected select downNothing selected select downNothing selected select downNothing selected select downNothing 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 modelsDrag 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@M1 atom, 1 model selected color radiall #2 center sel rainbow Expected a keyword color radiall #2 center sel volume zone #2 nearAtoms #3 range 350 newMap true color radiall #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.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 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 up95 atoms, 1 model selected select up95 atoms, 9 models selected select down95 atoms, 1 model selected select down1 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 radiall #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 radiall #5 center sel volume #5 level 3825 select up96 atoms, 1 model selected select down2 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 selDeleted 2 markers marker delete selDeleted 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 upNothing selected select upNothing selected select downNothing selected select downNothing selected select downNothing selected surface dust #7 size 220 color radiall #7 center sel Drag select of color radiall #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 radiall #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 radiall #7 center sel palette 1,gold:0.5,red color radiall #7 center sel palette 0.5,gold:0.5,red color radiall #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 radiall #7 center sel palette 5,gold:0.1,red color radiall #7 center sel palette .2,gold:0.1,red color radiall #7 center sel palette 0.2,gold:0.1,red color radiall #7 center sel palette 0.2,gold:0.5,red color radiall #7 center sel palette 0.2,gold:0.2,red color radiall #7 center sel palette 0.2,gold:0.3,red color radiall #7 center sel palette 10,gold:5,red color radiall #7 center sel palette 10,gold:50,red color radiall #7 center sel palette 40,gold:50,red color radiall #7 center sel palette 50,gold:40,red color radiall #7 center sel palette 50,gold:45,red palette listNo 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 radiall #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.cmmOpened 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.cmmOpened 1 marker sets containing 140 markers hide #1 models show #1 models hide #2 models hide #!4 modelsDrag 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 #3Drag 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 modelsDrag select of Drag select of 71 atoms show #!4 models hide #!4 models show #!3 models hide #1 models select up211 atoms, 6 models selected select up211 atoms, 6 models selected select down71 atoms, 1 model selected select down71 atoms, 1 model selected color radiall sel center sel palette accent show #2 models hide #2 models show #1 models hide #1 models show #1 models hide #1 models color radiall #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 #1Nothing selected select #2140 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 up211 atoms, 2 models selected select up211 atoms, 6 models selected select down211 atoms, 2 models selected select down141 atoms, 2 models selected color radiall #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 radiall #3 center sel palette gold:red color radiall #3 center sel palette gold:red color radiall #3 center sel palette 0.3,gold:0.7,red color radiall #3 center sel palette 0.3,gold:0.07,red color radiall #3 center sel palette 0.3,gold:0.1,red color radiall #3 center sel palette 0.3,gold:0.3,red color radiall #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 radiall #3 center sel palette 0,gold:0.7,red:0.29,pink color radiall #3 center sel palette 0.5,gold:0.7,red:0.29,pink color radiall #3 center sel palette 0.5,gold:0.6,red:0.29,pink color radiall #3 center sel palette 10,gold:10,red:10,pink color radiall #3 center sel palette 30,gold:20,red:10,pink color radiall #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@M1 atom, 1 model selected select #1/M:48@M1 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@M1 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@M1 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 0.3No 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@M1 atom, 1 model selected marker change #1:108 position 344.9,536.5,136.9 select #1/M:110@M1 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 #33 models selected select clear select clear select clear select clear hide #!3 modelsDrag 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@M1 atom, 1 model selected marker change #1:111 position 350.8,509.3,171.9 select #1/M:112@M1 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 trueTraceback (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 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' -> -> : 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 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' -> -> : 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 falseTraceback (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 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' -> -> : 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 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' -> -> : 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 down2 atoms, 1 model selected select up82 atoms, 1 model selected select up222 atoms, 4 models selected select up222 atoms, 4 models selected select down82 atoms, 1 model selected select down2 atoms, 1 model selected select down2 atoms, 1 model selected select down2 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 #1Wrote 1 marker sets containing 82 markers 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 rename #1 mem rename #2 clathrin save /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/Figures/Clathrin/vesicleclathrin.cxs includeMaps falseTraceback (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 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' -> -> : 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 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' -> -> : 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.cxsTraceback (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 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' -> -> : 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 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 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 *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' -> -> : 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.