id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3382 Map replacement results in session-save failure: self.positions is None g.zanetti@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0rc202005292300 (2020-05-29 23:00:06 UTC) Description I had a session where I opened an mrc file with charge attributes (coulomb_model3.mrc), which I had obtained with Coulomb potential in chimera. That session was saved fine. Then I removed the coulomb_model3.mrc file from the session, and opened another one, calculated again from chimera and saved with a different name (coulomb_model3_wcharges.mrc). I get this error when I try to save the session after changing the charge file. I get the error bot if I try and overwrite the previous chimera session or write a new one. Log: UCSF ChimeraX version: 1.0rc202005292300 (2020-05-29) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/chimera_session_model3.cxs > format session /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Autosharpen_62/sharpened_map_mask.mrc: invalid cell angles 0,0,0 must be between 0 and 180. /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked90.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Log from Mon Jun 8 07:07:36 2020UCSF ChimeraX version: 1.0rc202005292300 (2020-05-29) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/fittedC2.pdb > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/fittedC1.pdb > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/fitted2.pdb > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/fitted1.pdb Chain information for fittedC2.pdb #1 --- Chain | Description A | No description available fittedC1.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) cterm [more info...] Chain information for fittedC1.pdb #2 --- Chain | Description A | No description available Chain information for fitted2.pdb #3 --- Chain | Description A | No description available B | No description available fitted1.pdb title: The structure of the copii coat assembled on membranes [more info...] Chain information for fitted1.pdb #4 --- Chain | Description A | protein WEB1 B | protein transport protein SEC13 > open /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/rods_L_pp_mr38_B2200.mrc Opened rods_L_pp_mr38_B2200.mrc, grid size 128,128,128, pixel 2.66, shown at level 4.35, step 1, values float32 > set bgColor white > volume #5 level 4.35 > volume #5 color black > volume #5 color #00000019 > preset cartoons/nucleotides cylinders/stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > select #3/B:245 9 atoms, 8 bonds, 1 model selected > select up 33 atoms, 32 bonds, 1 model selected > select up 2196 atoms, 2256 bonds, 1 model selected > select up 4876 atoms, 4976 bonds, 1 model selected > select up 11438 atoms, 11666 bonds, 6 models selected > select down 4876 atoms, 4976 bonds, 1 model selected > select down 2196 atoms, 2256 bonds, 1 model selected > select up 4876 atoms, 4976 bonds, 1 model selected > select down 2196 atoms, 2256 bonds, 1 model selected > volume #5 color grey > color sel dim gray > select #4/B:105 7 atoms, 6 bonds, 1 model selected > select up 51 atoms, 52 bonds, 1 model selected > select up 2196 atoms, 2256 bonds, 1 model selected > color sel dim gray > select clear > select up 225 atoms, 225 bonds, 2 models selected > select up 1686 atoms, 1714 bonds, 2 models selected > volume #5 color #fc0107 > color sel purple > ui tool show ""Color Actions"" > color sel chocolate > color sel orange red > color sel chocolate > color sel tomato > color sel chocolate > select clear > select #3/A:589 8 atoms, 7 bonds, 1 model selected > select up 200 atoms, 203 bonds, 1 model selected > select up 2680 atoms, 2720 bonds, 1 model selected > color sel deep pink > select #4/A:621 11 atoms, 10 bonds, 1 model selected > select up 148 atoms, 147 bonds, 1 model selected > select up 2680 atoms, 2720 bonds, 1 model selected > color sel pale violet red > color sel aquamarine > color sel light coral > color sel dark violet > color sel orchid > color sel pale violet red > color sel rosy brown > select clear > volume #5 color black > volume #5 color #00000019 > view orient > ui tool show ""Side View"" > volume #5 level 5.011 > hide #1 models > hide #2 models > volume #5 level 5 > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting shadows true > select #4/A:656 9 atoms, 8 bonds, 1 model selected > select up 281 atoms, 286 bonds, 1 model selected > select up 2680 atoms, 2720 bonds, 1 model selected > ui tool show ""Color Actions"" > color sel light pink > color sel thistle > color sel light pink > color sel pink > color sel light pink > select clear > volume #5 level 6 > volume #5 level 5.5 > volume #5 level 5.2 > volume #5 level 5.5 > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/top1.png > width 795 height 730 supersample 3 > turn x -90 > volume #5 color white > volume #5 color #fffffff8 > volume #5 color #ffffffeb > volume #5 color #ffffffcd > volume #5 color #ffffffbd > volume #5 color #ffffffb2 > volume #5 color #ffffffac > volume #5 color #ffffffab > volume #5 color #ffffffaa > volume #5 color #ffffffa6 > volume #5 color #ffffff98 > volume #5 color #ffffff89 > volume #5 color #ffffff80 > volume #5 color #ffffff89 > volume #5 color #ffffff8a > volume #5 color #ffffff8b > volume #5 color #ffffff8e > volume #5 color #ffffff91 > volume #5 color #ffffff92 > volume #5 color #ffffff96 > volume #5 color #ffffff99 > volume #5 color #ffffff9b > volume #5 color #ffffff9f > volume #5 color #ffffffa3 > volume #5 color #ffffffa5 > volume #5 color #ffffffa7 > volume #5 color #ffffffa8 > volume #5 color #ffffffa9 > volume #5 color #ffffffaa > volume #5 color #ffffffad > volume #5 color #ffffffb0 > volume #5 color #ffffffb1 > volume #5 color #ffffffb2 > volume #5 color #ffffffb3 > volume #5 color #ffffffb4 > volume #5 color #ffffffb5 > volume #5 color #ffffffb6 > volume #5 color black > volume #5 color #00000019 > volume #5 color #0000001a > volume #5 color #0000001b > volume #5 color #0000001d > volume #5 color #0000001f > volume #5 color #00000022 > volume #5 color #00000023 > volume #5 color #00000025 > volume #5 color #00000028 > volume #5 color #0000002d > volume #5 color #00000036 > volume #5 color #0000003a > volume #5 color #0000003c > volume #5 color #0000003d > volume #5 color #0000003e > volume #5 color #00000040 > volume #5 color #00000041 > volume #5 color #00000043 > volume #5 color #00000046 > volume #5 color #0000004c > volume #5 color #0000004e > volume #5 color #00000050 > volume #5 color #0000004f > volume #5 color #0000004e > volume #5 color #0000004d > volume #5 color #0000004b > volume #5 color #0000004a > volume #5 color #00000049 > volume #5 color #00000048 > volume #5 color #00000047 > volume #5 color #00000045 > volume #5 color #00000042 > volume #5 color #00000040 > volume #5 color #0000003e > volume #5 color #0000003d > volume #5 color #0000003c > volume #5 color #0000003b > volume #5 color #0000003a > volume #5 color #00000039 > volume #5 color #00000037 > volume #5 color #00000036 > volume #5 color #00000034 > volume #5 color #00000033 > volume #5 color #00000034 > volume #5 color #00000035 > volume #5 color #00000036 > volume #5 color #00000037 > volume #5 color #0000003a > volume #5 color #00000041 > volume #5 color #00000045 > volume #5 color #00000047 > volume #5 color #00000048 > volume #5 color #00000047 > volume #5 color #00000044 > volume #5 color #0000003e > volume #5 color #0000003a > volume #5 color #00000038 > volume #5 color #00000039 > volume #5 color #0000003b > volume #5 color #0000003d > volume #5 color #00000040 > volume #5 color #00000043 > volume #5 color #00000044 > volume #5 color #00000043 > volume #5 color #00000042 > volume #5 color #0000003f > volume #5 color #0000003a > volume #5 color #00000035 > volume #5 color #00000033 > volume #5 color #00000030 > volume #5 color #0000002f > volume #5 color #00000030 > volume #5 color #0000003a > volume #5 color #00000045 > volume #5 color #00000054 > volume #5 color #00000058 > volume #5 color #0000005c > volume #5 color #0000005d > volume #5 color #0000005f > volume #5 color #0000005d > volume #5 color #0000005a > volume #5 color #00000053 > volume #5 color #00000049 > volume #5 color #00000046 > volume #5 color #00000045 > volume #5 color #00000044 > volume #5 color #00000043 > volume #5 color #0000003f > volume #5 color #0000003d > volume #5 color #0000003b > volume #5 color #0000003a > volume #5 color #00000037 > volume #5 color #0000002d > volume #5 color #00000026 > volume #5 color #00000024 > volume #5 color #00000019 > lighting simple > lighting simple > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > volume #5 color white > volume #5 color #fffffffd > volume #5 color #fffffffa > volume #5 color #fffffff4 > volume #5 color #ffffffef > volume #5 color #ffffffe6 > volume #5 color #ffffffdf > volume #5 color #ffffffd8 > volume #5 color #ffffffcf > volume #5 color #ffffffc5 > volume #5 color #ffffffb9 > volume #5 color #ffffffae > volume #5 color #ffffffa1 > volume #5 color #ffffff95 > volume #5 color #ffffff8b > volume #5 color #ffffff84 > volume #5 color #ffffff7f > volume #5 color #ffffff77 > volume #5 color #ffffff72 > volume #5 color #ffffff6f > volume #5 color #ffffff6d > volume #5 color #ffffff6c > volume #5 color #ffffff6d > volume #5 color #ffffff6e > volume #5 color #ffffff6f > volume #5 color #ffffff71 > volume #5 color #ffffff74 > volume #5 color #ffffff76 > volume #5 color #ffffff77 > volume #5 color #ffffff78 > volume #5 color #ffffff76 > volume #5 color #ffffff75 > volume #5 color #ffffff73 > volume #5 color #ffffff72 > volume #5 color #ffffff71 > volume #5 color #ffffff70 > volume #5 color #ffffff6f > volume #5 color #ffffff6d > volume #5 color #ffffff6b > volume #5 color #ffffff67 > volume #5 color #ffffff5e > volume #5 color #ffffff5a > volume #5 color #ffffff58 > volume #5 color #ffffff57 > volume #5 color #ffffff58 > volume #5 color #ffffff5a > volume #5 color #ffffff5c > volume #5 color #ffffff5d > volume #5 color #ffffff5f > volume #5 color #ffffff60 > volume #5 color #ffffff61 > volume #5 color #ffffff62 > volume #5 color #ffffff63 > volume #5 color #ffffff68 > volume #5 color #ffffff6b > volume #5 color #ffffff6f > volume #5 color #ffffff72 > volume #5 color #ffffff74 > volume #5 color #ffffff75 > volume #5 color #ffffff76 > volume #5 color #ffffff81 > volume #5 color #ffffff91 > volume #5 color #ffffffa0 > volume #5 color #ffffffa5 > volume #5 color #ffffffa6 > volume #5 color #ffffffa7 > lighting full > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > volume #5 color black > volume #5 color #00000019 > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/side1.png > width 795 height 730 supersample 3 > turn x 90 > volume #5 color white > volume #5 color #fffffffd > volume #5 color #fffffff7 > volume #5 color #ffffffe7 > volume #5 color #ffffffd2 > volume #5 color #ffffffc9 > volume #5 color #ffffffbe > volume #5 color #ffffffb3 > volume #5 color #ffffffa9 > volume #5 color #ffffffa2 > volume #5 color #ffffff9e > volume #5 color #ffffff99 > volume #5 color #ffffff93 > volume #5 color #ffffff91 > volume #5 color #ffffff8a > volume #5 color #ffffff84 > volume #5 color #ffffff7c > volume #5 color #ffffff73 > volume #5 color #ffffff6a > volume #5 color #ffffff64 > volume #5 color #ffffff5d > volume #5 color #ffffff56 > volume #5 color #ffffff53 > volume #5 color #ffffff50 > volume #5 color #ffffff4b > volume #5 color #ffffff49 > volume #5 color #ffffff47 > volume #5 color #ffffff48 > volume #5 color #ffffff4a > volume #5 color #ffffff4b > volume #5 color #ffffff4e > volume #5 color #ffffff51 > volume #5 color #ffffff55 > volume #5 color #ffffff56 > volume #5 color #ffffff57 > volume #5 color #ffffff58 > volume #5 color #ffffff5a > volume #5 color #ffffff5c > volume #5 color #ffffff5f > volume #5 color #ffffff61 > volume #5 color #ffffff64 > volume #5 color #ffffff69 > volume #5 color #ffffff6d > volume #5 color #ffffff71 > volume #5 color #ffffff72 > volume #5 color #ffffff73 > volume #5 color #ffffff74 > volume #5 color #ffffff76 > volume #5 color #ffffff78 > volume #5 color #ffffff7a > volume #5 color #ffffff79 > volume #5 color #ffffff77 > volume #5 color #ffffff73 > volume #5 color #ffffff71 > turn x -90 > toolshed show > ui tool show ""Side View"" > lighting gentle > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting intensity 2 > lighting intensity 0.5 > lighting intensity 1 > lighting intensity 0.5 > lighting fillIntensity 1 > lighting fillIntensity 0.5 > lighting fillIntensity 0.2 > lighting fillIntensity 0.5 > lighting fillDirection -0.5,-0.5,-0.5 > lighting simple > lighting fillIntensity 1 > lighting intensity 1 > lighting intensity 2 > lighting fillIntensity 2 > lighting fillIntensity 0.5 > lighting intensity 1 > lighting fillIntensity 0.25 > lighting fillIntensity 0.1 > lighting fillIntensity 0.25 > lighting ambientIntensity 0.25 > volume #5 color #ffffff74 > volume #5 color #ffffff77 > volume #5 color #ffffff7e > volume #5 color #ffffff85 > volume #5 color #ffffff8a > volume #5 color #ffffff8f > volume #5 color #ffffff94 > volume #5 color #ffffff96 > volume #5 color #ffffff98 > volume #5 color #ffffff9c > volume #5 color #ffffff9f > volume #5 color #ffffffa1 > volume #5 color #ffffffa3 > volume #5 color #ffffffa4 > volume #5 color #ffffffa5 > volume #5 color #ffffffa7 > volume #5 color #ffffffaa > volume #5 color #ffffffad > volume #5 color #ffffffaf > volume #5 color #ffffffae > volume #5 color #ffffffad > volume #5 color #ffffffac > volume #5 color #ffffffaa > volume #5 color #ffffffa7 > volume #5 color #ffffffa6 > volume #5 color #ffffffa4 > volume #5 color #ffffffa2 > volume #5 color #ffffffa1 > volume #5 color #ffffffa0 > volume #5 color #ffffff9f > volume #5 color #ffffff9e > volume #5 color #ffffff9d > volume #5 color #ffffff9c > volume #5 color #ffffff9b > volume #5 color #ffffff9a > volume #5 color #ffffff99 > volume #5 color #ffffff97 > volume #5 color #ffffff98 > volume #5 color #ffffff99 > volume #5 color #ffffff9b > volume #5 color #ffffff9c > volume #5 color #ffffff9d > volume #5 color #ffffff9e > volume #5 color #ffffff9f > volume #5 color #ffffff9d > volume #5 color #ffffff9c > volume #5 color #ffffff9b > volume #5 color #ffffff9a > volume #5 color #ffffff98 > volume #5 color #ffffff97 > volume #5 color #ffffff93 > volume #5 color #ffffff90 > volume #5 color #ffffff8d > volume #5 color #ffffff8b > volume #5 color #ffffff8a > volume #5 color #ffffff8b > volume #5 color #ffffff8c > volume #5 color #ffffff8d > volume #5 color #ffffff8e > volume #5 color #ffffff8f > volume #5 color #ffffff90 > volume #5 color #ffffff91 > volume #5 color #ffffff92 > volume #5 color #ffffff93 > volume #5 color #ffffff94 > volume #5 color #ffffff95 > volume #5 color #ffffff96 > volume #5 color #ffffff97 > volume #5 color #ffffff98 > volume #5 color #ffffff99 > volume #5 color #ffffff9a > volume #5 color #ffffff9c > volume #5 color #ffffff9d > volume #5 color #ffffff9e > volume #5 color #ffffffa1 > volume #5 color #ffffffa2 > volume #5 color #ffffffa4 > volume #5 color #ffffffa6 > volume #5 color #ffffffaa > volume #5 color #ffffffad > volume #5 color #ffffffb6 > volume #5 color #ffffffba > volume #5 color #ffffffbb > volume #5 color #ffffffba > volume #5 color #ffffffb9 > volume #5 color #ffffffb8 > volume #5 color #ffffffb7 > volume #5 color #ffffffb6 > volume #5 color #ffffffb4 > volume #5 color #ffffffb3 > volume #5 color #ffffffb1 > volume #5 color #ffffffaf > volume #5 color #ffffffae > volume #5 color #ffffffad > volume #5 color #ffffffac > volume #5 color #ffffffab > volume #5 color #ffffffaa > volume #5 color #ffffffa9 > volume #5 color #ffffffa7 > volume #5 color #ffffffa4 > volume #5 color #ffffffa3 > volume #5 color #ffffffa1 > volume #5 color #ffffffa0 > volume #5 color #ffffff9f > volume #5 color #ffffff9e > volume #5 color #ffffff9d > volume #5 color #ffffff9c > volume #5 color #ffffff99 > volume #5 color #ffffff96 > volume #5 color #ffffff95 > volume #5 color #ffffff94 > volume #5 color #ffffff93 > volume #5 color #ffffff92 > volume #5 color #ffffff91 > volume #5 color #ffffff90 > volume #5 color #ffffff8f > volume #5 color #ffffff8d > volume #5 color #ffffff8c > volume #5 color #ffffff8b > volume #5 color #ffffff89 > volume #5 color #ffffff88 > volume #5 color #ffffff87 > volume #5 color #ffffff85 > volume #5 color #ffffff84 > volume #5 color #ffffff82 > volume #5 color #ffffff81 > volume #5 color #ffffff80 > volume #5 color #ffffff76 > volume #5 color #ffffff74 > volume #5 color #ffffff72 > volume #5 color #ffffff71 > volume #5 color #ffffff70 > volume #5 color #ffffff6e > volume #5 color #ffffff6d > volume #5 color #ffffff6c > volume #5 color #ffffff6d > volume #5 color #ffffff6e > volume #5 color #ffffff72 > volume #5 color #ffffff78 > volume #5 color #ffffff7b > volume #5 color #ffffff7d > volume #5 color #ffffff80 > volume #5 color #ffffff89 > volume #5 color #ffffff8d > volume #5 color #ffffff94 > volume #5 color #ffffff99 > volume #5 color #ffffff9d > volume #5 color #ffffffa0 > volume #5 color #ffffffa6 > volume #5 color #ffffffa8 > volume #5 color #ffffffaa > volume #5 color #ffffffb1 > volume #5 color #ffffffbc > volume #5 color #ffffffcd > volume #5 color #ffffffe6 > volume #5 color #fffffff5 > volume #5 color white > volume #5 color #fffffff3 > volume #5 color #ffffffed > volume #5 color #ffffffe8 > volume #5 color #ffffffe6 > volume #5 color #ffffffe4 > volume #5 color #ffffffe2 > volume #5 color #ffffffe0 > volume #5 color #ffffffdd > volume #5 color #ffffffda > volume #5 color #ffffffd5 > volume #5 color #ffffffd1 > volume #5 color #ffffffcc > volume #5 color #ffffffc5 > volume #5 color #ffffffbe > volume #5 color #ffffffba > volume #5 color #ffffffb5 > volume #5 color #ffffffb3 > volume #5 color #ffffffb2 > volume #5 color #ffffffb1 > volume #5 color #ffffffb0 > volume #5 color #ffffffaf > volume #5 color #ffffffac > volume #5 color #ffffffa2 > volume #5 color #ffffff9d > volume #5 color #ffffff91 > volume #5 color #ffffff88 > volume #5 color #ffffff7d > volume #5 color #ffffff6e > volume #5 color #ffffff65 > volume #5 color #ffffff64 > volume #5 color #ffffff65 > volume #5 color #ffffff67 > volume #5 color #ffffff69 > volume #5 color #ffffff70 > volume #5 color #ffffff82 > volume #5 color #ffffff91 > volume #5 color #ffffff9e > volume #5 color #ffffffa4 > volume #5 color #ffffffa7 > volume #5 color #ffffffa8 > volume #5 color #ffffffac > volume #5 color #ffffffb9 > volume #5 color #ffffffde > volume #5 color #ffffffe3 > volume #5 color #ffffffe1 > volume #5 color #ffffffdd > volume #5 color #ffffffd4 > volume #5 color #ffffffd0 > volume #5 color #ffffffce > volume #5 color #ffffffcd > volume #5 color #ffffffcc > volume #5 color #ffffffc5 > volume #5 color #ffffffc2 > volume #5 color #ffffffc1 > volume #5 color #ffffffc0 > volume #5 color #ffffffbf > volume #5 color #ffffffbe > select #3 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select #4 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select #3 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select #4 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select #3 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select #4 4876 atoms, 4976 bonds, 6 pseudobonds, 2 models selected > select up 5103 atoms, 5205 bonds, 6 pseudobonds, 3 models selected > select up 7556 atoms, 7696 bonds, 6 pseudobonds, 3 models selected > select up 7655 atoms, 7798 bonds, 6 pseudobonds, 3 models selected > select up 9752 atoms, 9952 bonds, 6 pseudobonds, 3 models selected > color zone #5 near sel distance 10 > volume #5 color white > volume #5 color #fffffffb > volume #5 color #fffffff2 > volume #5 color #ffffffdb > volume #5 color #ffffffcb > volume #5 color #ffffffc4 > volume #5 color #ffffffbb > volume #5 color #ffffffb3 > volume #5 color #ffffff9e > volume #5 color #ffffff94 > volume #5 color #ffffff8b > volume #5 color #ffffff76 > volume #5 color #ffffff6c > volume #5 color #ffffff68 > volume #5 color #ffffff66 > volume #5 color #ffffff65 > volume #5 color #ffffff64 > volume #5 color #ffffff63 > volume #5 color #ffffff62 > volume #5 color #ffffff60 > volume #5 color #ffffff5d > volume #5 color #ffffff59 > volume #5 color #ffffff56 > volume #5 color #ffffff54 > volume #5 color #ffffff55 > volume #5 color #ffffff56 > volume #5 color #ffffff58 > volume #5 color #ffffff59 > volume #5 color #ffffff5a > volume #5 color #ffffff5b > volume #5 color #ffffff5c > volume #5 color #ffffff5d > volume #5 color #ffffff5e > volume #5 color #ffffff5f > select clear > graphics silhouettes true > graphics silhouettes false > volume #5 color #ffffff61 > volume #5 color #ffffff64 > volume #5 color #ffffff6b > volume #5 color #ffffff74 > volume #5 color #ffffff78 > volume #5 color #ffffff7b > volume #5 color #ffffff7f > volume #5 color #ffffff80 > volume #5 color #ffffff8a > volume #5 color #ffffff8d > volume #5 color #ffffff8f > volume #5 color #ffffff90 > volume #5 color #ffffff93 > volume #5 color #ffffff94 > volume #5 color #ffffff95 > volume #5 color #ffffff96 > volume #5 color #ffffff97 > volume #5 color #ffffff98 > volume #5 color #ffffff99 > volume #5 color #ffffff98 > volume #5 color #ffffff97 > volume #5 color #ffffff96 > volume #5 color #ffffff95 > volume #5 color #ffffff94 > volume #5 color #ffffff93 > volume #5 color #ffffff94 > volume #5 color #ffffff95 > volume #5 color #ffffff96 > volume #5 color #ffffff97 > volume #5 color #ffffff98 > volume #5 color #ffffff99 > volume #5 color #ffffff9a > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/side2.png > width 795 height 730 supersample 3 > turn x 90 > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/top2.png > width 795 height 730 supersample 3 > volume #5 level 5 > volume #5 color black > volume #5 color #00000019 > volume #5 color white > volume #5 color #ffffff00 > volume #5 color #ffffff80 > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting ambientIntensity 0.25 > lighting ambientIntensity 0.1 > volume #5 level 5.2 > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/detail1.png > width 795 height 730 supersample 4 > volume #5 level 5 > surface cap true > surface cap false > surface cap true > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/detail2.png > width 795 height 730 supersample 4 > view orient > volume #5 level 4 > show #1 models > show #2 models > select #1/A:97 9 atoms, 8 bonds, 1 model selected > select up 169 atoms, 171 bonds, 1 model selected > select up 843 atoms, 857 bonds, 1 model selected > view sel > volume #5 level 2.833 > volume #5 level 2.056 > select clear > volume #5 level 1.978 > volume #5 level 2.095 > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/fitC- > WMod.png width 795 height 730 supersample 3 > hide #1 models > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/fitC- > WOMod.png width 795 height 730 supersample 3 Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 1 - updating layer to match. Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x600001b24f00> contents scale of 2 - updating layer to match. > save /Users/ubgzan01/Documents/lab/yeast_COPII/EM/cryo- > inhouse/KRIOS_Jan19/outer_coat/after_clean/final_maps/figure_rods_L/chimeraX/session_070620.cxs > close session > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/two_protomers_no_sec31_headstripped_real_space_refined_3.pdb Chain information for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D H | No description available E | No description available F | No description available G | No description available > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Autosharpen_62/sharpened_map.mrc Opened sharpened_map.mrc, grid size 196,196,196, pixel 1.33, shown at level 3.35, step 1, values float32 > ui tool show ""Map Coordinates"" > volume #2 level 1.194 > volume #2 level 1 > close #2 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Autosharpen_62/sharpened_map_mask.mrc Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Autosharpen_62/sharpened_map_mask.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Autosharpen_62/sharpened_map_mask.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened sharpened_map_mask.mrc, grid size 196,196,196, pixel 1, shown at level 1.76, step 1, values float32 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod.mrc Opened denmod.mrc, grid size 196,196,196, pixel 1.33, shown at level 0.267, step 1, values float32 > volume #3 level 0.2867 > volume #3 level 0.08 > close #3 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod.mrc Opened denmod.mrc, grid size 196,196,196, pixel 1.33, shown at level 0.267, step 1, values float32 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked.mrc Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened denmod_masked.mrc, grid size 196,196,196, pixel 1, shown at level 0.186, step 1, values float32 > volume #4 level 0.01822 > ui tool show ""Map Coordinates"" > volume #4 level 0.03514 > volume #4 level 0.07574 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened denmod_masked95.mrc, grid size 196,196,196, pixel 1, shown at level 0.186, step 1, values float32 > volume #5 level 0.0471 > close #5 > close #4 > close #3 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked97.mrc Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked95.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked97.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked97.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened denmod_masked95.mrc, grid size 196,196,196, pixel 1, shown at level 0.188, step 1, values float32 Opened denmod_masked97.mrc, grid size 196,196,196, pixel 1, shown at level 0.191, step 1, values float32 > volume #4 level 0.1915 > volume #3 level 0.04653 > volume #4 level 0.06286 > volume #3 level 0.0761 > close #3 > close #4 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked90.mrc Summary of feedback from opening /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked90.mrc --- note | /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/ResolveCryoEM_57/denmod_masked90.mrc: invalid cell angles 0,0,0 must be between 0 and 180. Opened denmod_masked90.mrc, grid size 196,196,196, pixel 1, shown at level 0.186, step 1, values float32 > view orient > volume #2 level 1.756 > volume #2 level 1 > volume #3 level 0.1864 > volume #3 level 0.08 > preset cartoons/nucleotides cylinders/stubs Changed 26852 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > volume #2 color white > volume #2 color #fffffffe > volume #2 color #fffffff6 > volume #2 color #ffffffb4 > volume #2 color #ffffff9c > volume #2 color #ffffff9b > volume #2 color #ffffff98 > volume #2 color #ffffff8f > volume #2 color #ffffff7a > volume #2 color #ffffff72 > volume #2 color #ffffff71 > volume #2 color #ffffff6f > volume #2 color #ffffff6b > volume #2 color #ffffff68 > volume #2 color #ffffff66 > volume #2 color #ffffff65 > volume #2 color #ffffff66 > volume #3 level 0.08 > volume #2 color white > volume #2 color #ffffff66 > volume #3 color white > volume #3 color #ffffff66 > lighting simple > lighting soft > lighting full > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes true > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select /C:55 14 atoms, 15 bonds, 1 model selected > show sel target ab > select /A:710 11 atoms, 10 bonds, 1 model selected > show sel target ab > hide sel target a > select clear > select /C:55 14 atoms, 15 bonds, 1 model selected > hide sel target a > select clear > select /D:1802 7 atoms, 7 bonds, 1 model selected > select up 21 atoms, 23 bonds, 1 model selected > select up 26964 atoms, 27566 bonds, 1 model selected > select down 21 atoms, 23 bonds, 1 model selected > show sel target ab > select clear > select /A:384 12 atoms, 12 bonds, 1 model selected > select up 79 atoms, 80 bonds, 1 model selected > select up 5898 atoms, 6037 bonds, 1 model selected > select up 6025 atoms, 6166 bonds, 1 model selected > select up 7266 atoms, 7436 bonds, 1 model selected > addh #1 Summary of feedback from adding hydrogens to two_protomers_no_sec31_headstripped_real_space_refined_3.pdb #1 --- warning | Skipped 17 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb (#1) chain A; guessing termini instead No usable SEQRES records for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb (#1) chain B; guessing termini instead No usable SEQRES records for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb (#1) chain C; guessing termini instead No usable SEQRES records for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb (#1) chain D; guessing termini instead No usable SEQRES records for two_protomers_no_sec31_headstripped_real_space_refined_3.pdb (#1) chain E; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /A ASP 2, /B ARG 133, /C HIS 23, /D PRO 1801, /E ASP 2, /F ARG 133, /G HIS 23, /H PRO 1804 Chain-initial residues that are not actual N termini: /A HIS 483, /B GLY 779, /E HIS 483, /F GLY 779 Chain-final residues that are actual C termini: /C ILE 190 Chain-final residues that are not actual C termini: /A ALA 768, /A ALA 466, /B LYS 926, /B THR 770, /D PRO 1803, /E ALA 768, /E THR 465, /F LYS 926, /F PRO 769, /G TYR 189, /H PRO 1806 Skipping possible acceptor with bad geometry: /G GNP 201 O6 Wrong number of grandchild atoms for phi/psi acceptor /G GNP 201 O6 Skipping possible acceptor with bad geometry: /C TYR 189 O Wrong number of grandchild atoms for phi/psi acceptor /C TYR 189 O Skipping possible acceptor with bad geometry: /C GNP 201 O6 Wrong number of grandchild atoms for phi/psi acceptor /C GNP 201 O6 Skipping possible acceptor with bad geometry: /G GNP 201 O6 Wrong number of grandchild atoms for phi/psi acceptor /G GNP 201 O6 Skipping possible acceptor with bad geometry: /C GNP 201 O6 Wrong number of grandchild atoms for phi/psi acceptor /C GNP 201 O6 12 messages similar to the above omitted 2406 hydrogen bonds Adding 'H' to /A HIS 483 Adding 'H' to /B GLY 779 Adding 'H' to /E HIS 483 Adding 'H' to /F GLY 779 /A ALA 768 is not terminus, removing H atom from 'C' /A ALA 466 is not terminus, removing H atom from 'C' /B LYS 926 is not terminus, removing H atom from 'C' /B THR 770 is not terminus, removing H atom from 'C' /D PRO 1803 is not terminus, removing H atom from 'C' 6 messages similar to the above omitted 26715 hydrogens added > show sel cartoons > show sel surfaces > surface style (#!1 & sel) dot > surface style (#!1 & sel) solid > surface style (#!1 & sel) mesh > select /E:110 19 atoms, 18 bonds, 1 model selected > select up 88 atoms, 88 bonds, 1 model selected > select up 11674 atoms, 11813 bonds, 1 model selected > show sel surfaces > select clear > select /E:385@CD1 1 atom, 1 model selected > select clear > color electrostatic #1 range -10,10 Missing required ""map"" argument > mlp Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -28.32, mean -2.668, maximum 25.72 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -29.86, mean -2.254, maximum 27.76 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -28.05, mean -2.72, maximum 27.85 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -13.67, mean -1.355, maximum 8.623 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -28.79, mean -2.68, maximum 26.93 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -29.21, mean -2.06, maximum 26.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -27.17, mean -2.715, maximum 25.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -14.06, mean -1.236, maximum 8.777 > hide surfaces > color electrostatic #1 map #3 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -0.6741, mean -0.1393, maximum 0.9385 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -0.7242, mean -0.1113, maximum 0.968 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -0.6721, mean -0.1155, maximum 0.6463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -0.5736, mean -0.113, maximum 0.6337 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -0.2208, mean 0.07038, maximum 0.4461 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -0.4832, mean -0.06848, maximum 0.463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -0.4162, mean -0.03963, maximum 0.7165 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -0.04677, mean 0.004341, maximum 0.09154 > surface #1 > volume #3 hide > color electrostatic #1 map #3 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -0.6741, mean -0.1393, maximum 0.9385 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -0.7242, mean -0.1113, maximum 0.968 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -0.6721, mean -0.1155, maximum 0.6463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -0.5736, mean -0.113, maximum 0.6337 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -0.2208, mean 0.07038, maximum 0.4461 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -0.4832, mean -0.06848, maximum 0.463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -0.4162, mean -0.03963, maximum 0.7165 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -0.04677, mean 0.004341, maximum 0.09154 > color electrostatic #1 map #3 range -1,1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -0.6741, mean -0.1393, maximum 0.9385 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -0.7242, mean -0.1113, maximum 0.968 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -0.6721, mean -0.1155, maximum 0.6463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -0.5736, mean -0.113, maximum 0.6337 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -0.2208, mean 0.07038, maximum 0.4461 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -0.4832, mean -0.06848, maximum 0.463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -0.4162, mean -0.03963, maximum 0.7165 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -0.04677, mean 0.004341, maximum 0.09154 > color electrostatic #1 map #3 range -0.5,0.5 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -0.6741, mean -0.1393, maximum 0.9385 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -0.7242, mean -0.1113, maximum 0.968 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -0.6721, mean -0.1155, maximum 0.6463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -0.5736, mean -0.113, maximum 0.6337 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -0.2208, mean 0.07038, maximum 0.4461 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -0.4832, mean -0.06848, maximum 0.463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -0.4162, mean -0.03963, maximum 0.7165 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -0.04677, mean 0.004341, maximum 0.09154 > color electrostatic #1 map #3 range -0.1,0.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -0.6741, mean -0.1393, maximum 0.9385 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -0.7242, mean -0.1113, maximum 0.968 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -0.6721, mean -0.1155, maximum 0.6463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -0.5736, mean -0.113, maximum 0.6337 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -0.2208, mean 0.07038, maximum 0.4461 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -0.4832, mean -0.06848, maximum 0.463 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -0.4162, mean -0.03963, maximum 0.7165 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -0.04677, mean 0.004341, maximum 0.09154 > hide surfaces > show surfaces > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/coulomb_model3.mrc Opened coulomb_model3.mrc, grid size 210,210,94, pixel 1, shown at level 19.6, step 1, values float32 > color electrostatic #1 map #4 range -0.1,0.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 > color electrostatic #1 map #4 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 > hide surfaces > show surfaces > hide surfaces > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/all_protomers.pdb Chain information for all_protomers.pdb #5 --- Chain | Description A I | No description available B J K | No description available C L | No description available D H M | No description available E | No description available F | No description available G | No description available > preset cartoons/nucleotides ribbons/slabs Changed 46494 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > volume #3 color #fc0280 > volume #3 color #800002 > volume #3 color #fc0280 > volume #3 color #fc0107 > volume #3 color #fc0280 > ui tool show ""Color Actions"" > volume #3 color #cc0032 > color zone #3 near #5 distance 3 > volume #3 level 0.09 > volume #3 level 0.08 > volume #3 level 0.09 > volume #3 level 0.08 > hide #!5 models > select #1/A:664 19 atoms, 18 bonds, 1 model selected > select up 115 atoms, 117 bonds, 2 models selected > select up 11684 atoms, 11823 bonds, 2 models selected > ui tool show ""Color Actions"" > color sel dodger blue > select #1/C:94 19 atoms, 18 bonds, 1 model selected > select up 109 atoms, 109 bonds, 2 models selected > select up 2710 atoms, 2741 bonds, 2 models selected > color sel goldenrod > select #1/C:201@N3 1 atom, 1 model selected > select up 45 atoms, 47 bonds, 1 model selected > color sel gray > select #1/B:404 15 atoms, 14 bonds, 1 model selected > select up 266 atoms, 267 bonds, 2 models selected > select up 12424 atoms, 12553 bonds, 2 models selected > color sel yellow green > select #1/F:308 20 atoms, 20 bonds, 1 model selected > select up 102 atoms, 103 bonds, 2 models selected > select up 12410 atoms, 12539 bonds, 2 models selected > color sel yellow green > select #1/E:238 19 atoms, 18 bonds, 1 model selected > select up 174 atoms, 174 bonds, 2 models selected > select up 11674 atoms, 11813 bonds, 2 models selected > color sel dodger blue > select clear > select #1/D:1803 14 atoms, 14 bonds, 1 model selected > select up 44 atoms, 46 bonds, 2 models selected > select up 53679 atoms, 54281 bonds, 2 models selected > select down 44 atoms, 46 bonds, 9 models selected > show (#!1 & sel) target ab > select H 26715 atoms, 1 model selected > hide (#!1 & sel) target a > select #1/D:1802 14 atoms, 14 bonds, 1 model selected > select up 44 atoms, 46 bonds, 2 models selected > hide sel cartoons > color sel orange red > select clear > graphics silhouettes false > open /Users/ubgzan01/Downloads/Chimera/PDB/2QTV.pdb 2QTV.pdb title: Structure of SEC23-SAR1 complexed with the active fragment of SEC31 [more info...] Chain information for 2QTV.pdb #6 --- Chain | Description A | protein transport protein SEC23 B | small copii coat gtpase SAR1 D | protein WEB1 Non-standard residues in 2QTV.pdb #6 --- GNP — phosphoaminophosphonic acid-guanylate ester MG — magnesium ion ZN — zinc ion > matchmaker #6/a to #1/a Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker two_protomers_no_sec31_headstripped_real_space_refined_3.pdb, chain A (#1) with 2QTV.pdb, chain A (#6), sequence alignment score = 3590.1 RMSD between 675 pruned atom pairs is 1.116 angstroms; (across all 733 pairs: 1.286) > select #6/D 282 atoms, 280 bonds, 1 model selected > select ~sel 107679 atoms, 109252 bonds, 40 pseudobonds, 13 models selected > select #6/B 1363 atoms, 1361 bonds, 8 pseudobonds, 3 models selected > delete atoms (#!6 & sel) > delete bonds (#!6 & sel) > select #6/A 5974 atoms, 5915 bonds, 8 pseudobonds, 3 models selected > delete atoms (#!6 & sel) > delete bonds (#!6 & sel) > select #6/D 282 atoms, 280 bonds, 1 model selected > color sel magenta > select clear > view orient > volume #3 color #cc003280 > color zone #3 near #5 distance 3 > ui tool show ""Side View"" > lighting simple > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting ambientIntensity 0.1 > lighting ambientIntensity 0.5 > lighting ambientIntensity 0.3 > show #!1,6 surfaces > hide #!1,6 surfaces > save > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/chimera_session_model3.cxs > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/outer_bind_1.bmp > width 795 height 730 supersample 4 > molmap #5 4.5 > volume #7 level 0.4166 > molmap #5 5 > volume #7 level 0.3546 > molmap #5 4.5 > volume subtract #7 #3 > volume #8 level -0.07345 > volume #8 level -0.07763 > close #8 > volume subtract #3 #7 > volume #8 level 0.07231 > select #1 53679 atoms, 54281 bonds, 9 pseudobonds, 11 models selected > show sel surfaces > select up 53679 atoms, 54281 bonds, 9 pseudobonds, 19 models selected > select up 100624 atoms, 102256 bonds, 9 pseudobonds, 31 models selected > select up 100624 atoms, 102256 bonds, 9 pseudobonds, 32 models selected > color electrostatic #1 map #4 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 Map values for surface ""cap far"": minimum -1481, mean -3.84, maximum 665.6 Map values for surface ""cap near"": minimum 4.281, mean 8.838, maximum 17.47 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""cap far"": minimum -218.1, mean 3.114, maximum 5399 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""cap far"": minimum -1221, mean -4.612, maximum 594.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""cap far"": minimum -363.8, mean 0.8744, maximum 2050 Map values for surface ""cap near"": minimum -118.5, mean -5.908, maximum 158.4 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""cap far"": minimum -359.9, mean 1.511, maximum 1963 Map values for surface ""cap near"": minimum -385.4, mean -5.111, maximum 1113 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""cap far"": minimum -2011, mean -13.77, maximum 126.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 > ~select #1 46945 atoms, 47975 bonds, 21 models selected > hide sel & #!6 surfaces > hide sel & #!6 surfaces > select #1 53679 atoms, 54281 bonds, 9 pseudobonds, 11 models selected > hide sel surfaces > ~select #1 8 models selected > select #1/A:692 15 atoms, 14 bonds, 1 model selected > select up 285 atoms, 285 bonds, 3 models selected > select up 14394 atoms, 14564 bonds, 3 models selected > show sel surfaces > select #1 53679 atoms, 54281 bonds, 9 pseudobonds, 11 models selected > select clear > hide #!1,6 surfaces > select #5 46663 atoms, 47695 bonds, 15 pseudobonds, 2 models selected > show #!5 models > select subtract #1/D#5/D 46642 atoms, 47672 bonds, 15 pseudobonds, 2 models selected > molmap sel 4.5 > color electrostatic #1 map #4 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 > select #1 53679 atoms, 54281 bonds, 9 pseudobonds, 11 models selected > ~select #1 8 models selected > close #7 > volume subtract #3 #9 > close #8 > volume #7 level 0.08385 > select #1 53679 atoms, 54281 bonds, 9 pseudobonds, 11 models selected > select subtract #1/D 53635 atoms, 54235 bonds, 9 pseudobonds, 19 models selected > show sel surfaces > select clear > volume #7 color #41eb3a > volume #7 color #6ed3e3 > volume #7 color #e6e387 > volume #7 color #0a0e07 > volume #7 color #322f0d > volume #7 color #534f11 > volume #7 color #685312 > volume #7 color #957613 > volume #7 color #e500da > volume #7 color #e795e1 > volume #7 color #baeeeb > volume #7 color #82e987 > volume #7 color #b8eb96 > volume #7 color #020000 > volume #7 style mesh > volume #7 > volume #7 subdivideSurface true > volume #7 subdivideSurface false > volume #7 smoothLines true > volume #7 squareMesh false > volume #7 smoothLines true > volume #7 style surface style image Repeated keyword argument ""style"" > volume #7 style mesh > volume #7 step 2 > volume #7 step 1 > volume #7 subdivideSurface false > volume #7 subdivideSurface true > volume #7 squareMesh true > volume #7 squareMesh false > volume #7 style surface > volume #7 change image level -1.373,1 level -0.04838,0.8 level 0,0 level 0,0 > level 0.04838,0.8 level 0.7084,1 > volume #7 color #020000f3 > volume #7 color #020000b7 > volume #7 color #0200009b > volume #7 color #02000097 > volume #7 color #02000096 > volume #7 color #02000095 > volume #7 color #0200008f > volume #7 color #02000088 > volume #7 color #02000082 > volume #7 color #02000080 > volume #7 color #02000075 > volume #7 color #02000071 > volume #7 color #0200006f > volume #7 color #0200000a > volume #7 color #02000066 > volume #7 color #02000080 > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/coulomb_diffmap1.bmp > width 795 height 730 supersample 4 > volume #7 style mesh > volume #7 color #02000084 > volume #7 color #02000097 > volume #7 color #020000 > volume #7 color #020000c6 > volume #7 color #020000c7 > volume #7 color #020000c9 > volume #7 color #020000 > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/coulomb_diffmap2.bmp > width 795 height 730 supersample 4 > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > volume #7 style surface > volume #7 color #02000080 > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/coulomb_diffmap3.bmp > width 795 height 730 supersample 4 > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > save > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/chimera_session_model3.cxs Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 opened ChimeraX session > color electrostatic #1 map #4 range -17,17 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -452.1, mean -3.76, maximum 1723 Map values for surface ""cap far"": minimum -568.7, mean -3.758, maximum 396 Map values for surface ""cap near"": minimum 4.281, mean 8.838, maximum 17.47 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -803, mean -4.43, maximum 429.1 Map values for surface ""cap far"": minimum -133.3, mean 0.5421, maximum 657.4 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -2828, mean -4.726, maximum 569.8 Map values for surface ""cap far"": minimum -393.3, mean -2.591, maximum 598.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -644.3, mean -2.238, maximum 1525 Map values for surface ""cap far"": minimum -910.9, mean 3.889, maximum 713.8 Map values for surface ""cap near"": minimum -118.5, mean -5.908, maximum 158.4 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -31.13, mean -5.751, maximum 16.97 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -458.4, mean -2.337, maximum 895.2 Map values for surface ""cap far"": minimum -324.8, mean 14.34, maximum 563.6 Map values for surface ""cap near"": minimum -385.4, mean -5.111, maximum 1113 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum -1930, mean -4.614, maximum 398.1 Map values for surface ""cap far"": minimum -1167, mean -4.486, maximum 994.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum -64.75, mean -5.209, maximum 15.21 > hide surfaces > view orient > hide #!5 models > close #4 > open > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/coulomb_model3_wcharges.mrc Opened coulomb_model3_wcharges.mrc, grid size 117,102,84, pixel 1, shown at level 26.8, step 1, values float32 > hide #!4 models > color electrostatic #1 map #4 range -17,17 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -481.1, mean -2.369, maximum 384.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -3169, mean -3.567, maximum 891.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -655.5, mean -0.4983, maximum 184.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -1638, mean -0.2455, maximum 390.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -95.94, mean -5.641, maximum 109.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -1.128, mean -2.87e-06, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum 0, mean 0, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum 0, mean 0, maximum 0 > show #!1,6 surfaces > hide #!6 models > hide #!7 models > show #!7 models > color electrostatic #1 map #4 range -15,15 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -481.1, mean -2.369, maximum 384.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -3169, mean -3.567, maximum 891.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -655.5, mean -0.4983, maximum 184.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -1638, mean -0.2455, maximum 390.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -95.94, mean -5.641, maximum 109.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -1.128, mean -2.87e-06, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum 0, mean 0, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum 0, mean 0, maximum 0 > color electrostatic #1 map #4 range -10,0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -481.1, mean -2.369, maximum 384.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -3169, mean -3.567, maximum 891.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -655.5, mean -0.4983, maximum 184.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -1638, mean -0.2455, maximum 390.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -95.94, mean -5.641, maximum 109.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -1.128, mean -2.87e-06, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum 0, mean 0, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum 0, mean 0, maximum 0 > color electrostatic #1 map #4 range -10,10 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -481.1, mean -2.369, maximum 384.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -3169, mean -3.567, maximum 891.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -655.5, mean -0.4983, maximum 184.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -1638, mean -0.2455, maximum 390.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -95.94, mean -5.641, maximum 109.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -1.128, mean -2.87e-06, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum 0, mean 0, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum 0, mean 0, maximum 0 > color electrostatic #1 map #4 range -12,12 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_A SES surface"": minimum -481.1, mean -2.369, maximum 384.1 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_C SES surface"": minimum -3169, mean -3.567, maximum 891.2 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_E SES surface"": minimum -655.5, mean -0.4983, maximum 184.9 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_B SES surface"": minimum -1638, mean -0.2455, maximum 390.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_D SES surface"": minimum -95.94, mean -5.641, maximum 109.7 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_F SES surface"": minimum -1.128, mean -2.87e-06, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_G SES surface"": minimum 0, mean 0, maximum 0 Map values for surface ""two_protomers_no_sec31_headstripped_real_space_refined_3.pdb_H SES surface"": minimum 0, mean 0, maximum 0 > hide #!1 surfaces > select #1/C:117 20 atoms, 20 bonds, 1 model selected > select up 245 atoms, 246 bonds, 3 models selected > select up 14394 atoms, 14564 bonds, 3 models selected > show sel surfaces > select clear > save > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/chimera_session_model3.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. > save > /Users/ubgzan01/Documents/lab/yeast_COPII/EM/EMBL_dec19/inner_coat/fine3_phenix/Alan_build/chimera_session_model3_wcharges.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. > view orient > hide #!1 surfaces > select #1/E:219 16 atoms, 15 bonds, 1 model selected > select up 97 atoms, 98 bonds, 2 models selected > select up 11674 atoms, 11813 bonds, 2 models selected > ui tool show ""Color Actions"" > color sel dark blue > select clear > lighting ambientIntensity 0.3 > lighting ambientIntensity 0.5 > lighting ambientIntensity 0.7 > lighting simple > lighting ambientIntensity 0.7 > lighting ambientIntensity 0.5 > ui tool show ""Side View"" > lighting ambientIntensity 0.7 > lighting ambientIntensity 0.3 > show #!6 models > hide #!1,6 surfaces > surface cap false > hide #!3 models > show #!3 models > hide #!7 models > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/outer_bind_2.bmp > width 911 height 733 supersample 4 > show #!1,6 surfaces > select #6/D:932@CA 1 atom, 1 model selected > select #6 282 atoms, 280 bonds, 1 model selected > hide sel surfaces > select clear > show #!7 models > hide #!1,6 surfaces > select #1/A:696 19 atoms, 18 bonds, 1 model selected > select up 233 atoms, 233 bonds, 3 models selected > select up 14394 atoms, 14564 bonds, 3 models selected > show sel surfaces > select clear > lighting ambientIntensity 0.4 > lighting ambientIntensity 0.5 > lighting ambientIntensity 0.2 > volume #7 color #ffff0a > volume #7 color #ffff66 > volume #7 color #ccff66 > volume #7 color #ffff66 > volume #7 color #fecc66 > volume #7 color #ffff66 > volume #7 color white > volume #7 color #999999 > volume #7 color #333333 > volume #7 color #ffff66 > volume #7 color #fecc66 > volume #7 color #ffff66 > volume #7 color #ffff66fb > volume #7 color #ffff66f3 > volume #7 color #ffff66ef > volume #7 color #ffff66ec > volume #7 color #ffff66ea > volume #7 color #ffff66e7 > volume #7 color #ffff66e6 > volume #7 color #ffff66e5 > volume #7 color #ffff66e4 > volume #7 color #ffff66df > volume #7 color #ffff66d8 > volume #7 color #ffff66d2 > volume #7 color #ffff66c2 > volume #7 color #ffff66b7 > volume #7 color #ffff66b0 > volume #7 color #ffff66a9 > volume #7 color #ffff66a1 > volume #7 color #ffff669b > volume #7 color #ffff669a > volume #7 color #ffff66b3 > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/coulomb_diffmap4.bmp > width 911 height 733 supersample 4 > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/figure5.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. > save > /Users/ubgzan01/Documents/lab/yeast_COPII/paper_Apr20/inner_snaps/chimeraX/figure5.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1782, in take_snapshot 'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 329, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.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-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'coulomb_model3.mrc' File ""/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 283, in process raise RuntimeError(msg) from e See log for complete Python traceback. OpenGL version: 4.1 ATI-3.5.5 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 204.0.0.0.0 SMC Version (system): 2.45f1 Software: System Software Overview: System Version: macOS 10.15.3 (19D76) Kernel Version: Darwin 19.3.0 Time since boot: 1 day 20:16 Graphics/Displays: Intel HD Graphics 630: Chipset Model: Intel HD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591b Revision ID: 0x0004 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro 560: Chipset Model: Radeon Pro 560 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c0 ROM Revision: 113-C980AJ-927 VBIOS Version: 113-C9801AU-A02 EFI Driver Version: 01.A0.927 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Displays: HP 22f: 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: 3CM014015T 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 }}} " defect closed normal Sessions 1.0rc1 fixed Greg Couch all ChimeraX