#3382 closed defect (fixed)
Map replacement results in session-save failure: self.positions is None
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | 1.0rc1 |
Keywords: | Cc: | Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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 <lambda> 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> 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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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 <lambda> 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> 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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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 <lambda> 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> 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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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 <lambda> 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> 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' -> <chimerax.surface.updaters.SurfaceUpdaters object at 0x139255d50> -> <chimerax.surface.colorvol.VolumeColor object at 0x1392901d0> -> <chimerax.map.volume.Volume object at 0x1280b4cd0> '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
Change History (4)
comment:1 by , 5 years ago
Cc: | added |
---|---|
Component: | Unassigned → Sessions |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Map replacement results in session-save failure: self.positions is None |
Version: | → 1.0rc1 |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Fixed in ChimeraX 1.1, not in 1.0.
We plan to make a ChimeraX 1.0 release in the next day or two that will not contain this fix. After release, daily builds on the ChimeraX download page will have the fix.
The cause of this problem is coloring a surface by electrostatic potential, then deleting the potential map, then trying to save a session. The coloring uses the map to recolor. Until you get a fixed ChimeraX, avoid deleting the potential map uses to color a surface. Even after the fix if you delete the potential map and save the session, the session will not preserve the coloring. I'll make a separate bug report for that problem.
follow-up: 4 comment:4 by , 5 years ago
OK thanks a lot, that was a quick response! I will make sure to keep my ChimeraX up to date. Brilliant software by the way :) Giulia
Reported by Giulia Zanetti