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#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
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Reported by Giulia Zanetti