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#7123 closed defect (fixed)
Basic Actions saving session: 'QEventLoop' object has no attribute 'exec_'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Nothing special, I have only updated chimerax to v 1.4 while the original session was generated with v 1.3
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown
at level 0.44, step 1, values float32
Opened denmod_map_i4_copy.ccp4 zone as #4, grid size 199,196,146, pixel 1.34,
shown at level 0.572, step 1, values float32
Log from Sun Mar 27 22:51:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2c_overall.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown
at level 0.098, step 1, values float32
Log from Tue Mar 1 22:41:50 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_bHairpinsP.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown
at level 0.098, step 1, values float32
Log from Tue Mar 1 18:09:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_AGFcxs.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown
at level 0.098, step 1, values float32
Log from Fri Aug 13 11:00:00 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT4.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Fri Jun 18 15:39:00 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cutvertical.cxs
> format session
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.1, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Mon Jun 7 22:54:12 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.1, step 1, values float32
Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35,
shown at level 0.0225, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Mon Jun 7 18:44:10 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs
> format session
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35,
shown at level 0.0225, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Mon Jun 7 13:38:40 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
> format session
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.12, step 1, values float32
Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35,
shown at level 0.0225, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Mon Jun 7 08:05:30 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.085, step 1, values float32
Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35,
shown at level 0.0225, step 1, values float32
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Log from Sun Jun 6 23:35:17 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> set bgColor white
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/density_mod_phenix/ResolveCryoEM_3/denmod_map_i4.ccp4
Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at
level 0.263, step 1, values float32
> volume #1 level 0.085
> ui tool show "Hide Dust"
> surface dust #1 size 8.04
> lighting full
> surface dust #1 size 10
> surface dust #1 size 10
> save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3
> transparentBackground true
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/Clps_Daris_map/body001_masked_PbestDari.mrc
> /Users/marta.carroni/Documents/ClpCPA_rosa/Clps_Daris_map/body001_masked_crown.mrc
Opened body001_masked_PbestDari.mrc as #2.1, grid size 400,400,400, pixel
1.35, shown at level 8.48e-06, step 2, values float32
Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35,
shown at level 1.02e-05, step 2, values float32
> volume #2.1 step 1
> volume #2.1 level 0.03791
> close #2.1
> volume #2.2 level 0.02248
> volume #2.2 step 1
> select #2.2
2 models selected
> ~select #2.2
Nothing selected
> toolshed show
> ui mousemode right select
> select #2.2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2.2,0.95243,0.28449,-0.10926,-23.172,-0.30406,0.91121,-0.27792,210.94,0.02049,0.29792,0.95437,-69.175
> view matrix models
> #2.2,0.31072,0.32437,0.89344,-238.67,0.56388,0.69379,-0.44799,99.698,-0.76518,0.64299,0.032666,396.73
> view matrix models
> #2.2,0.4619,0.61924,0.63498,-262.08,0.5366,0.37492,-0.75597,309.67,-0.70619,0.68991,-0.15911,440.36
> view matrix models
> #2.2,0.60401,0.54486,0.58164,-260.16,0.42333,0.399,-0.81338,355.36,-0.67525,0.73752,0.010342,355.21
> view matrix models
> #2.2,0.774,0.43541,0.45973,-230.41,0.25538,0.44972,-0.85588,402.96,-0.57941,0.77985,0.23689,232.46
> view matrix models
> #2.2,0.71519,0.51369,0.47395,-241.13,0.15844,0.54129,-0.82577,392.94,-0.68074,0.66567,0.30574,264.85
> view matrix models
> #2.2,0.68147,0.17566,0.71045,-229.45,0.32864,0.79393,-0.51154,159.99,-0.65391,0.58208,0.48331,213.36
> ui mousemode right "move picked models"
> view matrix models
> #2.2,0.68147,0.17566,0.71045,-221.14,0.32864,0.79393,-0.51154,155.43,-0.65391,0.58208,0.48331,213.34
> view matrix models
> #2.2,0.68147,0.17566,0.71045,-142.1,0.32864,0.79393,-0.51154,143.34,-0.65391,0.58208,0.48331,143.22
> volume #1 style image region 0,0,72,198,195,72 step 1 showOutlineBox true
> volume #1 region 0,0,0,198,195,145 step 1
> volume #1 region 0,0,0,198,195,145 step 1
> volume #1 level -0.03658,0 level 0.5295,0.8 level 1.338,1
> volume #1 level -0.03658,0 level 0.1251,0.7231 level 1.338,1
> volume #1 level -0.03658,0 level 0.1251,0.7231 level 0.6891,0.2923
> volume #1 showOutlineBox false
> save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3
> transparentBackground true
> volume #1 level -0.03658,0 level 0.1251,0.7231 level 0.6997,0.8
> save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3
> transparentBackground true
> save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3
> transparentBackground false
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/session_bodies_190117_semplified_allonC.pyc
Python code was compiled for a different version of Python
> volume #1 style surface
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/manuscript_parts/final_pdbs_nov2020/combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
Chain information for
combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb #3
---
Chain | Description
A C E N | No description available
B G | No description available
D | No description available
F | No description available
H M | No description available
I | No description available
J K | No description available
L | No description available
S | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
> hide atoms
> show cartoons
> ui tool show "Model Panel"
> select #2
3 models selected
> ~select #2
Nothing selected
> hide #!1 models
> select #3: .A-N
Expected an objects specifier or a keyword
> select #3:.A-N
Expected an objects specifier or a keyword
> select 3:.A-N
Expected an objects specifier or a keyword
> select add /A
2948 atoms, 2967 bonds, 191 residues, 1 model selected
> select add /B
5865 atoms, 5903 bonds, 380 residues, 1 model selected
> select add /C
8813 atoms, 8870 bonds, 571 residues, 1 model selected
> select add /D
11700 atoms, 11775 bonds, 1 pseudobond, 758 residues, 2 models selected
> select add /F
14574 atoms, 14667 bonds, 2 pseudobonds, 945 residues, 2 models selected
> select add /G
17488 atoms, 17600 bonds, 2 pseudobonds, 1134 residues, 2 models selected
> select add /G
17488 atoms, 17600 bonds, 2 pseudobonds, 1134 residues, 2 models selected
> select add /H
20349 atoms, 20479 bonds, 3 pseudobonds, 1320 residues, 2 models selected
> select add /I
23180 atoms, 23328 bonds, 4 pseudobonds, 1504 residues, 2 models selected
> select add /L
26020 atoms, 26186 bonds, 5 pseudobonds, 1688 residues, 2 models selected
> select add /M
28881 atoms, 29065 bonds, 6 pseudobonds, 1874 residues, 2 models selected
> select add /N
31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected
> select add /B
31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected
> select add /C
31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected
> select add /M
31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected
> select add /K
34676 atoms, 34897 bonds, 7 pseudobonds, 2250 residues, 2 models selected
> color (#!3 & sel) dark gray
> select /a
4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected
> select /E
2948 atoms, 2967 bonds, 191 residues, 1 model selected
> color sel dark gray
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> color sel black
> select /a
4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected
> ui tool show "Color Actions"
> color sel fire brick
> select /b
4264 atoms, 4317 bonds, 6 pseudobonds, 532 residues, 2 models selected
> color sel salmon
> select /c
4434 atoms, 4488 bonds, 4 pseudobonds, 559 residues, 2 models selected
> color sel gold
> select /d
4136 atoms, 4187 bonds, 5 pseudobonds, 520 residues, 2 models selected
> color sel olive drab
> select /e
8166 atoms, 8213 bonds, 6 pseudobonds, 512 residues, 2 models selected
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> select /f
8278 atoms, 8325 bonds, 5 pseudobonds, 516 residues, 2 models selected
> color sel dodger blue
> select clear
> select /J
2854 atoms, 2872 bonds, 1 pseudobond, 185 residues, 2 models selected
> color (#!3 & sel) dark gray
> select clear
> open /Users/marta.carroni/Dropbox/chimera_sessions_ClpPCA/MD_ND_MecA.pdb
MD_ND_MecA.pdb title:
Structure of S.aureus CLPC In complex with meca [more info...]
Chain information for MD_ND_MecA.pdb #4
---
Chain | Description
C I O U a m | class III stress response-related atpase, aaa+ superfamily
E K Q W c o | atp-dependent CLP protease atp-binding subunit CLPC
F L R X d p | atp-dependent CLP protease atp-binding subunit CLPC
e f g h i j | adapter protein meca
> select #4
5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models #4,1,0,0,56.288,0,1,0,-60.01,0,0,1,25.306
> view matrix models #4,1,0,0,78.14,0,1,0,-87.575,0,0,1,52.561
> view matrix models #3,1,0,0,8.1169,0,1,0,-9.9621,0,0,1,8.992
> view matrix models #4,1,0,0,89.358,0,1,0,-107.73,0,0,1,91.076
> view matrix models #4,1,0,0,109.21,0,1,0,-127.66,0,0,1,94.941
> view matrix models #4,1,0,0,225.03,0,1,0,-11.788,0,0,1,55.494
> view matrix models #4,1,0,0,205.99,0,1,0,-26.324,0,0,1,61.327
> view matrix models #4,1,0,0,198.97,0,1,0,-30.061,0,0,1,63.242
> ui mousemode right "move picked models"
> ui mousemode right select
> select #4/L:20@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel atoms
> select #4/I:443@CA
1 atom, 1 residue, 1 model selected
> select #4
5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected
> ~select #4
Nothing selected
> select #4
5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> cartoon style (#!4 & sel) modeHelix tube sides 20
> preset cartoons/nucleotides cylinders/stubs
Changed 79256 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
> show sel atoms
> view sel
> color sel bychain
> hide #!4 models
> view
Drag select of 956 residues, 2 pseudobonds
> select clear
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> 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
> 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 licorice/ovals
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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show #!4 models
> close #4
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> undo
> undo
> undo
> undo
Traceback (most recent call last):
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 522, in undo
a.undo()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 396, in undo
self._update_owner(owner, attribute, old_value, option, deleted_check)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 430, in _update_owner
getattr(owner, attribute)(value)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/ribbon.py", line 1939, in set_sheet_end_arrow
self._set_gc_ribbon()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/ribbon.py", line 2066, in _set_gc_ribbon
s._graphics_changed |= s._RIBBON_CHANGE
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError
undo failed: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError:
AttributeError: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> undo
Traceback (most recent call last):
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 522, in undo
a.undo()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 396, in undo
self._update_owner(owner, attribute, old_value, option, deleted_check)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/undo.py", line 434, in _update_owner
getattr(owner, attribute)(*value)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/ribbon.py", line 1864, in set_sheet_arrow_scale
self._set_gc_ribbon()
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/ribbon.py", line 2066, in _set_gc_ribbon
s._graphics_changed |= s._RIBBON_CHANGE
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError
undo failed: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError:
AttributeError: Execution of 'Structure' object's '_graphics_changed' property
raised AttributeError
File
"/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Changed 73766 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
> lighting full
> lighting full
> lighting soft
> view
> ui tool show "Color Actions"
> ui windowfill toggle
> ui windowfill toggle
> select add/.A-N
Expected an objects specifier or a keyword
> select add /.A-N
Expected an objects specifier or a keyword
> select add /A
2948 atoms, 2967 bonds, 191 residues, 1 model selected
> select add /A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 3 models selected
> color (#!3 & sel) dark gray
> select add /a
44824 atoms, 45134 bonds, 13 pseudobonds, 3172 residues, 16 models selected
> select replace /a
Expected an objects specifier or a keyword
> select /a
4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected
> colour /a red brick
> color /a red brick
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> colour /a fire brick
> colour /b salmon
> colour /c gold
> colour /d olive grab
> color /d olive grab
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> colour /d olive drab
> colour /e light blue
> colour /f dodger blue
> select clear
> colour /S black
> show #!1 models
> ui mousemode right translate
> ui tool show "Fit in Map"
Fit molecule
combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb (#3)
to map denmod_map_i4.ccp4 (#1) using 74184 atoms
average map value = 0.01291, steps = 128
shifted from previous position = 2.44
rotated from previous position = 3.15 degrees
atoms outside contour = 59923, contour level = 0.085
Position of
combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb (#3)
relative to denmod_map_i4.ccp4 (#1) coordinates:
Matrix rotation and translation
0.99909996 0.04219753 0.00431685 -4.93809295
-0.04202069 0.99850096 -0.03507283 11.57437078
-0.00579037 0.03485986 0.99937544 -0.99304355
Axis 0.63613447 0.09193917 -0.76608101
Axis point 274.64910232 103.03635904 0.00000000
Rotation angle (degrees) 3.15095997
Shift along axis -1.31640130
Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb
map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1,
values float32
Fit map
combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5
in map denmod_map_i4.ccp4 using 174685 points
correlation = 0.471, correlation about mean = 0.6133, overlap = 7407
steps = 144, shift = 13.8, angle = 3.15 degrees
Position of
combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5
(#4) relative to denmod_map_i4.ccp4 (#1) coordinates:
Matrix rotation and translation
0.99999997 -0.00010445 -0.00023506 0.04814859
0.00010438 0.99999995 -0.00030190 0.09674212
0.00023510 0.00030188 0.99999993 -0.16286802
Axis 0.76116794 -0.59271984 0.26326139
Axis point 0.00000000 484.12865811 195.55736650
Rotation angle (degrees) 0.02272424
Shift along axis -0.06356868
Average map value = 0.1906 for 74184 atoms, 29821 outside contour
> view
> ui windowfill toggle
> view
> color zone #1 near #3 distance 8.04
> select /a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
——— End of log from Sun Jun 6 23:35:17 2021 ———
opened ChimeraX session
> select clear
> turn x 90
> hide #!3 models
> ui tool show "Volume Viewer"
> ui tool show "Side View"
> turn y 60
> undo
> turn z 60
> turn z 60
> turn z 60
> surface cap mesh true
> surface cap mesh false
> surface cap subdivision 5.0
> surface cap subdivision 5.0
> surface cap subdivision 2.0
> surface cap subdivision 20.0
> surface cap subdivision 20.0
> surface cap false
> surface cap true
> surface cap mesh true
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!3 models
> color zone #1 near #3 distance 8.04
> hide #!3 models
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
> ui windowfill toggle
> save ../Documents/ClpCP_aaa2fig1.png width 1600 height 1600 supersample 3
> transparentBackground true
> ui windowfill toggle
> ui mousemode right clip
> ui mousemode right clip
> ui mousemode right clip
> ui tool show "Side View"
> ui mousemode right clip
> ui windowfill toggle
> ui mousemode right select
> ui mousemode right translate
> view
> save ../Documents/ClpCP_aaa1fig1.png width 1600 height 1600 supersample 3
> transparentBackground true
> view
> ui tool show "Side View"
> select /a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!3 models
> volume zone #1 nearAtoms sel & #3 range 8.04
> hide #!3 models
> ui windowfill toggle
> lighting simple
> lighting full
> select /a-d
17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected
> show #!3 models
> color zone #1 near sel & #3 distance 8.04
> undo
> volume zone #1 nearAtoms sel & #3 range 8.04
> hide #!3 models
> ui windowfill toggle
> ui tool show "Side View"
> volume #1 level 0.1
> ui windowfill toggle
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #3 distance 1.34
> show #!3 models
> surface zone #1 nearAtoms #3 distance 1.34
> select /a-d
17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected
> surface zone #1 nearAtoms #3 distance 1.34
> surface zone #1 nearAtoms sel distance 1.34
> hide #!3 models
> ui windowfill toggle
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 1.34
> surface zone #1 nearAtoms sel distance 2
> surface zone #1 nearAtoms sel distance 2
> select /a-d
17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected
> ui windowfill toggle
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 3 models selected
> ui tool show "Model Panel"
> show #!3 models
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected
> surface zone #1 nearAtoms sel distance 2
> hide #!3 models
> ui windowfill toggle
> surface dust #1 size 13.4
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> ui tool show "Model Panel"
> show #!3 models
> volume zone #1 nearAtoms sel & #3 range 8.04
> hide #!3 models
> ui windowfill toggle
> volume #1 level 0.12
> ui windowfill toggle
> ui tool show "Hide Dust"
> surface dust #1 size 9.14
> surface dust #1 size 3
> surface dust #1 size 30
> surface dust #1 size 30
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected
> show #!3 models
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected
> volume zone #1 nearAtoms sel & #3 range 8.04
> hide #!3 models
> ui windowfill toggle
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 2
> ui windowfill toggle
> ui tool show "Hide Dust"
> select add /S,a-d
17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected
> surface dust #1 size 3.4
> surface dust #1 size 3.43
> surface dust #1 size 91.03
> surface dust #1 size 91.92
> surface dust #1 size 105.03
> ui windowfill toggle
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save ../Documents/ClpCP_spiralfig1.png width 1600 height 1600 supersample 3
> transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
> view matrix
camera position:
0.47201,0.8521,-0.22613,176.23,0.29575,-0.39468,-0.86992,-244.58,-0.83051,0.34373,-0.4383,-4.4071
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,0.68147,0.17566,0.71045,-142.1,0.32864,0.79393,-0.51154,143.34,-0.65391,0.58208,0.48331,143.22,#2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,-0.00010445,-0.00023506,0.048149,0.00010438,1,-0.0003019,0.096742,0.0002351,0.00030188,1,-0.16287,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#3.6,1,0,0,0,0,1,0,0,0,0,1,0,#3.7,1,0,0,0,0,1,0,0,0,0,1,0,#3.8,1,0,0,0,0,1,0,0,0,0,1,0,#3.9,1,0,0,0,0,1,0,0,0,0,1,0,#3.10,1,0,0,0,0,1,0,0,0,0,1,0,#3.11,1,0,0,0,0,1,0,0,0,0,1,0,#3.12,1,0,0,0,0,1,0,0,0,0,1,0,#3.13,1,0,0,0,0,1,0,0,0,0,1,0,#3.14,1,0,0,0,0,1,0,0,0,0,1,0,#3.15,1,0,0,0,0,1,0,0,0,0,1,0,#3.16,1,0,0,0,0,1,0,0,0,0,1,0,#3.17,1,0,0,0,0,1,0,0,0,0,1,0,#3.18,1,0,0,0,0,1,0,0,0,0,1,0,#3.19,1,0,0,0,0,1,0,0,0,0,1,0,#3.20,1,0,0,0,0,1,0,0,0,0,1,0,#3.21,1,0,0,0,0,1,0,0,0,0,1,0,#3.22,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,-0.00010445,-0.00023506,0.048149,0.00010438,1,-0.0003019,0.096742,0.0002351,0.00030188,1,-0.16287,#4.1,1,0,0,0,0,1,0,0,0,0,1,0
> ui windowfill toggle
> view name spiral
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs
——— End of log from Mon Jun 7 08:05:30 2021 ———
opened ChimeraX session
> select /a
4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected
> show #!3 models
> color (#!3 & sel) orange red
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> ui tool show "Model Panel"
> hide #!3 models
> ~select #3
21 models selected
> lighting simple
> lighting full
> ui tool show "Side View"
> ui windowfill toggle
> ui tool show "Side View"
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> hide #!3 models
> ~select #3
21 models selected
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> graphics silhouettes false
> save ../Documents/ClpCP_cut.png width 1600 height 1600 supersample 3
> transparentBackground true
> view name cut
> turn x 90
> ui tool show "Surface Zone"
> surface unzone #1
> ui windowfill toggle
> view name cut_horizontal
> save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs
——— End of log from Mon Jun 7 13:38:40 2021 ———
opened ChimeraX session
> view
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lavender
> ui tool show "Model Panel"
> show #!3 models
> color zone #1 near sel & #3 distance 8.04
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> select /A-N:1-20
3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected
> color (#!3 & sel) dim gray
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> color zone #1 near #3 distance 8.04
> surface dust #1 size 13.4
> volume #1 level 0.1
> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
> ui tool show "Model Panel"
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> hide #!3 target m
> ui tool show "Side View"
> show #!3 target m
> color zone #1 near sel & #3 distance 8.04
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> color (#!3 & sel) hot pink
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> show #!3 target m
> color zone #1 near sel & #3 distance 8.04
> hide #!3 models
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> color #1.1#!1-2 lime
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> show #!3 models
> hide #!1 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light green
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> show #!1 models
> color zone #1 near sel & #3 distance 8.04
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ~select #3
21 models selected
> hide #!3 models
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> color #1.1#!1-2 magenta
> show #!3 models
> select /S
82 atoms, 81 bonds, 8 residues, 1 model selected
> color (#!3 & sel) magenta
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> graphics silhouettes false
> color zone #1 near sel & #3 distance 8.04
> ~select #3
21 models selected
> hide #!3 models
> turn y 10
> turn y 10
> turn y 10
> turn y -10
> turn y -10
> turn y -10
> ui tool show "Model Panel"
> show #!3 models
> hide #!1 models
> select /A-N:98,123,172
560 atoms, 532 bonds, 42 residues, 1 model selected
> style sel sphere
Changed 560 atom styles
> show sel atoms
> color (#!3 & sel) hot pink
> color (#!3 & sel) purple
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> show #!1 models
> color zone #1 near sel & #3 distance 8.04
> ~select #3
21 models selected
> hide #!3 models
> view name cut_vertical
> matrix
Unknown command: matrix
> matrix list
Unknown command: matrix list
> save ../Documents/ClpCP_cut_vertical.png width 1600 height 1600 supersample
> 3 transparentBackground true
> turn x 90
> ui tool show "Volume Viewer"
> ui tool show "Side View"
> view name cut_horizontal
> save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs
——— End of log from Mon Jun 7 18:44:10 2021 ———
opened ChimeraX session
> select /a
4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected
> show #!3 models
> close #2
> ui tool show "Color Actions"
> color sel fire brick
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> ~select #3
21 models selected
> hide #!3 models
> ui mousemode right zoom
> ui mousemode right clip
> ui mousemode right zoom
> lighting full
> lighting soft
> lighting soft
> lighting full
> lighting soft
> lighting full
> graphics silhouettes true
> lighting soft
> lighting soft
> graphics silhouettes false
> lighting full
> save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cuthorizontal.cxs
> turn x -90
> ui tool show "Side View"
> select /A-N:1-20
3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> select /A-N:1-20
3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected
> color (#!3 & sel) dim gray
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> select /A-N:1-20
3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected
> color (#!3 & sel) black
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> select /A-N:1-20
3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dim gray
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> hide #!3 models
> ~select #3
21 models selected
> select /A-N:98,123,172
560 atoms, 532 bonds, 42 residues, 1 model selected
> show #!3 models
> hide #!1 models
> ui tool show "Color Actions"
> color sel khaki
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> show #!1 models
> color zone #1 near sel & #3 distance 8.04
> select clear
> select /A-N:98,123,172
560 atoms, 532 bonds, 42 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> color sel lime
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> hide #!3 models
> ~select #3
21 models selected
> save ../Documents/ClpCP_cut_vertical.png width 1600 height 1600 supersample
> 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cutvertical.cxs
——— End of log from Mon Jun 7 22:54:12 2021 ———
opened ChimeraX session
> lighting soft
> lighting soft
> lighting full
> lighting full
> graphics silhouettes true
> surface cap false
> surface cap true
> surface cap mesh true
> surface cap mesh false
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> ~select #3
21 models selected
> hide #!3 models
> turn x 90
> hide #!1 models
> show #!3 models
> select /N,A,B,C,D,E,F:1-10
872 atoms, 872 bonds, 60 residues, 1 model selected
> select /N,A,B,C,D,E,F:10-16
621 atoms, 613 bonds, 1 pseudobond, 41 residues, 2 models selected
> color /N,A,B,C,D,E,F:10-16 redorange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sele redorange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /N,A,B,C,D,E,F:10-16 orangered
> select clear
> show #!1 models
> color zone #1 near #3 distance 8.04
> ui tool show "Side View"
> graphics silhouettes false
> lighting shadows false
> view
> view start
Expected an objects specifier or a view name or a keyword
> view start
Expected an objects specifier or a view name or a keyword
> view start
Expected an objects specifier or a view name or a keyword
> view #1 start
Expected an integer >= 1 or a keyword
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> clip near 40
> clip near -40
> clip near -20
> clip near 10
> clip far -30
> clip far -30
> clip far -10
> clip far -10
> select #1
5 models selected
> ~select #1
Nothing selected
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> ~select #3
21 models selected
> hide #!3 models
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> select clear
> hide #!3 models
> view name cutcontact
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT1.cxs
> includeMaps true
> ui windowfill toggle
> ui windowfill toggle
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> color zone #5 near #2 distance 8.78
> wait 40
> save /Users/marta.carroni/Desktop/image8.png supersample 3
> save /Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3
> transparentBackground true
Expected a keyword
> save ../Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3
> transparentBackground true
Expected a keyword
> save ../Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3
> transparentBackground true
Expected a keyword
> save ../Documents/PCA_Figure2a_cut.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT1.cxs
> show #!3 models
> hide #!1 models
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #3 distance 8.04
> undo move
Expected fewer arguments
> view start
Expected an objects specifier or a view name or a keyword
> view list
Named views: cut, cut_horizontal, cut_vertical, cutcontact, spiral
> view cut
> tunx x 90
Unknown command: tunx x 90
> tun x 90
Unknown command: tun x 90
> tun x 90
Unknown command: tun x 90
> show #!1 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
Nothing selected
> tun x 90
Unknown command: tun x 90
> turn x 90
> ui tool show "Side View"
> clip near far 20 20
Invalid "near" argument: Expected 'off' or a number
> clip near -20 far -20
> clip near 20 far 20
> clip near 20 far 20
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> surface zone #1 nearAtoms sele distance 8.04list
Invalid "nearAtoms" argument: invalid atoms specifier
> surface zone #1 nearAtoms #3/A-N distance 8.04list
Invalid "distance" argument: Expected a number
> surface zone #1 nearAtoms #3/A-N distance 8.04
> select clear
> hide #!3 models
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!3 models
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> hide #!3 models
> clip near 20 far 20
> clip near -20 far -20
> clip near -20 far -20
> clip near -5 far -5
> select #3/A-N:10-16
1030 atoms, 1010 bonds, 6 pseudobonds, 66 residues, 2 models selected
> show #!3 models
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> color zone #1 near sel distance 3
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> hide #!3 models
> clip near -5 far 10
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> color zone #1 near sel distance 3
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> color zone #1 near sel distance 8
> color zone #1 near sel distance 5
> color zone #1 near sel distance 4
> clip near 10
> color zone #1 near sel distance 3
> color zone #1 near sel distance 5
> color zone #1 near sel distance 8
> ui tool show "Side View"
> ui tool show "Volume Viewer"
> volume #1 level 0.12
> volume #1 level 0.125
> clip near -10
> volume #1 level 0.12
> color zone #1 near sel distance 3
> color zone #1 near sel distance 3
> color zone #1 near sel distance 3
> color zone #1 near sel distance 5
> color zone #1 near sel distance 3
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> show #!3 models
> color zone #1 near sel distance 3
> ~select #3
21 models selected
> hide #!3 models
> save ../Documents/PCA_Figure2a_cut2.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT2.cxs
> ui tool show "Side View"
> show #!3 models
> select #3/a-f:671-673
71 atoms, 69 bonds, 9 residues, 1 model selected
> style (#!3 & sel) sphere
Changed 71 atom styles
> show (#!3 & sel) target ab
> select #3/a-f:660-670,674-685
1059 atoms, 1058 bonds, 2 pseudobonds, 102 residues, 2 models selected
> show (#!3 & sel) target ab
> style (#!3 & sel) stick
Changed 1059 atom styles
> hide #3! ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3 ribbons
> select clear
> select #3/A,B,C,D,E,F,N
20463 atoms, 20594 bonds, 2 pseudobonds, 1327 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> clip far -10
> clip far 10
> clip far 10
> clip near -10
> clip near -10
> select #3/A-N:10-16
1030 atoms, 1010 bonds, 6 pseudobonds, 66 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> color zone #1 near sel & #3 distance 4
> color zone #1 near sel & #3 distance 8.04
> color zone #1 near sel & #3 distance 4
> clip near -10
> clip near -10
> ui tool show "Side View"
> select #3/a-f:665-675
452 atoms, 453 bonds, 42 residues, 1 model selected
> select #3/a-f:665-674
452 atoms, 453 bonds, 42 residues, 1 model selected
> select #3/a-f:669-674
203 atoms, 205 bonds, 19 residues, 1 model selected
> select #3/a-f:669-673
203 atoms, 205 bonds, 19 residues, 1 model selected
> style (#!3 & sel) sphere
Changed 203 atom styles
> select clear
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> ui windowfill toggle
> undo
> select clear
> zoom 0.85
> ui tool show "Side View"
> zoom -0.85
> view
> zoom -1.5
> view
> zoom 1.5
> ui tool show "Side View"
> clip near 10 far -10
clip far plane is in front of near plane
> clip near 10 far 10
clip far plane is in front of near plane
> clip near 10 far 10
clip far plane is in front of near plane
> clip near -10 far -10
clip far plane is in front of near plane
> clip near -10 far -10
clip far plane is in front of near plane
> clip near -10 far -10
clip far plane is in front of near plane
> clip near -10 far -10
clip far plane is in front of near plane
> clip far 10
clip far plane is in front of near plane
> clip far 10
clip far plane is in front of near plane
> clip far 10
> clip near -10 far -10
> clip near -10 far -10
> clip near -10 far -10
> clip far 10
> clip far 10
> clip far 10
> surface zone #1 nearAtoms #3/A-N distance 4
> zoom 1
> zoom 1.2
> zoom -1.2
> ui tool show "Side View"
> view
> zoom 1.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> clip near 20
> clip near -10
> clip near -10
> clip near -10
> clip near -10
> clip near -10
> clip near -10
> save ../Documents/PCA_Figure2a_cutPview.png format png width 1600 height
> 1600 supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT3.cxs
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT3.cxs
> includeMaps true
> graphics silhouettes false
> save ../Documents/PCA_Figure2a_cutP2.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 8.04
> surface unzone #1
> select clear
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> save ../Documents/PCA_Figure2a_cutP3.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> graphics silhouettes true
> save ../Documents/PCA_Figure2a_cutP3s.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT4.cxs
> includeMaps true
——— End of log from Fri Jun 18 15:39:00 2021 ———
opened ChimeraX session
> ui tool show "Side View"
> view
> select #3/A-N:98,127,172
420 atoms, 378 bonds, 42 residues, 1 model selected
> hide (#!3 & sel) target a
> color #3/A-N:29-72,186-197 magenta
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> color zone #1 near sel & #3 distance 5
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> volume zone #1 nearAtoms sel & #3 range 8.04
> volume zone #1 nearAtoms sel & #3 range 8.04
> hide #1.1 models
> show #1.1 models
> hide #!3 models
> show #!3 models
> select clear
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> volume zone #1 nearAtoms sel & #3 range 8.04
> volume zone #1 nearAtoms sel & #3 distance 5
Expected a keyword
> volume zone #1 nearAtoms sel & #3 range 5
> select clear
> select ::name="LIG"
336 atoms, 352 bonds, 8 residues, 1 model selected
> hide sel target a
> select #3/A-N
40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected
> volume zone #1 nearAtoms sel & #3 range 3
> select clear
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> lighting full
> lighting soft
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting full
> lighting soft
> lighting flat
> lighting flat
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> graphics silhouettes false
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c.cxs
> includeMaps true
> hide cartoons
> graphics silhouettes true
> graphics silhouettes false
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c1.cxs
> includeMaps true
> save /Users/marta.carroni/Desktop/image8.png supersample 3
> save ../Deskotop/Figure2c.png format png width 1600 height 1600 supersample
> 3 transparentBackground true
Directory "../Deskotop" does not exist
> save ../Desktop/Figure2c.png format png width 1600 height 1600 supersample 3
> transparentBackground true
> hide #!3 models
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> cartoon (#!3 & sel)
> hide #!1 models
> select #3/C,E:29-72,186-197
1550 atoms, 1556 bonds, 102 residues, 1 model selected
> select #3/C,E:29-72
1332 atoms, 1338 bonds, 88 residues, 1 model selected
> color #3/A-N:38-52,72-85,29-32,60-64,110-116,186-182 magenta
> color #3/A-N:38-52,72-85,29-32,60-64,110-116,186-182,86-95 magenta
> select clear
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> select up
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 23 models selected
> select up
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 27 models selected
> select up
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 28 models selected
> select up
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 28 models selected
> color zone #1 near sel & #3 range 5
Expected a keyword
> color zone #1 near sel & #3 distance 5
> show #!1 models
> cartoon hide (#!3 & sel)
> select clear
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_suba.cxs
> includeMaps true
> save ../Deskotop/Figure2c_suba.png format png width 1600 height 1600
> supersample 3 transparentBackground true
Directory "../Deskotop" does not exist
> save ../Desktop/Figure2c_suba.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> view
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subb.cxs
> includeMaps true
> save ../Desktop/Figure2c_subb.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> view
> save ../Desktop/Figure2c_subc.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subc.cxs
> includeMaps true
> view
> save ../Desktop/Figure2c_subd.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subd.cxs
> includeMaps true
> view
> save ../Desktop/Figure2c_sube.png format png width 1600 height 1600
> supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_sube.cxs
> includeMaps true
> view
> view
> view
> select #3/a-f:671-673
71 atoms, 69 bonds, 9 residues, 1 model selected
> hide #!4 models
> close #4
> open
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/density_mod_phenix/ResolveCryoEM_3/denmod_map_i4_copy.ccp4
Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown
at level 0.263, step 1, values float32
> volume #2 level 0.05545
> volume #2 level 0.09802
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_AGFcxs.cxs
> includeMaps true
——— End of log from Fri Aug 13 11:00:00 2021 ———
opened ChimeraX session
> hide #!2 models
> hide #!3 models
> show #!3 models
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_bHairpinsP.cxs
> includeMaps true
——— End of log from Tue Mar 1 18:09:05 2022 ———
opened ChimeraX session
> lighting soft
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select #3/A:1-28
437 atoms, 439 bonds, 27 residues, 1 model selected
> select #3/A-F,N:1-28
2907 atoms, 2919 bonds, 2 pseudobonds, 179 residues, 2 models selected
> select ~sel
71277 atoms, 71826 bonds, 37 pseudobonds, 5640 residues, 7 models selected
> hide sel cartoons
> select #3/a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> show sel cartoons
> select clear
> view
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> view
> view orient
> undo
Drag select of 3355 residues, 25 pseudobonds
> show sel surfaces
> select clear
> hide #!3 models
> show #!3 models
> ui tool show "Side View"
> turn x 90
> turn y 60
> turn x 90
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> hide #3.1 models
> hide #3.15 models
> hide #3.17 models
> hide #3.18 models
> hide #3.19 models
> show #3.19 models
> hide #3.19 models
> hide #3.20 models
> hide #3.21 models
> hide #3.22 models
> hide #!3 models
> show #!3 models
> view
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> show #3.3 models
> show #3.4 models
> show #3.5 models
> show #3.6 models
> show #3.7 models
> show #3.8 models
> show #3.9 models
> show #3.10 models
> show #3.11 models
> show #3.12 models
> show #3.13 models
> show #3.14 models
> show #3.15 models
> lighting shadows false
> select #3/a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> ui tool show "Basic Actions"
> hide /J target abp
[Repeated 3 time(s)]
> show /J target abp
[Repeated 3 time(s)]
> hide /J target abp
[Repeated 1 time(s)]
> cartoon style (#!3 & sel) modeHelix tube sides 20
> cartoon style (#!3 & sel) xsection oval modeHelix default
> cartoon style (#!3 & sel & coil) xsection oval
> cartoon style (#!3 & sel) xsection barbell modeHelix default
> cartoon style (#!3 & sel) modeHelix tube sides 20
> select clear
> save /Users/marta.carroni/Desktop/Figure2c_overall.png format png width 1600
> height 1600 supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2c_overall.cxs
> includeMaps true
——— End of log from Tue Mar 1 22:41:50 2022 ———
opened ChimeraX session
> cartoon style #3.2-15#!3 xsection oval modeHelix default
> hide #!3 models
> show #!3 models
> select #3/a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> select ~sel
40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 7 models selected
> hide sel cartoons
> ~select #1
40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 19 models selected
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3.1
74184 atoms, 74745 bonds, 5819 residues, 22 models selected
> select #3
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected
> ~select #3
21 models selected
> hide #!3 models
> show #!3 models
> select #3/a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> select ~sel
40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 7 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> surface hidePatches (#!3 & sel)
> select #3/a-f
33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected
> select #3/b/c/d/e/
Expected an objects specifier or a keyword
> select #3/b,c,d,e
21000 atoms, 21205 bonds, 21 pseudobonds, 2123 residues, 2 models selected
> hide sel cartoons
> select #3/a:LIG
82 atoms, 86 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/f:704
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> show #!2 models
> volume #2 style mesh
> volume #!2 style mesh
> undo
> select clear
> volume #2 level 0.2257
> volume #2 level 0.3162
> volume #2 level 0.3801
> select #3/a:LIG
82 atoms, 86 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #3/a:LIG
82 atoms, 86 bonds, 2 residues, 1 model selected
> volume zone #2 nearAtoms #3/a:LIG range 3 newMap true
Opened denmod_map_i4_copy.ccp4 zone as #4, grid size 199,196,146, pixel 1.34,
shown at step 1, values float32
> select up
4346 atoms, 4398 bonds, 546 residues, 1 model selected
> select up
74184 atoms, 74745 bonds, 5819 residues, 2 models selected
> select up
74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 23 models selected
> select #3/f:704
24 atoms, 23 bonds, 1 residue, 1 model selected
> color (#!3 & sel) byelement
> volume #4
> volume #4 level 0.3929
> style sel ball
Changed 24 atom styles
> style sel sphere
Changed 24 atom styles
> style sel ball
Changed 24 atom styles
> mesh fine
Unknown command: mesh fine
> ui tool show "Side View"
> volume #2 level 0.4404
> volume #4 level 0.5717
> select clear
> ui mousemode right label
> label #3/f:704
> ui mousemode right "move label"
> label #4#3.2-15,23#!3 attribute label_one_letter_code
> ui mousemode right label
> ~label #4#3.2-15,23#!3 atoms
> ~label #4#3.2-15,23#!3 residues
> ui mousemode right label
> label #3/f:704
> ui mousemode right "move label"
> label #4#3.2-15,23#!3 attribute label_one_letter_code
> label height 7
> label height 3
> ui mousemode right label
> ~label #4#3.2-15,23#!3 residues
> ui mousemode right label
> label #3/f:704
> ui mousemode right "move label"
> select clear
> label #4#3.2-15,23#!3 text R704
Too many labels (5819), label texture size (2048,17496) exceeded maximum
OpenGL texture size (16384), some labels will be blank.
> ~label #4#3.2-15,23#!3 residues
> save /Users/marta.carroni/Documents/figure3_ATP_suba.png width 1600 height
> 1600 supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs
> volume #4 style surface
> volume #4 color #b2b2b286
> volume #4 color #b2b2b24a
> volume #4 color #b2b2b2c5
> volume #4 color #b2b2b241
> save /Users/marta.carroni/Documents/figure3_ATP_suba_v1.png width 1600
> height 1600 supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs
> includeMaps true
——— End of log from Sun Mar 27 22:51:28 2022 ———
opened ChimeraX session
> hide hh
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide HH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide HH atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide hh
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide hh atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hideh
Unknown command: hideh
> hidehh
Unknown command: hidehh
> hide hh
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select N
7910 atoms, 5819 residues, 1 model selected
> select H
28621 atoms, 3652 residues, 1 model selected
> hide sel atoms
> select clear
> save /Users/marta.carroni/Documents/figure3a_pocketb.png width 1600 height
> 1600 supersample 3 transparentBackground true
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a_I.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fab208dcee0> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fab0f5b9280> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
Populating font family aliases took 600 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fab208dcee0> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fab0f5b9280> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_aI.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fab208dcee0> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fab0f5b9280> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fab208dcee0> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fab0f5b9280> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fab208dcee0> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fab0f5b9280> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook
Model Identifier: MacBook10,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1,3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 451.120.7.0.0
OS Loader Version: 540.120.3~6
SMC Version (system): 2.42f13
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 7:03
Graphics/Displays:
Intel HD Graphics 615:
Chipset Model: Intel HD Graphics 615
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x591e
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2304 x 1440 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (6)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Basic Actions saving session: 'QEventLoop' object has no attribute 'exec_' |
comment:2 by , 3 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
| Status: | accepted → assigned |
comment:3 by , 3 years ago
QEventLoop does not have an exec_() method in PyQt6, instead it has exec(), while PyQt5 had exec_(). Because of this ported code that wanted to support both looked like (from ui/src/gui.py)
if hasattr(menu, 'exec'):
menu.exec(p) # PyQt6
else:
menu.exec_(p) # PyQt5
The reason you thought QEventLoop has exec_() is because it does after qtpy is imported (the shim used by the ChimeraX shell). Apparently qtpy adds the exec_ method.
from Qt.QtCore import QEventLoop QEventLoop.exec_ Out[7]: <function qtpy.QtCore.<lambda>(self, *args, **kwargs)>
comment:4 by , 3 years ago
I think we no longer support Qt 5 so event_loop.exec_() can simply be changed to event_loop.exec().
But session saving is broken whenever Basic Actions is shown in 1.4. Not sure how serious this will be.
comment:5 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
That did fix session saving/restoring. We might put the new version on the toolshed.
follow-up: 6 comment:6 by , 3 years ago
The trouble with putting a fix on the Toolshed is that everyone will be notified of an update. This is a bug that probably effects less 1% of users. So we are mostly just annoying everyone by asking everyone to do an update. We have discussed before making the update notification only notify people who actually have used the tool that is being updated. I've made a ticket for that #7152.
Note:
See TracTickets
for help on using tickets.
_Seems_ like a Qt6 wrapping issue somehow, so reassigning to Zach. Nonetheless, as far as I can tell, QEventLoop *does* have an exec_ method, so I don't know how the error occurs.