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Opened 4 years ago
Closed 4 years ago
#5258 closed defect (fixed)
Session code trying to take len() of 'SurfaceUpdaters'
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.3 |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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: 1.3.dev202109172329 (2021-09-17 23:29:10 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3.dev202109172329 (2021-09-17)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.cxs"
Opened j1474_j1475_combined.mrc as #1, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at level 0.8, step 1, values float32
Opened j1474_j1475_combined.mrc zone as #3, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at level 0.5, step 1, values float32
Opened j1474_j1475_combined.mrc zone as #4, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at level 0.5, step 1, values float32
Opened j1474_j1475_combined.mrc zone as #5, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at level 0.5, step 1, values float32
Log from Tue Sep 14 12:49:36 2021UCSF ChimeraX version: 1.3.dev202105250411
(2021-05-25)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/kookjookim/Dropbox/Band3_shared/ankyrin_complex/maps_and_models/j1474_j1475_combined/j1474_j1475_combined.mrc
Opened j1474_j1475_combined.mrc as #1, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at level 1.09, step 2, values float32
> open
> /Users/kookjookim/Dropbox/Band3_shared/ankyrin_complex/maps_and_models/j1474_j1475_combined/initial_model_26_jul_real_space_refined_001.pdb
Chain information for initial_model_26_jul_real_space_refined_001.pdb #2
---
Chain | Description
A | No description available
B | No description available
D | No description available
F | No description available
I | No description available
K | No description available
L | No description available
P | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> style stick
Changed 46010 atom styles
> volume #1 step 1
> hide atoms
> show atoms
> show cartoons
> select /K
5949 atoms, 6019 bonds, 5 pseudobonds, 380 residues, 2 models selected
> select /K,L,B
18024 atoms, 18247 bonds, 7 pseudobonds, 1161 residues, 2 models selected
> select ~sel
27986 atoms, 28112 bonds, 6 pseudobonds, 1926 residues, 4 models selected
> hide sel atoms
> hide sel cartoons
Drag select of 12091 atoms, 1158 residues, 7 pseudobonds, 11274 bonds
> hide sel atoms
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> show sel atoms
> select H
23058 atoms, 2944 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select /K
5949 atoms, 6019 bonds, 5 pseudobonds, 380 residues, 2 models selected
> color sel #8338EC
> select /L
6061 atoms, 6139 bonds, 1 pseudobond, 390 residues, 2 models selected
> color sel #3A86FF
> color /B #002F7A
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> hide sel atoms
> show #!1 models
> set bgColor white
> select /K,L,B
18024 atoms, 18247 bonds, 7 pseudobonds, 1161 residues, 2 models selected
> volume zone #1 nearAtoms sel range 5 newMap true
Opened j1474_j1475_combined.mrc zone as #3, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> volume #3 level 0.492
> close #3
> volume zone #1 nearAtoms #2/K range 5 newMap true
Opened j1474_j1475_combined.mrc zone as #3, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> volume zone #1 nearAtoms #2/B range 5 newMap true
Opened j1474_j1475_combined.mrc zone as #4, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> volume zone #1 nearAtoms #2/L range 5 newMap true
Opened j1474_j1475_combined.mrc zone as #5, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> lighting soft
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #3
> volume zone #1 nearAtoms #2/K range 3 newMap false
> show #!1 models
> close #4-5
> volume zone #1 nearAtoms #2/K range 2 newMap false
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Hide Dust"
> surface dust #1 size 2.49
> surface dust #1 size 2.61
> surface dust #1 size 16.42
> surface dust #1 size 1.26
> surface dust #1 size 2.74
> surface dust #1 size 2.84
> surface dust #1 size 6.94
> surface dust #1 size 1.54
> surface dust #1 size 1.46
> surface dust #1 size 9.19
[Repeated 1 time(s)]
> surface dust #1 size 6.94
[Repeated 1 time(s)]
> surface dust #1 size 45.1
[Repeated 1 time(s)]
> surface dust #1 size 23.24
[Repeated 1 time(s)]
> surface dust #1 size 36.96
> surface dust #1 size 37.58
> surface dust #1 size 25.67
[Repeated 1 time(s)]
> surface dust #1 size 17.83
[Repeated 1 time(s)]
> surface dust #1 size 10.85
[Repeated 1 time(s)]
> volume zone #1 nearAtoms #2/K range 2 newMap false
> volume #1 level 0.5648
> volume zone #1 nearAtoms #2/K range 2 newMap false
> volume zone #1 nearAtoms #2/K range 2 newMap true
Opened j1474_j1475_combined.mrc zone as #3, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> surface dust #3 size 2.49
> surface dust #3 size 2.52
> surface dust #3 size 6.49
> volume zone #1 nearAtoms #2/L range 2 newMap true
Opened j1474_j1475_combined.mrc zone as #4, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> surface dust #4 size 2.49
> volume zone #1 nearAtoms #2/B range 2 newMap true
Opened j1474_j1475_combined.mrc zone as #5, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> surface dust #5 size 2.49
> color #3 #83b2b2 models
> color #3 #513377 models
[Repeated 1 time(s)]
> color #3 #8338ec models
> color #4 #3a86ff models
> color #5 #002F7A models
> hide #!2 models
> lighting soft
> lighting simple
> lighting full
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> view orient
> ui tool show "Side View"
> camera ortho
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!2 models
> view orient
> show #!2 models
> hide #!3 models
> view orient
> turn x 10
[Repeated 11 time(s)]
> turn x -5
> turn y 100
> show #!3 models
> hide #!2 models
> turn x 10
> turn x -5
> turn y 20
[Repeated 3 time(s)]
> turn x 30
> show #!2 models
> hide #!3 models
> turn x 30
[Repeated 1 time(s)]
> turn z 10
[Repeated 12 time(s)]
> turn z -5
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select clear
[Repeated 1 time(s)]
> hide #2/K target p
> hide #2/K,L,B target p
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting flat
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> turn z 2
[Repeated 3 time(s)]
> turn y 2
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.cxs"
> includeMaps true
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.png"
> width 3000 height 3000 supersample 3 transparentBackground true
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.png"
> width 3000 height 1200 supersample 3 transparentBackground true
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.png"
> width 3000 height 1500 supersample 3 transparentBackground true
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.png"
> width 3000 height 1800 supersample 3 transparentBackground true
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!2 models
> lighting soft
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_top_density_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> turn x 90
[Repeated 2 time(s)]
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_side_cx.png"
> width 3000 height 1800 supersample 3 transparentBackground true
> show #!3 models
> show #!4 models
> show #!5 models
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_density_cx.png" width 3000 height 1800 supersample 3
> transparentBackground true
> hide #!2 models
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_side_density_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> show #!2 models
> surface dust #3 size 6.38
> surface dust #3 size 2.17
> surface dust #3 size 2.25
> surface dust #3 size 1.14
> surface dust #3 size 1.16
> surface dust #3 size 0.75
> surface dust #3 size 0.78
> surface dust #3 size 2.88
> volume #3 level 0.462
> volume #3 level 0.4
> turn x 90
> surface dust #3 size 2.88
> surface dust #3 size 2.98
> surface dust #3 size 1.97
> surface dust #3 size 2
> surface dust #3 size 3.18
> surface dust #3 size 3.29
> surface dust #3 size 6.18
> surface dust #3 size 5.78
> surface dust #3 size 7.29
> surface dust #3 size 7.41
> surface dust #3 size 6.28
> volume #3 level 0.3
> volume #3 level 0.4
> volume #3 level 0.3
> turn x 90
> surface undust #3
[Repeated 1 time(s)]
> surface dust #3 size 6.28
> volume #3 level 0.2
> volume #3 level 0.4
> volume #3 level 0.5
> volume #3 level 0.4
> volume #3 level 0.45
> volume #3 level 0.5
> volume #3 level 0.4
> volume #4 level 0.4
> volume #5 level 0.4
> surface dust #3 size 6.28
> surface dust #3 size 7
[Repeated 1 time(s)]
> turn x 90
[Repeated 5 time(s)]
> surface dust #4 size 7
[Repeated 1 time(s)]
> turn x 90
> surface dust #5 size 2.7
> surface dust #5 size 7
> volume #3 level 0.3
> volume #3 level 0.6
> volume #3 level 0.5
> volume #3 level 0.4
> volume #3 level 0.5
> volume #4 level 0.5
> volume #5 level 0.5
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> volume #1 level 0.5
> volume #1 level 0.6
> volume #1 level 0.7
> volume #1 level 0.8
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.cxs"
> includeMaps true
——— End of log from Tue Sep 14 12:49:36 2021 ———
opened ChimeraX session
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2 newMap false
> show #!1 models
> volume #1 level 0.5
> volume #1 level 0.4
> volume #1 level 0.5
> volume zone #1 nearAtoms sel range 3 newMap false
> select clear
> graphics silhouettes false
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> turn x 90
> volume #1 level 0.3376
> volume zone #1 nearAtoms sel range 2.5 newMap true
no atoms specified for zone
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2.5 newMap true
Opened j1474_j1475_combined.mrc zone as #6, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> select clear
> ui tool show "Hide Dust"
> surface dust #6 size 2.49
> surface dust #6 size 2.44
> surface dust #6 size 2.7
> volume #6 color #fffb00
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> turn z 90
> turn z 270
> turn x 90
[Repeated 2 time(s)]
> hide #!2 models
> turn x 90
[Repeated 2 time(s)]
> hide #!6 models
> close #6
> select ::name="CLR"
222 atoms, 234 bonds, 3 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2 newMap true
Opened j1474_j1475_combined.mrc zone as #6, grid size 470,403,338, pixel
0.415,0.415,0.415, shown at step 1, values float32
> surface dust #6 size 2.49
> surface dust #6 size 2.4
> surface dust #6 size 2.88
> color #6 #fffb00 models
> volume #6 level 0.5
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ag_side_density_chl_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> zoom 1.1
[Repeated 1 time(s)]
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ag_side_density_chl_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> select clear
> graphics silhouettes true
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ag_side_chl_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> select H
23058 atoms, 2944 residues, 1 model selected
> hide sel atoms
> select clear
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ag_side_chl_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> turn y 180
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ce_side_chl_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!5 models
> show #!4 models
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ce_side_chl_density_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> turn x 90
[Repeated 3 time(s)]
> graphics silhouettes false
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_Ce_side_chl_density_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> turn x 90
[Repeated 2 time(s)]
> zoom 0.9
[Repeated 1 time(s)]
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_top_chl_density_cx.png" width 3000 height 1800
> supersample 3 transparentBackground true
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> graphics silhouettes true
> save "/Users/kookjookim/Dropbox/untitled
> folder/Figures/fig3_Rh_top_chl_cx.png" width 3000 height 1800 supersample 3
> transparentBackground true
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
> save "/Users/kookjookim/Dropbox/untitled folder/Figures/fig3_Rh_top_cx.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
TypeError: object of type 'SurfaceUpdaters' has no len()
TypeError: object of type 'SurfaceUpdaters' has no len()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.2.15
OpenGL renderer: AMD Radeon RX 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro5,1
Processor Name: 6-Core Intel Xeon
Processor Speed: 3.46 GHz
Number of Processors: 2
Total Number of Cores: 12
L2 Cache (per Core): 256 KB
L3 Cache (per Processor): 12 MB
Hyper-Threading Technology: Enabled
Memory: 96 GB
System Firmware Version: 9144.0.7.1.0
SMC Version (system): 1.39f5
SMC Version (processor tray): 1.39f5
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 4 days 1:13
Graphics/Displays:
Radeon RX 580:
Chipset Model: Radeon RX 580
Type: GPU
Bus: PCIe
Slot: Slot-1
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00e7
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
PA278QV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: LALMQS000226
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29.1
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
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: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109172329
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.1
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
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
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: 2.0.1
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2
ChimeraX-ModelPanel: 1.2
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: 1.7
ChimeraX-PDB: 2.6.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.3
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: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
distlib: 0.3.2
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.8.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.1
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (5)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session code trying to take len() of 'SurfaceUpdaters' |
comment:2 by , 4 years ago
| Milestone: | → 1.3 |
|---|---|
| Reporter: | changed from to |
comment:4 by , 4 years ago
Duplicate with:
open emdb:1080 format ccp4 fromDatabase emdb surface dust #1 size 2.49 save fubar.cxs
comment:5 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed by reverting session state manager API to look for subclasses of State, not StateManager. Instead, in daily builds, print developer warning if include_state (from StateManager) is missing. This works because SurfaceUpdaters subclasses from State, not StateManager.
Note:
See TracTickets
for help on using tickets.
From Christophe's mail to chimerax-users:
When I'm saving a session displaying 3D image stacks as surfaces into a csx file, I get this error:
TypeError: object of type 'SurfaceUpdaters' has no len()
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:
However if I switch the displayed stacks as volume, then there is no error on save.
This is with the daily build 1.3.dev202109160803 (2021-09-16) on OSX Big Sur (Intel architecture).