Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5126 closed defect (limitation)

'view' session data is None

Reported by: ewatson@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I can't restore a recent session, though the Log messages indicate that files are opened normally.  I tried in 2.1.4 and the new 2.1.5

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/ewatson/Dropbox (Scripps
> Research)/Cereblon/FIGURES/sessionfig3c.cxs"

Opened 2442_2458_2460_hingedclosed.mrc as #1, grid size 224,224,224, pixel
1.15, shown at step 1, values float32  
Opened 100postprocess_masked.mrc as #4, grid size 224,224,224, pixel 1.15,
shown at step 1, values float32  
Opened 100postprocess_masked.mrc gaussian as #5, grid size 224,224,224, pixel
1.15, shown at step 1, values float32  
Opened 100postprocess_masked.mrc gaussian as #7, grid size 224,224,224, pixel
1.15, shown at step 1, values float32  
Opened 100postprocess_masked.mrc gaussian as #8, grid size 224,224,224, pixel
1.15, shown at step 1, values float32  
Opened 19dec13_32run_class001.mrc as #9, grid size 224,224,224, pixel 0.91,
shown at step 1, values float32  
Opened cryosparc_P17_J2499_class_01_00162_volume.mrc as #10, grid size
128,128,128, pixel 1.8, shown at step 1, values float32  
Opened cryosparc_P17_J2499_class_01_00162_volume.mrc gaussian as #12, grid
size 128,128,128, pixel 1.8, shown at step 1, values float32  
Opened cryosparc_P17_J2499_class_01_00162_volume.mrc gaussian as #11, grid
size 128,128,128, pixel 1.8, shown at step 1, values float32  
Opened 22run_class001.mrc as #13, grid size 224,224,224, pixel 0.91, shown at
step 1, values float32  
Opened 117postprocess_masked.mrc as #14, grid size 224,224,224, pixel 0.91,
shown at step 1, values float32  
Opened 117postprocess_masked.mrc gaussian as #15, grid size 224,224,224, pixel
0.91, shown at step 1, values float32  
Opened 121postprocess_masked.mrc as #18, grid size 224,224,224, pixel 0.91,
shown at step 1, values float32  
Opened 19dec14c_68postprocess_masked.mrc as #19, grid size 224,224,224, pixel
0.91, shown at step 1, values float32  
Opened cryosparc_P17_J2212_006_volume_map_sharp.mrc as #20, grid size
200,200,200, pixel 1.15, shown at step 1, values float32  
Opened cryosparc_P17_J2635_map_sharp.mrc as #21.1, grid size 200,200,200,
pixel 1.15, shown at step 1, values float32  
Opened cryosparc_P17_J2636_map_sharp.mrc as #21.2, grid size 200,200,200,
pixel 1.15, shown at level 0.22, step 1, values float32  
Opened cryosparc_P17_J2634_map_sharp.mrc as #22, grid size 200,200,200, pixel
1.15, shown at level 0.105, step 1, values float32  
Opened postprocess147a01_masked.mrc as #29, grid size 200,200,200, pixel 0.91,
shown at step 1, values float32  
Opened 040run_class001.mrc as #30.1, grid size 200,200,200, pixel 0.91, shown
at level 0.00437, step 1, values float32  
Opened postprocess040a002_masked.mrc as #30.2, grid size 200,200,200, pixel
0.91, shown at level 0.0111, step 1, values float32  
Opened 19aug16c_closed_postprocess113_masked.mrc as #31, grid size
224,224,224, pixel 0.91, shown at step 1, values float32  
Opened postprocess147a01_masked.mrc gaussian as #35, grid size 200,200,200,
pixel 0.91, shown at step 1, values float32  
Opened postprocess040a002_masked.mrc gaussian as #36, grid size 200,200,200,
pixel 0.91, shown at level 0.00434, step 1, values float32  
Opened 19aug16c_closed_postprocess113_masked.mrc gaussian as #37, grid size
224,224,224, pixel 0.91, shown at level 0.00349, step 1, values float32  
Opened cryosparc_P17_J2635_map_sharp.mrc as #24, grid size 200,200,200, pixel
1.15, shown at step 1, values float32  
Opened cryosparc_P17_J2107_map_sharp.mrc as #27, grid size 224,224,224, pixel
1.15, shown at step 1, values float32  
Opened cryosparc_P17_J2147_006_volume_map_sharp.mrc as #28.1, grid size
224,224,224, pixel 1.15, shown at level 0.129, step 1, values float32  
Opened cryosparc_P17_J2148_005_volume_map_sharp.mrc as #28.2, grid size
224,224,224, pixel 1.15, shown at level 0.207, step 1, values float32  
Opened cryosparc_P17_J2149_006_volume_map_sharp.mrc as #28.3, grid size
224,224,224, pixel 1.15, shown at level 0.206, step 1, values float32  
Opened cryosparc_P17_J2147_006_volume_map_sharp.mrc gaussian as #33, grid size
224,224,224, pixel 1.15, shown at step 1, values float32  
Opened cryosparc_P17_J2148_005_volume_map_sharp.mrc gaussian as #34, grid size
224,224,224, pixel 1.15, shown at level 0.0853, step 1, values float32  
Opened cryosparc_P17_J2149_006_volume_map_sharp.mrc gaussian as #38, grid size
224,224,224, pixel 1.15, shown at level 0.122, step 1, values float32  
Opened cryosparc_P17_J2149_006_volume_map_sharp.mrc gaussian as #39, grid size
224,224,224, pixel 1.15, shown at level 0.161, step 1, values float32  
Opened cryosparc_P17_J2148_005_volume_map_sharp.mrc gaussian as #40, grid size
224,224,224, pixel 1.15, shown at level 0.18, step 1, values float32  
Opened cryosparc_P17_J2147_006_volume_map_sharp.mrc gaussian as #41, grid size
224,224,224, pixel 1.15, shown at step 1, values float32  
Opened try4_real_space_refined_008-coot-1_real_space_refined_010.pdb map 8 as
#42, grid size 48,67,53, pixel 2.67, shown at step 1, values float32  
Opened 6umlOPEN-linear_1.pdb map 8 as #43, grid size 47,65,56, pixel 2.67,
shown at step 1, values float32  
Opened map 8 as #50, grid size 52,66,62, pixel 2.67, shown at step 1, values
float32  
Opened map 8 as #49, grid size 51,65,59, pixel 2.67, shown at step 1, values
float32  
Opened map 8 as #51, grid size 47,67,56, pixel 2.67, shown at step 1, values
float32  
Opened TBDsub2.pdb map 4 as #47, grid size 22,26,23, pixel 1.33, shown at step
1, values float32  
Opened map 8 as #52, grid size 48,66,56, pixel 2.67, shown at step 1, values
float32  
Opened Morph - try4_real_space_refined_008-coot-1_real_space_refined_010.pdb
map 8 as #54, grid size 32,33,30, pixel 2.67, shown at step 1, values float32  
Opened Morph - try4_real_space_refined_008-coot-1_real_space_refined_010.pdb
map 8 as #56, grid size 36,39,34, pixel 2.67, shown at step 1, values float32  
Opened Morph - try4_real_space_refined_008-coot-1_real_space_refined_010.pdb
map 8 as #55, grid size 31,35,31, pixel 2.67, shown at step 1, values float32  
Opened tclcactvs0000GGsXQ.pdb map 4 as #58, grid size 35,24,22, pixel 1.33,
shown at level 0.0621, step 1, values float32  
Opened map 8 as #59, grid size 49,73,57, pixel 2.67, shown at step 1, values
float32  
Opened map 8 as #60, grid size 49,72,56, pixel 2.67, shown at step 1, values
float32  
Opened map 8 as #61, grid size 48,71,56, pixel 2.67, shown at step 1, values
float32  
Opened TBDsub2.pdb map 8 as #62, grid size 25,22,28, pixel 2.67, shown at
level 0.00591, step 1, values float32  
Opened 6umlOPEN-linear_1.pdb map 5 as #3, grid size 25,32,29, pixel 1.67,
shown at level 0.0101, step 1, values float32  
Opened 6bnb map 5 as #63, grid size 29,29,36, pixel 1.67, shown at level
0.0477, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/view.py", line 263, in restore_snapshot  
for k,v in data['view attrs'].items():  
TypeError: 'NoneType' object is not subscriptable  
  
Traceback (most recent call last):  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 713, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/view.py", line 263, in restore_snapshot  
for k,v in data['view attrs'].items():  
TypeError: 'NoneType' object is not subscriptable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 357, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 531, in reset  
container.clear()  
AttributeError: 'Fake' object has no attribute 'clear'  
  
AttributeError: 'Fake' object has no attribute 'clear'  
  
File
"/private/var/folders/qm/n97hnpnn5533_m7dn6_v5xx00000gn/T/AppTranslocation/FEE5F80B-661B-4ADF-86D2-CDC9AF569358/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 531, in reset  
container.clear()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 8 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (13)

comment:1 by Eric Pettersen, 4 years ago

Cc: Greg Couch added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 'view' session data is None

Reported by Edmond Watson

comment:2 by Tom Goddard, 4 years ago

You say this ChimeraX session that does not restore is "recent". What version of ChimeraX wrote that session file? Was it ChimeraX 1.2.5? Or was it a very old ChimeraX version?

The problem may be that the session file was written incorrectly. I recall seeing this kind of error with sessions written by very old versions of ChimeraX.

Have you ever opened this session file successfully since it was written?

in reply to:  3 ; comment:3 by ewatson@…, 4 years ago 

It may have been written originally by 0.9.0, but I believe it was written by 1.2.4.   I only downloaded 1.2.5 today as an attempted fix, along with restarting computer etc.

The session has been updated and renamed and resaved several times, and some older versions still open in each chimera instance, but the two newest versions don't open under any circumstances.  

I can not say for certain that I have had success opening this exact session file before.

Thanks for looking into it,
Edmond

On 8/30/21, 12:05 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #5126: 'view' session data is None
    --------------------------------+-------------------------
              Reporter:  ewatson@…  |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Sessions   |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Tom Goddard):

     You say this ChimeraX session that  does not restore is "recent".  What
     version of ChimeraX wrote that session file?  Was it ChimeraX 1.2.5?  Or
     was it a very old ChimeraX version?

     The problem may be that the session file was written incorrectly.  I
     recall seeing this kind of error with sessions written by very old
     versions of ChimeraX.

     Have you ever opened this session file successfully since it was written?

    --
    Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5126#comment:2>
    ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:4 by Tom Goddard, 4 years ago

If this session that does not open is one of your newest it seems unlikely it was written by ChimeraX 0.9 unless you have been using 0.9 recently. That would be a bad idea since so many bugs have been fixed in the year and a half since 0.9 came out.

The exact same error is reported in bug #1816 two years ago in ChimeraX 0.8. That ticket claims it was an error saving the session.

Ticket #1668 from 3 years ago with ChimeraX 0.9 also reports exactly the same error as reported in this bug report.

These old ChimeraX 0.9 bug reports don't give any way to recover because the session file written by ChimeraX 0.9 was for some reason defective. I definitely want to know if the session reported in this bug was written by a newer version than ChimeraX 0.9, but my suspicion is it was written by that very old ChimeraX.

comment:5 by Greg Couch, 4 years ago

If you run the ChimeraX command "debug session.cxs session.txt" you get a textual version of the session. It is not suitable for restoring the session, but you can see what the ChimeraX-branch, ChimeraX_commit, and ChimeraX-date are. And that will tell you which version of ChimeraX wrote the session.

in reply to:  6 ; comment:6 by ewatson@…, 4 years ago 

I'm sorry I can't figure out how to do to this to get you this information.  I have typed it in the GUI command line quite a few ways either with the broken session or with currently open sessions saved locally: Unknown command: debug session4.cxs session.txt

I also just launched ChimeraX from command line (terminal on Mac) which I never do and cannot get a debug option to work there:

 (base) wireless-122-123:Applications ewatson$ open ChimeraX /Users/ewatson/Desktop/sessionfig3c.cxs --debug
open: unrecognized option `--debug'
Usage: open [-e] [-t] [-f] [-W] [-R] [-n] [-g] [-h] [-s <partial SDK name>][-b <bundle identifier>] [-a <application>] [filenames] [--args arguments]
Help: Open opens files from a shell.
      By default, opens each file using the default application for that file.  
      If the file is in the form of a URL, the file will be opened as a URL.
Options: 
      -a                Opens with the specified application.
      -b                Opens with the specified application bundle identifier.
      -e                Opens with TextEdit.
      -t                Opens with default text editor.
      -f                Reads input from standard input and opens with TextEdit.
      -F  --fresh       Launches the app fresh, that is, without restoring windows. Saved persistent state is lost, excluding Untitled documents.
      -R, --reveal      Selects in the Finder instead of opening.
      -W, --wait-apps   Blocks until the used applications are closed (even if they were already running).
          --args        All remaining arguments are passed in argv to the application's main() function instead of opened.
      -n, --new         Open a new instance of the application even if one is already running.
      -j, --hide        Launches the app hidden.
      -g, --background  Does not bring the application to the foreground.
      -h, --header      Searches header file locations for headers matching the given filenames, and opens them.
      -s                For -h, the SDK to use; if supplied, only SDKs whose names contain the argument value are searched.
                        Otherwise the highest versioned SDK in each platform is used.
(base) wireless-122-123:Applications ewatson$ open ChimeraX /Users/ewatson/Desktop/sessionfig3c.cxs -e
The file /Applications/ChimeraX does not exist.
(base) wireless-122-123:Applications ewatson$ open ChimeraX-1.2.5.app /Users/ewatson/Desktop/sessionfig3c.cxs -e

I attempted the -e for TextEdit and my texteditor says it will not open Application files.

I'm willing to concede it was likely generated in ChimeraX version 0.9 because I use them interchangeably depending on the need for soft-lighting with surface coloring with transparency with superposition, since I think the there are circumstances where the old version works and the new does not.

Thanks for your time, or further explanation if you want to pursue further.
Randy

On 8/30/21, 2:46 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #5126: 'view' session data is None
    --------------------------------+-------------------------
              Reporter:  ewatson@…  |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Sessions   |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Greg Couch):

     If you run the ChimeraX command "debug session.cxs session.txt" you get a
     textual version of the session.  It is not suitable for restoring the
     session, but you can see what the ChimeraX-branch, ChimeraX_commit, and
     ChimeraX-date are.  And that will tell you which version of ChimeraX wrote
     the session.

    --
    Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5126#comment:5>
    ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:7 by Greg Couch, 4 years ago

Ack. I screwed up the command. It is "debug sdump session.cxs session.txt" -- forgot the sdump. You need to substitute the actual file name of the session for session.cxs, e.g., ~/project/interesting.cxs. And same for session.txt, e.g., /usr/tmp/foobar.txt.

in reply to:  8 ; comment:8 by ewatson@…, 4 years ago 

Thanks, I was able to generate the .txt file.   I think it reveals that the file was initially generated with ChimeraX 0.9

I will try to stick with newer versions of chimeraX to avoid these bugs.  Thank you for your help.  Let me know if you want more info from the 750MB text file.

 'created': '2021-07-26T22:32:16.703064Z',
 'creator': 'ewatson',
 'dateCopyrighted': '© 2021 ewatson',
 'generator': 'UCSF-ChimeraX/0.9 (Darwin), http://www.rbvi.ucsf.edu/chimerax/',
 'modified': '2021-08-12T23:01:49.633863Z',
 'session_version': 3}


Randy


On 8/30/21, 3:29 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #5126: 'view' session data is None
    --------------------------------+-------------------------
              Reporter:  ewatson@…  |      Owner:  Tom Goddard
                  Type:  defect     |     Status:  assigned
              Priority:  normal     |  Milestone:
             Component:  Sessions   |    Version:
            Resolution:             |   Keywords:
            Blocked By:             |   Blocking:
    Notify when closed:             |   Platform:  all
               Project:  ChimeraX   |
    --------------------------------+-------------------------

    Comment (by Greg Couch):

     Ack.  I screwed up the command.  It is "debug sdump session.cxs
     session.txt" -- forgot the sdump.  You need to substitute the actual file
     name of the session for session.cxs, e.g., ~/project/interesting.cxs.  And
     same for session.txt, e.g., /usr/tmp/foobar.txt.

    --
    Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5126#comment:7>
    ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:9 by Tom Goddard, 4 years ago

Resolution: → limitation
Status: assigned → closed

Hi Randy,

Thanks for checking the session. And thanks Greg, I forgot about that command that dumps session info. I'm afraid the best solution here is that you should stick to a recent ChimeraX version. Using a version before 1.0 is especially precarious. That said, if these sessions are high value to you I can explain how to insert a line into the ChimeraX Python in your distribution to get around this error.

Tom

in reply to:  10 ; comment:10 by ewatson@…, 4 years ago 

It would be very helpful if that's possible, these were relatively time-consuming and in-depth sessions.  I have help on our side as well to make sure things go smoothly. 

On 8/30/21, 4:49 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #5126: 'view' session data is None
    ---------------------------------+-------------------------
              Reporter:  ewatson@…   |      Owner:  Tom Goddard
                  Type:  defect      |     Status:  closed
              Priority:  normal      |  Milestone:
             Component:  Sessions    |    Version:
            Resolution:  limitation  |   Keywords:
            Blocked By:              |   Blocking:
    Notify when closed:              |   Platform:  all
               Project:  ChimeraX    |
    ---------------------------------+-------------------------
    Changes (by Tom Goddard):

     * status:  assigned => closed
     * resolution:   => limitation


    Comment:

     Hi Randy,

       Thanks for checking the session.  And thanks Greg, I forgot about that
     command that dumps session info.  I'm afraid the best solution here is
     that you should stick to a recent ChimeraX version.  Using a version
     before 1.0 is especially precarious.  That said, if these sessions are
     high value to you I can explain how to insert a line into the ChimeraX
     Python in your distribution to get around this error.

       Tom

    --
    Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5126#comment:9>
    ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:11 by Tom Goddard, 4 years ago

Ok, not sure you won't run into other problems restoring this session but here is how to avoid the reported error. Modify with a text editor file, e.g. Mac TextEdit

ChimeraX-1.2.5.app/Contents/lib/python3.8/site-packages/chimerax/std_commands/view.py

near line 260 you will find lines

def restore_snapshot(session, data):

nv = NamedView.new(NamedView)
for k,v in dataview attrs.items():

and add a line after the def line:

def restore_snapshot(session, data):

if data is None: return None
nv = NamedView.new(NamedView)
for k,v in dataview attrs.items():

File should be saved as raw text.

in reply to:  12 ; comment:12 by ewatson@…, 4 years ago 

Thank you so much, this worked and my session is open!!   Much appreciated

Randy

On 8/30/21, 5:31 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #5126: 'view' session data is None
    ---------------------------------+-------------------------
              Reporter:  ewatson@…   |      Owner:  Tom Goddard
                  Type:  defect      |     Status:  closed
              Priority:  normal      |  Milestone:
             Component:  Sessions    |    Version:
            Resolution:  limitation  |   Keywords:
            Blocked By:              |   Blocking:
    Notify when closed:              |   Platform:  all
               Project:  ChimeraX    |
    ---------------------------------+-------------------------

    Comment (by Tom Goddard):

     Ok, not sure you won't run into other problems restoring this session but
     here is how to avoid the reported error.  Modify with a text editor file,
     e.g. Mac TextEdit

       ChimeraX-1.2.5.app/Contents/lib/python3.8/site-
     packages/chimerax/std_commands/view.py

     near line 260 you will find lines

         def restore_snapshot(session, data):
             nv = NamedView.__new__(NamedView)
             for k,v in data['view attrs'].items():

     and add a line after the def line:

         def restore_snapshot(session, data):
             if data is None: return None
             nv = NamedView.__new__(NamedView)
             for k,v in data['view attrs'].items():

     File should be saved as raw text.

    --
    Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5126#comment:11>
    ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

in reply to:  13 ; comment:13 by goddard@…, 4 years ago 

Great!
Note: See TracTickets for help on using tickets.