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#9869 accepted defect

Restoring new session in old ChimeraX

Reported by:	jae-hun.jeoung@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/adminjh/Documents/ChimeraX/SulE/Missense3D/csx/E53D-msCysAsp_v1.cxs

Log from Tue Jul 11 11:43:02 2023 Startup Errors  
---  
error | Bundle 'ChimeraX-Dicom' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/__init__.py", line 17, in <module>  
from .dicom import (  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/__init__.py", line 3, in <module>  
from .ui import DICOMBrowserTool, DICOMDatabases  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/__init__.py", line 16, in <module>  
from .dicom_databases import *  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/ui/dicom_databases.py", line 29, in <module>  
from ..databases import TCIADatabase  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/__init__.py", line 1, in <module>  
from .tcia import TCIADatabase  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dicom/dicom/databases/tcia.py", line 24, in <module>  
from tcia_utils import nbia  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tcia_utils/__init__.py", line 2, in <module>  
from . import datacite  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tcia_utils/datacite.py", line 1, in <module>  
import pandas as pd  
ModuleNotFoundError: No module named 'pandas'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's
module: No module named 'pandas'  
notes | available bundle cache has not been initialized yet  
2023-07-11 11:32:55,154:INFO:OpenGL_accelerate module loaded  
2023-07-11 11:32:55,173:INFO:Using accelerated ArrayDatatype  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.dev202307100059 (2023-07-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/adminjh/Desktop/Missense3D/PDB-7ppt-coot-0-A-53ASP.sc.pdb format
> pdb

Chain information for PDB-7ppt-coot-0-A-53ASP.sc.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/adminjh/Documents/ChimeraX/SulE/SulE_MB_202x/model_maps/E95D_FeFe/Job_173/XYZOUT.pdb

XYZOUT.pdb title:  
\--- [more info...]  
  
Chain information for XYZOUT.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Non-standard residues in XYZOUT.pdb #2  
---  
CL — (CL)  
FE — (FE)  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PDB-7ppt-coot-0-A-53ASP.sc.pdb, chain A (#1) with XYZOUT.pdb, chain
C (#2), sequence alignment score = 751.3  
RMSD between 139 pruned atom pairs is 0.392 angstroms; (across all 143 pairs:
0.877)  
  

> toolshed show

> show #1/A:53

> hide #2 models

> show #2 models

> close #2

> open
> /Users/adminjh/Documents/ChimeraX/SulE/SulE_MB_202x/model_maps/E53D_FeFe/Job_171/XYZOUT.pdb

XYZOUT.pdb title:  
\--- [more info...]  
  
Chain information for XYZOUT.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  
Non-standard residues in XYZOUT.pdb #2  
---  
CL — (CL)  
FE — (FE)  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PDB-7ppt-coot-0-A-53ASP.sc.pdb, chain A (#1) with XYZOUT.pdb, chain
C (#2), sequence alignment score = 756  
RMSD between 143 pruned atom pairs is 0.264 angstroms; (across all 144 pairs:
0.568)  
  

> hide #2

> show #2

> style stick

Changed 9916 atom styles  

> select #2/G:3@FE

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> select add #2/C:53@OD1

3 atoms, 3 residues, 1 model selected  

> select up

10 atoms, 7 bonds, 3 residues, 1 model selected  

> hide #2

> show sel

> select #1/A:23

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> open /Users/adminjh/Desktop/Missense3D/PDB-7ppt-coot-0-A-53CYS.sc.pdb

Chain information for PDB-7ppt-coot-0-A-53CYS.sc.pdb #3  
---  
Chain | Description  
A | No description available  
  

> show #3/A:53

> select #2/C:53@OD1

1 atom, 1 residue, 1 model selected  

> select add #2/G:3@FE

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between XYZOUT.pdb #2/C ASP 53 OD1 and /G FE 3 FE: 2.066Å  

> select #2/C:53@OD1

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between XYZOUT.pdb #2/C ASP 53 OD1 and /G FE 4 FE: 2.533Å  

> select #3/A:53@SG

1 atom, 1 residue, 1 model selected  

> select #2/C:53@CG

1 atom, 1 residue, 1 model selected  

> select add #2/G:3@FE

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between XYZOUT.pdb #2/C ASP 53 CG and /G FE 3 FE: 3.059Å  

> select clear

> select #2/C:53@CG

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance between XYZOUT.pdb #2/C ASP 53 CG and /G FE 4 FE: 2.948Å  

> save /Users/adminjh/Desktop/Missense3D/csx/E53D-msCysAsp_v1.cxs

——— End of log from Tue Jul 11 11:43:02 2023 ———

opened ChimeraX session  

> select #2/G:3@FE

1 atom, 1 residue, 1 model selected  

> select #2/G:4@FE

1 atom, 1 residue, 1 model selected  

> select #2/G:3@FE

1 atom, 1 residue, 1 model selected  

> select #2/G:4@FE

1 atom, 1 residue, 1 model selected  

> select #2/G:3@FE

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> contacts sel makePseudobonds false reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    30 contacts
             atom1                                atom2                       overlap  distance
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 236 OE2   0.160    1.890
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 236 OE2   0.160    1.890
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A HIS 56 ND1    0.155    2.115
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A HIS 56 ND1    0.155    2.115
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/C HIS 56 ND1                        0.136    2.134
    XYZOUT.pdb #2/G FE 4 FE  XYZOUT.pdb #2/D GLU 126 OE1                       0.002    2.048
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/D GLU 126 OE2                       -0.008    2.058
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/C ASP 53 OD1                        -0.016    2.066
    XYZOUT.pdb #2/G FE 4 FE  XYZOUT.pdb #2/D HIS 129 ND1                       -0.051    2.321
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 20 CD     -0.077    2.587
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 20 CD     -0.077    2.587
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/S HOH 21 O                          -0.085    2.175
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/C GLU 20 CD                         -0.097    2.607
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 270 OE2   -0.123    2.173
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 270 OE2   -0.123    2.173
    XYZOUT.pdb #2/G FE 4 FE  XYZOUT.pdb #2/D GLU 92 OE2                        -0.173    2.223
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 20 OE2    -0.178    2.228
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 20 OE2    -0.178    2.228
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 270 OE1   -0.200    2.250
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 270 OE1   -0.200    2.250
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A HIS 273 ND1   -0.216    2.486
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A HIS 273 ND1   -0.216    2.486
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/C GLU 20 OE2                        -0.221    2.271
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 270 CD    -0.254    2.764
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 270 CD    -0.254    2.764
    XYZOUT.pdb #2/G FE 3 FE  XYZOUT.pdb #2/C GLU 20 OE1                        -0.266    2.316
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 236 CD    -0.281    2.791
    XYZOUT.pdb #2/G FE 4 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 236 CD    -0.281    2.791
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A GLU 20 OE1    -0.319    2.369
    XYZOUT.pdb #2/G FE 3 FE  PDB-7ppt-coot-0-A-53ASP.sc.pdb #1/A GLU 20 OE1    -0.319    2.369
    

  
30 contacts  

> select clear

> hide #4.1 models

> hide #3 models

> show #3 models

> hide #1 models

> color #3 #5070e1ff

> color #3 #76b6e1ff

> color #3 #65e1daff

> color #3 #77d4e1ff

> color N blue target a

> color O red target a

> color S yellow target a

> color Fe firebrick

> select add #2/G:3@FE

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> select clear

> select #3/A:53@SG

1 atom, 1 residue, 1 model selected  

> select add #2/G:3@FE

2 atoms, 2 residues, 2 models selected  

> distance sel

Distance between PDB-7ppt-coot-0-A-53CYS.sc.pdb #3/A CYS 53 SG and XYZOUT.pdb
#2/G FE 3 FE: 3.694Å  

> select #2/G:4@FE

1 atom, 1 residue, 1 model selected  

> select add #3/A:53@SG

2 atoms, 2 residues, 2 models selected  

> distance sel

Distance between XYZOUT.pdb #2/G FE 4 FE and PDB-7ppt-coot-0-A-53CYS.sc.pdb
#3/A CYS 53 SG: 3.225Å  

> select #2/G:4@FE

1 atom, 1 residue, 1 model selected  

> select #2/G:4@FE

1 atom, 1 residue, 1 model selected  

> select add #2/C:53@CG

2 atoms, 2 residues, 1 model selected  

> hide sel

[Repeated 1 time(s)]

> color sel red

> color sel blue

> set bgColor white

> select clear

> show #1 models

> show #4.1 models

> hide #4.1 models

> save
> /Users/adminjh/Documents/ChimeraX/SulE/Missense3D/csx/E53D-msCysAsp_v1.cxs

> hide #1 models

> select #2/C:53@CG

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> distance sel

Distance already exists; modify distance properties with 'distance style'  

> show #4.1 models

> select clear

[Repeated 1 time(s)]

> select #2/C:53@CG

1 atom, 1 residue, 1 model selected  

> select add #2/G:4@FE

2 atoms, 2 residues, 1 model selected  

> show sel distance

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1018, in <lambda>  
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 669, in file_close_cb  
run(session, 'close session')  
File
"/Applications/ChimeraX-1.6.1.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-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state  
self.clear()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations  
for rotater in self.bond_rotaters.values():  
AttributeError: 'list' object has no attribute 'values'  
  
AttributeError: 'list' object has no attribute 'values'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations  
for rotater in self.bond_rotaters.values():  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16R000QGD/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 19 days, 16 hours, 56 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U3223QE:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.6.6
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 2 years ago

Component:	Unassigned → Sessions
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Restoring new session in old ChimeraX

comment:2 by pett, 2 years ago

Hi Jae-Hun,

ChimeraX session files are typically not backwards compatible, which means they may not be able to be restored in versions of ChimeraX older than the version they were saved from. In this case, you would need a ChimeraX daily build to restore that session file without having the later problems you ran into.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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