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Opened 2 years ago
Closed 2 years ago
#10026 closed defect (limitation)
Restore new session in old ChimeraX
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: Linux-3.10.0-1160.95.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /nfs/home/pksingh/DATA/PilB_PA/1013_Clean_files_for_next/0906_Model_Water_Zn_2.pdb
Chain information for 0906_Model_Water_Zn_2.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/D 1.2/E | No description available
1.2/C 1.2/F | No description available
> show atoms
> hide atoms
> show cartoons
> sel#1/A:ADP
Unknown command: sel#1/A:ADP
> sel#1/A
Unknown command: sel#1/A
> select #1/a
6059 atoms, 6102 bonds, 384 residues, 1 model selected
> select #1/a:ADP
Nothing selected
> open "/run/media/pksingh/Pradip_Hutu/0906_Fitting_with
> ligands/0906_Model_02_iso_1_apply_ncs_7_water3-coot-2.pdb"
Chain information for 0906_Model_02_iso_1_apply_ncs_7_water3-coot-2.pdb #2
---
Chain | Description
A B D E | No description available
C F | No description available
> select #2/a:ADP
Nothing selected
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #2 atoms
> show #2 cartoons
> select #2/a:ZN
Nothing selected
> open "/run/media/pksingh/Pradip_Hutu/0906_Fitting_with ligands/0906Fitted
> ligand_ADP2-coot-1.pdb"
> hide #2 models
> hide #3 models
> show #3 models
> hide #3 models
> color #3 #e9b96e transparency 0
> show #3 models
> hide #3 models
> show #2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> close #1.2
> close
> open
> /nfs/home/pksingh/DATA/PilB_PA/Mac_mini/0914_PilBpa_Ligands_Zn_water/0817composite_map.ccp4
Opened 0817composite_map.ccp4 as #1, grid size 226,226,226, pixel 1.08, shown
at level 3.79, step 1, values float32
> open
> /nfs/home/pksingh/DATA/PilB_PA/Mac_mini/0914_PilBpa_Ligands_Zn_water/0911_Model_Water_Zn-
> ADP-Coot_0.pdb
Chain information for 0911_Model_Water_Zn-ADP-Coot_0.pdb #2
---
Chain | Description
A B D E | No description available
C F | No description available
> hide atoms
> show cartoons
> transparency #1 50
> select #2
36542 atoms, 36806 bonds, 2318 residues, 1 model selected
> color sel bychain
> ~select #2
Nothing selected
> hide #!1 models
> select #2/ADP
Nothing selected
> select #2/A:Zn
Nothing selected
> select #2/A:ADP
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/zn
Nothing selected
> select #Zn
Expected an objects specifier or a keyword
> show surfaces
> show atoms
> hide surfaces
> hide atoms
> select # Zn
Expected an objects specifier or a keyword
> select # ZN
Expected an objects specifier or a keyword
> select ligand
162 atoms, 174 bonds, 6 residues, 1 model selected
> select ZN
Expected an objects specifier or a keyword
> select Zn
6 atoms, 6 residues, 1 model selected
> show sel atoms
> size Zn atomRadius +2
Changed 6 atom radii
> select ligand
162 atoms, 174 bonds, 6 residues, 1 model selected
> show sel atoms
> open
> /nfs/home/pksingh/DATA/PilB_PA/Mac_mini/0914_PilBpa_Ligands_Zn_water/1017_model_01.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1346, in restore_snapshot
s.set_state_from_snapshot(session, data)
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1353, in set_state_from_snapshot
Structure.set_state_from_snapshot(self, session, data['structure state'])
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 214, in set_state_from_snapshot
StructureData.set_state_from_snapshot(self, session, data['structure state'])
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1799, in set_state_from_snapshot
f(self._c_pointer, data['version'], tuple(data['ints']),
tuple(data['floats']), tuple(data['misc']))
TypeError: Don't know how to restore new session data; update your version of
ChimeraX
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: X10SRA
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 15G 2.6G 7.4G 772M 5.4G 11G
Swap: 7.5G 4.0G 3.5G
Graphics:
02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11b2]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
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: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
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
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
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: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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: 2.0.4
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: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
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: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
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: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
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: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
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
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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Hi Pradip,
--Eric