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#8658 closed defect (fixed)

'PickedPseudobond' object has no attribute 'group'

Reported by:	bshaanan@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-144-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.dev202303040240 (2023-03-04 02:40:47 UTC)
Description
I am coloring a ligand surface by electrostatic potential (.dx)

I am not where to look for the log file. Please guide me. Thanks

Log:
UCSF ChimeraX version: 1.6.dev202303040240 (2023-03-04)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /home/boaz/data/esrf_jul09/b28/xds_2021/test_surface_D_electrostatics.cxs
> format session

Log from Tue Aug 31 00:16:55 2021UCSF ChimeraX version: 1.3.dev202108240721
(2021-08-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/boaz/data/EladB_2021/i393a+_b6/Jan_2021/refmac/0006-01_CDEF_pdbset1.pdb
> format pdb

Summary of feedback from opening
/home/boaz/data/EladB_2021/i393a+_b6/Jan_2021/refmac/0006-01_CDEF_pdbset1.pdb  
---  
warnings | Ignored bad PDB record found on line 217  
REMARK [No title given]  
  
Cannot find LINK/SSBOND residue CYS (588 )  
Cannot find LINK/SSBOND residue CYS (588 )  
Cannot find LINK/SSBOND residue UQ0 (962 )  
Cannot find LINK/SSBOND residue MG (601 )  
Cannot find LINK/SSBOND residue ASP (446 )  
14 messages similar to the above omitted  
  
0006-01_CDEF_pdbset1.pdb title:  
\--- [more info...]  
  
Chain information for 0006-01_CDEF_pdbset1.pdb #1  
---  
Chain | Description  
C D E F | No description available  
  
Non-standard residues in 0006-01_CDEF_pdbset1.pdb #1  
---  
ALU — (ALU)  
CSO — (CSO)  
FAD — (FAD)  
MG — (MG)  
PGE — (PGE)  
TDK — (TDK)  
UQ0 — (UQ0)  
  

> select D

Nothing selected  

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select clear

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> hide sel target a

> select /C:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> cartoon hide sel

> hide sel target a

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /E:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> select /E:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /C:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /C:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /E:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> select /F:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> cartoon hide sel

> hide sel target a

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> surface sel

> surface hidePatches (#!1 & sel)

> select D:51

Expected an objects specifier or a keyword  

> ~select

Nothing selected  

> surface

> surface hidePatches

> select /D:2-593

4529 atoms, 4621 bonds, 592 residues, 1 model selected  

> surface (#!1 & sel)

> surface style #1.2 mesh

> surface style #1.2 dot

> surface style #1.2 solid

> transparency (#!1 & sel) 50

> save /home/boaz/data/esrf_jul09/b28/xds_2021/test_surface_D.cxs

> toolshed show

[Repeated 1 time(s)]

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CSO (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp9x4nv4bq/ante.in.mol2 -fi mol2 -o /tmp/tmp9x4nv4bq/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(CSO) ``  
(CSO) `Welcome to antechamber 20.0: molecular input file processor.`  
(CSO) ``  
(CSO) `Info: Finished reading file (/tmp/tmp9x4nv4bq/ante.in.mol2); atoms read
(24), bonds read (23).`  
(CSO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CSO) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CSO) ``  
(CSO) ``  
(CSO) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CSO) `Info: Total number of electrons: 102; net charge: 0`  
(CSO) ``  
(CSO) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`  
(CSO) ``  
(CSO) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(CSO) ``  
(CSO) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CSO) ``  
Charges for residue CSO determined  
Coulombic values for 0006-01_CDEF_pdbset1.pdb_D SES surface #1.2: minimum,
-15.25, mean -2.58, maximum 9.89  
To also show corresponding color key, enter the above coulombic command and
add key true  

> save
> /home/boaz/data/esrf_jul09/b28/xds_2021/test_surface_D_electrostatics.cxs

——— End of log from Tue Aug 31 00:16:55 2021 ———

opened ChimeraX session  

> select up

4533 atoms, 4623 bonds, 593 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> select add /C:701@C5A

4534 atoms, 4623 bonds, 593 residues, 2 models selected  

> ~select

Nothing selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

34 atoms, 35 bonds, 1 residue, 1 model selected  

> ~select

Nothing selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

34 atoms, 35 bonds, 1 residue, 1 model selected  

> select up

4640 atoms, 4735 bonds, 599 residues, 1 model selected  

> hide (#!1 & sel) target a

> select up

4642 atoms, 4736 bonds, 600 residues, 2 models selected  

> select up

4693 atoms, 4793 bonds, 600 residues, 2 models selected  

> hide (#!1 & sel) target a

> select add /C:802@C8

4694 atoms, 4793 bonds, 601 residues, 2 models selected  

> select up

4706 atoms, 4806 bonds, 601 residues, 2 models selected  

> select up

9235 atoms, 9428 bonds, 1193 residues, 2 models selected  

> hide (#!1 & sel) target a

> select up

9237 atoms, 9429 bonds, 1194 residues, 3 models selected  

> select up

9269 atoms, 9463 bonds, 1194 residues, 3 models selected  

> select up

9281 atoms, 9472 bonds, 1197 residues, 3 models selected  

> hide (#!1 & sel) target a

> select add /F:801@PB

9282 atoms, 9472 bonds, 1198 residues, 3 models selected  

> select up

9283 atoms, 9473 bonds, 1198 residues, 3 models selected  

> select up

9315 atoms, 9507 bonds, 1198 residues, 3 models selected  

> select up

13921 atoms, 14207 bonds, 1796 residues, 3 models selected  

> hide (#!1 & sel) target a

> select /D801

Nothing selected  

> select /D 801

Expected a keyword  

> select /D TDK 801

Expected a keyword  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

34 atoms, 35 bonds, 1 residue, 1 model selected  

> surface sel

> open
> /home/boaz/data/EladB_2021/b24_iavd/XDS_2022/SG-19/apbs/salt/dslep1csdt-
> pot.dx

Opened dslep1csdt-pot.dx as #2, grid size 257,257,225, pixel
0.502,0.504,0.525, shown at level -60.3,60.3, step 1, values float32  

> hide #!2 models

> ui tool show "Surface Color"

> color radial #1.6 palette #ff0000:#ffffff:#0000ff

> color single #1.6

> color radial #1.6 palette -30,#ff0000:0,#ffffff:30,#0000ff

> color radial #1.6 palette #ff0000:#ffffff:#0000ff

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 488, in
_report_surface_value_at_mouse  
reported = _report_surface_value(self.session, win_x, win_y)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 522, in _report_surface_value  
surf = surf_pick.drawing()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2233, in drawing  
return self.group  
AttributeError: 'PickedPseudobond' object has no attribute 'group'  
  
Error processing trigger "new frame":  
AttributeError: 'PickedPseudobond' object has no attribute 'group'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2233, in drawing  
return self.group  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.161.03
OpenGL renderer: Quadro T2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 5540
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9850H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       2.7Gi        10Gi       121Mi       2.0Gi        12Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Mobile) [8086:3e9b] (rev 02)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell UHD Graphics 630 (Mobile) [1028:0906]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.9
    ChimeraX-AtomicLibrary: 10.0.5
    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: 1.2.1
    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-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.dev202303040240
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 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-LinuxSupport: 1.0.1
    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: 2.0.11
    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: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    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: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    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: 1.27.3
    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: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.2.0
    jupyterlab-widgets: 3.0.5
    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: 23.0
    pandas: 1.5.3
    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: 3.1.0
    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: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4
    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: 1.0.2
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5
    zipp: 3.15.0

Change History (6)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Graphics
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → 'PickedPseudobond' object has no attribute 'group'

comment:2 by Eric Pettersen, 3 years ago

Hi Boaz,

Thanks for reporting this problem -- it will be fixed in tomorrow's build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to: 3 ; follow-up: 3 comment:3 by bshaanan@…, 3 years ago

Hi Eric,

That'll be great,thanks. BTW the bug report panel asks to attach the log file, is this the equivalent of the reply-log in Chimera? In any case, where is hiding ?
Thanks,
Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710




________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, March 16, 2023 11:55 PM
Cc: בעז שאנן <bshaanan@bgu.ac.il>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8658: 'PickedPseudobond' object has no attribute 'group' (was: ChimeraX bug report submission)

#8658: 'PickedPseudobond' object has no attribute 'group'
---------------------------------+----------------------
          Reporter:  bshaanan@…  |      Owner:  pett
              Type:  defect      |     Status:  accepted
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:              |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+----------------------
Changes (by pett):

 * status:  new => accepted
 * component:  Unassigned => Graphics
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => pett


--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f8658%23comment%3a1&umid=489CD26C-F70B-8305-A43A-38A05B3D5524&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-c9f0b9204249716078db674f5b36e262b2241d2e>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=489CD26C-F70B-8305-A43A-38A05B3D5524&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-10ccf63b3dd883998e84778da3c0481cade61578>
ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 3 years ago

Hi Boaz,

The "log" is the contents of the Log tool, which shows automatically at startup unless you've disabled it from autostarting. Tools→General→Log will show it if for some reason it's not being shown in your ChimeraX.

--Eric

in reply to: 5 ; follow-up: 5 comment:5 by bshaanan@…, 3 years ago

Hi Pett,

Ah, it was open in front of my eyes, just didn't realize that this was the log file (I should have, of course).

Thanks a lot,

           Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710




________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, March 17, 2023 2:09 AM
Cc: בעז שאנן <bshaanan@bgu.ac.il>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8658: 'PickedPseudobond' object has no attribute 'group'

#8658: 'PickedPseudobond' object has no attribute 'group'
---------------------------------+----------------------
          Reporter:  bshaanan@…  |      Owner:  pett
              Type:  defect      |     Status:  accepted
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:              |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+----------------------

Comment (by pett):

 Hi Boaz,
         The "log" is the contents of the Log tool, which shows
 automatically at startup unless you've disabled it from autostarting.
 Tools→General→Log will show it if for some reason it's not being shown in
 your ChimeraX.

 --Eric

--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f8658%23comment%3a4&umid=CE252CF7-F70D-6605-AE72-CA7321CC754C&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-d11a181e2617705c0bc094f4493175c3dc45349e>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=CE252CF7-F70D-6605-AE72-CA7321CC754C&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-bbebcf6940500aae17186f42ed1bf4b29eca3db0>
ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 3 years ago

Resolution:	→ fixed
Status:	accepted → closed

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