Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5623 closed defect (fixed)

rotamers table: 'setVisibile'

Reported by: doyeon.kim@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202110080903 (2021-10-08 09:03:01 UTC)
Description
Hello, I am Doyeon Kim and I was trying to use the Rotamers tool. I selected a residue and changed it to another amino acid, and an error message that says "AttributeError: 'QHeaderView' object has no attribute 'setVisibile'" appeared. I attached the result in print screen in case it would helf figure out what the problem is. How can I resolve this?
Thank you.

Log:
UCSF ChimeraX version: 1.3.dev202110080903 (2021-10-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5I57 format mmcif fromDatabase pdb

Summary of feedback from opening 5I57 fetched from pdb  
---  
warnings | Unknown polymer entity '3' near line 5964  
Unknown polymer entity '4' near line 5969  
Atom OXT is not in the residue template for GLY /A:1001  
Atom OXT is not in the residue template for GLU /B:301  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
5i57 title:  
Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains [more
info...]  
  
Chain information for 5i57 #1  
---  
Chain | Description | UniProt  
A | Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA
1 | NMDZ1_RAT  
B | Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA
2A | NMDE1_RAT  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select
> /A:6-10,18-21,42-47,58-64,82-86,95-97,104-106,120-121,136-137,142-151,173-174,220-224,238-250,253-254

570 atoms, 575 bonds, 69 residues, 1 model selected  

> select /A:83

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:83

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel target ab

> select sel @< 5

57 atoms, 47 bonds, 15 residues, 1 model selected  

> select up

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

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

/A GLU 83: phi -132.6, psi 138.3 trans  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 111, in launch_rotamers  
run(self.session, "swapaa interactive sel %s rotLib %s" % (res_type,
lib_name))  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 127, in rotamers  
RotamerDialog(session, "%s Side-Chain Rotamers" % r, mgr, res_type, rot_lib)  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 184, in __init__  
self.finalize_init(*args)  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 223, in finalize_init  
self.table.verticalHeader().setVisibile(False)  
AttributeError: 'QHeaderView' object has no attribute 'setVisibile'  
  
AttributeError: 'QHeaderView' object has no attribute 'setVisibile'  
  
File "C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site-
packages\chimerax\swap_res\tool.py", line 223, in finalize_init  
self.table.verticalHeader().setVisibile(False)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: SAMSUNG ELECTRONICS CO., LTD.
Model: 950XBE
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 8,473,681,920
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: ko-KR
Locale: ('ko_KR', 'cp949')
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: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110080903
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.2
    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: 1.2.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.4
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    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: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
File attachment: Rotamer error 21-11-17 Doyeon Kim.png

Rotamer error 21-11-17 Doyeon Kim.png​

Attachments (1)

Rotamer error 21-11-17 Doyeon Kim.png​ (155.9 KB ) - added by doyeon.kim@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

by doyeon.kim@…, 4 years ago

Attachment: Rotamer error 21-11-17 Doyeon Kim.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → rotamers table: 'setVisibile'

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Hi Doyeon,

Thanks for reporting this problem. It was fixed about 5 days after the version you have, so if you get a current build you will be able to use Rotamers successfully.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  4 comment:3 by doyeon.kim@…, 4 years ago 

Hi Eric,

Thanks for the reply! Now in the latest version, I can change the residue using Rotamer. I will download a new version regularly. Or is there a way to update automatically?

Best regards,
Doyeon
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: November 18, 2021 3:29 PM
Cc: Doyeon Kim <doyeon.kim@sickkids.ca>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5623: rotamers table: 'setVisibile'

#5623: rotamers table: 'setVisibile' ----------------------------------------+---------------------------- Reporter: doyeon.kim@… | Owner: Eric Pettersen Type: defect | Status: closed Priority: normal | Milestone: Component: Structure Editing 

#5623: rotamers table: 'setVisibile'
----------------------------------------+----------------------------
          Reporter:  doyeon.kim@…       |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Hi Doyeon,
         Thanks for reporting this problem.  It was fixed about 5 days
 after the version you have, so if you get a current build you will be able
 to use Rotamers successfully.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5623*comment:2__;Iw!!D0zGoin7BXfl!pgHAfhM6LSTfI65xyPnq4tZhmGQuH51HEExiY34T-d84vOjm60twddVOIwZKdnaKn19U$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!D0zGoin7BXfl!pgHAfhM6LSTfI65xyPnq4tZhmGQuH51HEExiY34T-d84vOjm60twddVOIwZKdnWfDZsQ$ >
ChimeraX Issue Tracker


________________________________

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

comment:4 by Eric Pettersen, 4 years ago

Well, starting with the 1.3 production release (which should be out at the end of this month), you will be alerted when a new production release or release candidate becomes available. We don't alert about new daily builds since, well, they come out every day. :-)

in reply to:  6 comment:5 by doyeon.kim@…, 4 years ago 

Hello Eric,

That is good news. I did realize that daily builds are updated every day after inquiring, so I thought I would not get a reply. Thanks for the information, and I will look forward to the 1.3 production release.
Have a nice week! 🙂
Best regards,
Doyeon
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: November 22, 2021 8:28 PM
Cc: Doyeon Kim <doyeon.kim@sickkids.ca>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5623: rotamers table: 'setVisibile'

#5623: rotamers table: 'setVisibile' ----------------------------------------+---------------------------- Reporter: doyeon.kim@… | Owner: Eric Pettersen Type: defect | Status: closed Priority: normal | Milestone: Component: Structure Editing 

#5623: rotamers table: 'setVisibile'
----------------------------------------+----------------------------
          Reporter:  doyeon.kim@…       |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------

Comment (by Eric Pettersen):

 Well, starting with the 1.3 production release (which should be out at the
 end of this month), you will be alerted when a new production release or
 release candidate becomes available.  We don't alert about new daily
 builds since, well, they come out every day. :-)

--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5623*comment:4__;Iw!!D0zGoin7BXfl!vc981Cd5Ge7KZIhBCsoKzSu51FE7dJRMPEcYHbS9uIKSoXWd0Q54gqpJAYXYlKhBgpxe$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!D0zGoin7BXfl!vc981Cd5Ge7KZIhBCsoKzSu51FE7dJRMPEcYHbS9uIKSoXWd0Q54gqpJAYXYlOohR-dl$ >
ChimeraX Issue Tracker


________________________________

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