Opened 5 years ago

Closed 5 years ago

#4453 closed defect (fixed)

Overlapping labels

Reported by: a9471163@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Dear expert： 
   I used "chimeraX 1.1 for windows 10 64-bit" to make animation. As can be seen in the movie provided in the file attachment, the labels of hydrogen bonding distance overlapped when I played the animation. However, when I used "Tools-Structure Analysis-Contacts" to show the labels of "Contacts", these labels did not exhibit the above-mentioned problem when I played the animation. I wonder how to solve the problem of the label overlap regarding hydrogen bonds because I want to make a movie to show all of the hydrogen bonds. 
Many thanks! 

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\0325yansuansihuansu\system3-pipi.pdb format pdb

Summary of feedback from opening D:\0325yansuansihuansu\system3-pipi.pdb  
---  
warning | Ignored bad PDB record found on line 346  
END  
  

> set bgColor #ffffff00

> open D:\0325yansuansihuansu\testamber\final20zhen.trr structureModel #1

Replaced existing frames of system3-pipi.pdb #1 with 20 new frames  

> ui tool show H-Bonds

> hbonds radius 0.105 showDist true interModel false intraMol false intraRes
> false reveal true

40 hydrogen bonds found in 20 coordsets  

> hbonds radius 0.105 showDist true interModel false intraMol false intraRes
> false reveal true

40 hydrogen bonds found in 20 coordsets  

> coordset slider #1 pauseFrames 60

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  

> ui tool show H-Bonds

> hbonds radius 0.105 interModel false intraMol false intraRes false reveal
> true

40 hydrogen bonds found in 20 coordsets  

> hbonds radius 0.105 showDist true interModel false intraMol false intraRes
> false reveal true

40 hydrogen bonds found in 20 coordsets  

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  

> save "D:/0325yansuansihuansu/A session that exhibits the bug.cxs"

> ui tool show H-Bonds

> hbonds radius 0.105 showDist true interModel false intraModel false saltOnly
> true intraMol false intraRes false reveal true

0 hydrogen bonds found in 20 coordsets  

> ui tool show Contacts

> contacts interModel false intraMol false showDist true

44 contacts  

> contacts interModel false intraMol false radius 0.045 showDist true

44 contacts  

> contacts interModel false intraMol false radius 0.025 showDist true

44 contacts  

> contacts interModel false intraMol false radius 0.005 showDist true

44 contacts  

> contacts interModel false intraMol false radius 0.015 showDist true

44 contacts  

> contacts interModel false intraMol false radius 0.025 showDist true

44 contacts  

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  

> ui tool show Contacts

> contacts intraModel false intraMol false radius 0.025 showDist true

No contacts  

> ui tool show H-Bonds

> hbonds radius 0.105 showDist true interModel false intraModel false saltOnly
> true intraMol false intraRes false reveal true

0 hydrogen bonds found in 20 coordsets  

> hbonds radius 0.105 showDist true interModel false intraMol false intraRes
> false reveal true

40 hydrogen bonds found in 20 coordsets  

> hbonds radius 0.105 showDist true interModel false intraMol false intraRes
> false reveal true

40 hydrogen bonds found in 20 coordsets  

> movie record

> movie encode C:\Users\Disiyuan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\Disiyuan/Desktop/movie.mp4  
  




OpenGL version: 3.3.0 NVIDIA 457.20
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HASEE Computer
Model: NH5x_7xRCx,RDx              
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 17,009,004,544
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1
File attachment: movie-hydrogen bonds.mp4

movie-hydrogen bonds.mp4​

Attachments (2)

movie-hydrogen bonds.mp4​ (494.9 KB ) - added by a9471163@… 5 years ago.
Added by email2trac
A session that exhibits the bug.cxs​ (153.1 KB ) - added by a9471163@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

by a9471163@…, 5 years ago

Attachment: movie-hydrogen bonds.mp4​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Cc: Tom Goddard added
Component: Unassigned → Graphics
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Overlapping labels

comment:2 by Eric Pettersen, 5 years ago

Status: accepted → feedback

Hi Jack,

The use of hydrogens bonds In conjunction with coordinate sets hasn't gotten a lot of testing in ChimeraX, so it's possible there's a bug there. Would it be possible for you to send a session file demonstrating the problem?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  4 comment:3 by a9471163@…, 5 years ago 



Dear expert:
    I have followed your suggestion and the session file demonstrating the problem is provided in the attachment.














在 2021-04-06 00:38:43，"ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> 写道：

A session that exhibits the bug.cxs​

by a9471163@…, 5 years ago

Attachment: A session that exhibits the bug.cxs​ added

Added by email2trac

comment:4 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: feedback → closed

Hi Jack,
The fix will be in tomorrow's daily build. If you restore your session you will initially see the overlapping labels because the (bad) session state is restored exactly, but If you then play through your trajectory the overlap will disappear.

--Eric

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