Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#10001 closed defect (fixed)

Clip plane motion problem

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
To supplement previous bug report. Another solution is to do all clip using command, eg' clip near +1 far -1', for all views, then changing views using 'view p3 60' will have clipping planes gradually changing.

Ruizhi

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

> open "C:\\\Users\\\kfzr5\\\OneDrive - Florida State
> University\\\Drp1\\\volumes\\\PAorig\\\PA_raw.mrc"

Opened PA_raw.mrc as #1, grid size 224,224,224, pixel 4.04, shown at level
689, step 1, values float32  

> set bgColor white

> ui tool show "Side View"

> view name p1

> volume #1 level 383.5

> view name p2

> view name p3

> view p1

> view p2 60

> view p3 60

> view p2

> turn x 90

> clip near +20

[Repeated 18 time(s)]

> clip far -20

[Repeated 16 time(s)]

> view name p3

> view p2

> view p3 60

> view p2

> turn x 90

> view name p3

> view p2

> view p3 60

> view p2

> turn x 90

> view p2

> clip near +20

[Repeated 13 time(s)]

> clip far -20

[Repeated 12 time(s)]

> view p3

> view p2

> clip near +20

[Repeated 17 time(s)]

> clip far -20

[Repeated 14 time(s)]

> view name p3

> view p2

> view p3 60

> view p2

> camera ortho

> view p2

> view p3 60

> view p2

> view p3

> view name p3

> view p2

> view p3 60

> view p2

> turn x 90

> view name p3

> view p2

> view p3 60

> view p2

> turn x 90

> clip near 50

[Repeated 5 time(s)]

> clip far -50

[Repeated 6 time(s)]

> view name p3

> view p2

> view p3 60

> view name p3

> view p2

> wait 10

> view p3 60

> view p2

> clip off

> clip on

Expected a keyword  

> clip near 1

> clip near -1

> clip off

> clip near +1

> clip -50

Expected a keyword  

> clip -50

Expected a keyword  

> clip -50

Expected a keyword  

> clip -50

Expected a keyword  

> clip -50

Expected a keyword  

> clip near -50

[Repeated 5 time(s)]

> clip far -1

> clip far +50

[Repeated 4 time(s)]

> view name p2

> turn x 90

> clip near +20

[Repeated 12 time(s)]

> clip far -20

[Repeated 7 time(s)]

> view name p3

> view p2

> view p3 60

> view name p3

> view p2

> view p3 60

> view p2

> view name p2

> turn x 90

> clip near +50

[Repeated 4 time(s)]

> clip far -50

[Repeated 4 time(s)]

> view name p3

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> clip off

> clip near 1

> clip near -50

[Repeated 6 time(s)]

> view far -1

Expected an objects specifier or a view name or a keyword  

> clip far -1

> clip far +50

[Repeated 6 time(s)]

> view name p2

> turn x 90

> clip near +20

[Repeated 14 time(s)]

> clip far -20

[Repeated 14 time(s)]

> view name p3

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> view p3 60

> viwe p2

Unknown command: viwe p2  

> view p2

> turn x 90

> view name p3

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> view p3 60

> view p2

> clip off

> view name p2

> turn x 90

> clip near +20

[Repeated 17 time(s)]

> clip far -20

[Repeated 21 time(s)]

> view name p3

> view p2

> view p3 60

> view p2

> turn x 90

> view name p3

> view p2

> view p3 60




OpenGL version: 3.3.0 NVIDIA 526.98
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 68,642,189,312
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800X 8-Core Processor             
OSLanguage: en-US

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: 2023.5.7
    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-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-ISOLDE: 1.6.0
    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-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: 1.1
    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
    comtypes: 1.1.14
    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: 2022.9.26
    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: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    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: 2.4.1
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    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
    WMI: 1.5.1
    zipp: 3.15.0

Change History (8)

comment:1 by Tom Goddard, 2 years ago

Component: Unassigned → Depiction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clip plane motion problem

Follow-up to ticket #10000.

Just reply to the previous bug report email in order to make a comment on a submitted report instead of making a new report.

comment:2 by Tom Goddard, 2 years ago

Resolution: → worksforme
Status: assigned → closed

I set the near plane with the side view, then "view name p1", then rotated, and set the clip plane with "clip near -10" and used "view name p2". Then interpolating between these views "view p1 100" or "view p2 100" smoothly moves the clip planes as expected.

comment:3 by rpeng@…, 2 years ago 

Yeah, I noticed that we need to have clip plane on for both views to make it move smoothly too. But that's not the error I met. I repeated these same processes in this email in a newly opened chimerax window, but the clip planes are still not moving smoothly. Below is the log content. My manual operation is rotate the map using mouse between 'view name p1' and 'clip near 10'. Maybe it's only triggered under some cases.



UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open "XXXXXXXXXXPA_raw.mrc"Opened PA_raw.mrc as #1, grid size 224,224,224, pixel 4.04, shown at level 689, step 1, values float32
camera ortho
set bgColor white
ui tool show "Side View"
view name p1
clip near 10[Repeated 27 time(s)]
view name p2
view p1
view p2 60
view p1
view p2 60


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, October 17, 2023 3:09 PM
To: Ruizhi Peng <rpeng@fsu.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #10001: Clip plane motion problem

#10001: Clip plane motion problem
---------------------------------+-------------------------
          Reporter:  rpeng@\u2026     |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Depiction   |    Version:
        Resolution:  worksforme  |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => worksforme
 * status:  assigned => closed

Comment:

 I set the near plane with the side view, then "view name p1", then  rotated, and set the clip plane with "clip near -10" and used "view name  p2".  Then interpolating between these views "view p1 100" or "view p2  100" smoothly moves the clip planes as expected.
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10001*comment:2__;Iw!!PhOWcWs!0lsYTXDQz0vKH_VAJAH4wAzmDlXeL1c2UCOJfu36CFrVALtWcs7cvXB3Ndq5MI2NQGKK8Gke237E-9dlhxVSJy9KUU556Q$ > ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!PhOWcWs!0lsYTXDQz0vKH_VAJAH4wAzmDlXeL1c2UCOJfu36CFrVALtWcs7cvXB3Ndq5MI2NQGKK8Gke237E-9dlhxVSJy-LquFyKA$ > ChimeraX Issue Tracker

comment:4 by rpeng@…, 2 years ago 

Correction, my manual operation also include setting a clip plane using side view window before 'view name p1'

Thanks for the help!
Best,
Ruizhi

-----Original Message-----
From: Ruizhi Peng 
Sent: Tuesday, October 17, 2023 4:01 PM
To: ChimeraX-bugs@cgl.ucsf.edu
Subject: RE: [ChimeraX] #10001: Clip plane motion problem

Yeah, I noticed that we need to have clip plane on for both views to make it move smoothly too. But that's not the error I met. I repeated these same processes in this email in a newly opened chimerax window, but the clip planes are still not moving smoothly. Below is the log content. My manual operation is rotate the map using mouse between 'view name p1' and 'clip near 10'. Maybe it's only triggered under some cases.



UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open "XXXXXXXXXXPA_raw.mrc"Opened PA_raw.mrc as #1, grid size 224,224,224, pixel 4.04, shown at level 689, step 1, values float32 camera ortho set bgColor white ui tool show "Side View"
view name p1
clip near 10[Repeated 27 time(s)]
view name p2
view p1
view p2 60
view p1
view p2 60


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 17, 2023 3:09 PM
To: Ruizhi Peng <rpeng@fsu.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #10001: Clip plane motion problem

#10001: Clip plane motion problem
---------------------------------+-------------------------
          Reporter:  rpeng@\u2026     |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Depiction   |    Version:
        Resolution:  worksforme  |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => worksforme
 * status:  assigned => closed

Comment:

 I set the near plane with the side view, then "view name p1", then  rotated, and set the clip plane with "clip near -10" and used "view name  p2".  Then interpolating between these views "view p1 100" or "view p2  100" smoothly moves the clip planes as expected.
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10001*comment:2__;Iw!!PhOWcWs!0lsYTXDQz0vKH_VAJAH4wAzmDlXeL1c2UCOJfu36CFrVALtWcs7cvXB3Ndq5MI2NQGKK8Gke237E-9dlhxVSJy9KUU556Q$ > ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!PhOWcWs!0lsYTXDQz0vKH_VAJAH4wAzmDlXeL1c2UCOJfu36CFrVALtWcs7cvXB3Ndq5MI2NQGKK8Gke237E-9dlhxVSJy-LquFyKA$ > ChimeraX Issue Tracker

comment:5 by Tom Goddard, 2 years ago

Resolution: worksforme
Status: closed → reopened

Fixed.

Thanks for the detailed steps. The rotation between the two views is a key step. The clip planes are not interpolated if the normal vectors are not the same. The near plane normal should always be parallel camera view direction so they should be the same (in camera coordinates), but due to rounding errors converting between scene and camera coordinates they were slightly different if a rotation is done between the two views. I've changed the code so it will still interpolate if the normals are within 0.01 degree of each other, so now your case works. Fix is in the daily build.

comment:6 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: reopened → closed

comment:7 by rpeng@…, 2 years ago 

Oh I see, so it's the mouse control producing some abnormal numbers of angles that cannot be processed for interpolation. That totally makes sense now. Thanks very much! Glad we solved this!

Ruizhi

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, October 17, 2023 4:39 PM
To: Ruizhi Peng <rpeng@fsu.edu>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #10001: Clip plane motion problem

#10001: Clip plane motion problem
--------------------------------+-------------------------
          Reporter:  rpeng@\u2026    |      Owner:  Tom Goddard
              Type:  defect     |     Status:  reopened
          Priority:  normal     |  Milestone:
         Component:  Depiction  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
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Changes (by Tom Goddard):

 * resolution:  worksforme =>
 * status:  closed => reopened

Comment:

 Fixed.

 Thanks for the detailed steps. The rotation between the two views is a key  step.  The clip planes are not interpolated if the normal vectors are not  the same.  The near plane normal should always be parallel camera view  direction so they should be the same (in camera coordinates), but due to  rounding errors converting between scene and camera coordinates they were  slightly different if a rotation is done between the two views.  I've  changed the code so it will still interpolate if the normals are within
 0.01 degree of each other, so now your case works.  Fix is in the daily  build.
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Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10001*comment:5__;Iw!!PhOWcWs!0BsGGPjPsj6acQYPHsIrQerkoMw6bOcpR_9OSOuouNK6G9NM1jiajRdSPfZzXQhseMEhIhoqxJglYIXvZJ0tQTuAaOIfcA$ > ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!PhOWcWs!0BsGGPjPsj6acQYPHsIrQerkoMw6bOcpR_9OSOuouNK6G9NM1jiajRdSPfZzXQhseMEhIhoqxJglYIXvZJ0tQTsg6dFk4Q$ > ChimeraX Issue Tracker

comment:8 by Tom Goddard, 2 years ago

The bug is related to the rotation between the two views and round-off error in transformations between scene and camera coordinates. It does not matter if the rotation is done by mouse or command, and I don't think it matters if the clipping is done by command or mouse.

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