'show' unexpectedly showing whole chains

[samuel.west@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
happened halfway through a session today. select now selects entire chain that residue or user defined selector belongs to. if selector contains multiple chains, than all the chains containing actuall inteded residues are selected. so "sel layer8" "show sel atoms" shows side chains for all residues in 4 chains (layer8 is made of 4 residues- one from each of 4 chains). however, "show layer8 atoms" only shows the sidechains for the correct 4 residues. quite confused.

OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 64 GB

Software:

    System Software Overview:

      System Version: macOS 12.3 (21E230)
      Kernel Version: Darwin 21.4.0
      Time since boot: 71 days 2:10

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
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    ChimeraX-Registration: 1.1
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    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
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    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
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    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
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    line-profiler: 3.4.0
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    matplotlib: 3.5.1
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    networkx: 2.6.3
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    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
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    Pillow: 9.0.1
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[Eric Pettersen]

Reported by Sam West

[Tom Goddard]

I'm confused too. That is very strange. The only thing I can think of is that somehow the up-arrow key is being pressed which extends the selection -- it takes a few presses to get from residue to helix to chain to all chains. Maybe that key is stuck on your keyboard? Another thought is that maybe you have installed some ChimeraX plugin that changes the selection mode. Have you installed any plugins?

If you try "select :55" or replace 55 with a residue number in your structure does it select (show the green outline) for just that residue, or for the whole chain? What does the ChimeraX Log panel say? It should show how many atoms and residues were selected.

It might help if you do some of these wrong selections and then use menu Help / Report a Bug... so I see the whole Log output, maybe that contains a clue what is going on.

[Tom Goddard]

Also does it happen with every atomic model? If you open a PDB structure, e.g. command "open 1gcn" can you select its individual residues?

[samuel.west@…]

Maybe that key is stuck on your keyboard? - nope! Also it only happens with one model to date (Also does it happen with every atomic model?- no)

Have you installed any plugins? No

If you try "select :55" or replace 55 with a residue number in your
structure does it select (show the green outline) for just that residue,
or for the whole chain? - 4 residues (this is as it should be. /c:55 is only 1 residue)

Just so I don’t have to do it again:

"sel layer8” output = 267 residues (it should be 4) "show sel atoms" shows side chains for all
residues in 4 chains (layer8 is made of 4 residues- one from each of 4
chains).

however and this is the interesting part, "show layer8 atoms" only shows the sidechains for the
correct 4 residues. (No output dialogue indicating number of residues, but only the 4 were modified)

One last thing: only happens with selections I make as I go or that I saved as user defined selectors yesterday. Older user defined selectors are fine!!!!

Select add, replace etc still work.

Thanks for the help!

Sam

On Oct 26, 2022, at 12:54, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

I'm confused too. That is very strange. The only thing I can think of is
that somehow the up-arrow key is being pressed which extends the selection
-- it takes a few presses to get from residue to helix to chain to all
chains. Maybe that key is stuck on your keyboard? Another thought is
that maybe you have installed some ChimeraX plugin that changes the
selection mode. Have you installed any plugins?

If you try "select :55" or replace 55 with a residue number in your
structure does it select (show the green outline) for just that residue,
or for the whole chain? What does the ChimeraX Log panel say? It should
show how many atoms and residues were selected.

It might help if you do some of these wrong selections and then use menu
Help / Report a Bug... so I see the whole Log output, maybe that contains
a clue what is going on.

[Tom Goddard]

Ok. So the bad behavior is only with named selections like "select layer8" and not with explicit selections like "select :55"?

We'll need a case we can reproduce. For example when I do these commands they work fine (tested in daily build).

open 1gcn
name frozen somefour :11-14
show somefour

If it only fails to work correctly for one particular structure can you make a simple test, just open the structure, define a selector, try the show command to see it doesn't work right, save a session file, then quit, reload the session and see if it still does not work, then send us the session. But bug reports are publicly visible so don't send if it is private data.

[samuel.west@…]

Ok. So the bad behavior is only with named selections like "select
layer8" and not with explicit selections like "select :55” -yes, only named. The moment I save a selection as a named selection and then try “select namedSelection” it selects the whole chain.

We'll need a case we can reproduce. For example when I do these commands
they work fine (tested in daily build).

open 1gcn
name frozen somefour :11-14
show somefour

If it only fails to work correctly for one particular structure can you
make a simple test, just open the structure, define a selector, try the
show command to see it doesn't work right, save a session file, then quit,
reload the session and see if it still does not work, then send us the
session. But bug reports are publicly visible so don't send if it is
private data. — some private data, hopefully this suffices. Also, saving and quitting doesn’t help.

On 1gcn: its fine…
[cid:002B2A1E-891B-4E6F-AFC1-F197D6A25E4D]


On my model, its not… (2 residues is correct)
[cid:991D0906-9AD4-4615-9A6A-88A7968E513A]

Thank you for the help. Im going a little crazy over here.
sam

On Oct 26, 2022, at 19:48, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

Ok. So the bad behavior is only with named selections like "select
layer8" and not with explicit selections like "select :55"?

We'll need a case we can reproduce. For example when I do these commands
they work fine (tested in daily build).

open 1gcn
name frozen somefour :11-14
show somefour

If it only fails to work correctly for one particular structure can you
make a simple test, just open the structure, define a selector, try the
show command to see it doesn't work right, save a session file, then quit,
reload the session and see if it still does not work, then send us the
session. But bug reports are publicly visible so don't send if it is
private data.

[samuel.west@…]

Added by email2trac

[samuel.west@…]

Added by email2trac

[Tom Goddard]

Excellent.  Can you give me a ChimeraX session file (save myses.cxs) for your case that does not work right.  Something is clearly broken.

[Tom Goddard]

No reply from reporter.