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#4617 closed defect (fixed)

Specifier for picked atom may need to use serial number in some situations

Reported by:	Tristan Croll	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Command Line	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(If I recall correctly this was fixed before, but appears to have been reverted)

If there are two atoms in a model* with the same name, residue number, and chain ID, then ctrl-clicking one selects both. Of course the situation of *having* two residues with the same identifier is itself pathological, but this behaviour makes it difficult to fix anything by (e.g.) deleting one.


* Mistake on my part in this case, while test-running addition of amino acids to a chain after Eric's fix to pseudobonds.

Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open test_session.cxs

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 1,1,1, pixel 0.723, shown at
level 0.298, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 1,1,1, pixel 0.723, shown at
level -0.0595,0.0595, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 1,1,1, pixel 0.723,
shown at level 0.598, step 1, values float32  
Log from Mon May 10 11:38:24 2021

> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0_cut.pdb

Chain information for 3io0_cut.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open 3io0.mtz structureModel #1

Summary of feedback from opening 3io0.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  
note | (CLIPPER) NOTE: No symmetry information found in model. Using symmetry
from MTZ file.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.298, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0595,0.0595, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.598, step 1, values float32  
Chain information for 3io0_cut.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Opened crystallographic dataset from 3io0.mtz  
Found experimental reflection data:  
(dataset) FOBS, SIGFOBS  
Rwork: 0.2093; Rfree: 0.2146  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_sharp_29  
Any unwanted maps may be safely closed via the Model panel.  

> save test_session.cxs

——— End of log from Mon May 10 11:38:24 2021 ———

opened ChimeraX session  

> select /A:83@CA

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel

> select /A:84@C

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:84@CA

1 atom, 1 residue, 1 model selected  

> select add /A:85@N

2 atoms, 2 residues, 1 model selected  

> select up

38 atoms, 37 bonds, 2 residues, 1 model selected  

> delete sel

> select /A:83@C

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:83@CA

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 1 residue, 1 model selected  

> delete sel

> select /A:82@C

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /A:82@C

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:83

19 atoms, 18 bonds, 1 residue, 1 model selected  

> delete sel

> select /A:82@C

1 atom, 1 residue, 1 model selected  

> isolde add aa GLY sel approxConformation helix

> select /A:83@C

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:84@CA

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:85@N

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:86@CA

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:87

19 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

> select /A:87@CA

1 atom, 1 residue, 1 model selected  

> isolde add aa LEU sel approxConformation helix

Selection is not a terminal residue!  

> select /A:88@CA

2 atoms, 2 residues, 1 model selected  

> isolde add aa LEU sel approxConformation helix

Please select a single residue!  

> select /A:88@CB

2 atoms, 2 residues, 1 model selected  

> isolde add aa LEU sel approxConformation helix

Please select a single residue!  

> select /A:88@O

2 atoms, 2 residues, 1 model selected  

> isolde add aa LEU sel approxConformation helix

Please select a single residue!  

> select clear

> select /A:88@CG

2 atoms, 2 residues, 1 model selected  

> select /A:87@CA

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

102 atoms, 101 bonds, 6 residues, 1 model selected  

> select /A:88@C

2 atoms, 2 residues, 1 model selected  

> select clear

Drag select of 12 atoms, 3 residues, 14 bonds  

> select clear

Drag select of 7 atoms, 1 residues, 6 bonds  

> select clear

> select /A:88@C

2 atoms, 2 residues, 1 model selected  

> select clear

> select /A:88@C

2 atoms, 2 residues, 1 model selected  

> select clear




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        5.5G         41G        270M         15G         56G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
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: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-DevelExtras: 0.4.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.dev38
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.2
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (8)

comment:1 by Eric Pettersen, 5 years ago

Cc:	Eric Pettersen added
Component:	Unassigned → Command Line
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Specifier for picked atom may need to use serial number in some situations

comment:2 by Tom Goddard, 5 years ago

Cc:	Tom Goddard added; Eric Pettersen removed
Owner:	changed from Tom Goddard to Eric Pettersen

I thought Eric fixed this. Here is the commit that I think was supposed to fix it.

https://github.com/RBVI/ChimeraX/commit/c2ba7277361d8b7e1d3e347ec14e9a3d84cac126

I could not find the ticket about this problem, but maybe you can -- it would probably help. Also attaching an example file with the problem would speed testing and fixing.

comment:3 by Eric Pettersen, 5 years ago

No that commit is for atoms with the same name within the same residue. So, for a small molecule coming, for example, from a mol2 file where all the carbons are named 'C', all the hydrogens 'H', etc. It's not for checking for atom spec collisions globally within a possibly large structure.

It's a little unclear where this check should occur, but my best guess is in PickedAtom.specifier(). I'll see what I can do.

comment:4 by Eric Pettersen, 5 years ago

Status:	assigned → feedback

I have pushed out a putative fix for this problem. Tristan, you'll have to let us know if it works.

comment:5 by Tristan Croll, 5 years ago

That doesn't work, I'm afraid. Looks like the problem is that all atoms added using the addaa command have serial numbers of -1.

comment:6 by Eric Pettersen, 5 years ago

You need to assign unique serial numbers to atoms you add. If you were using chimerax.atomic.struct_edit.add_atom that would be done automatically for you.

in reply to: 7 ; follow-up: 7 comment:7 by Tristan Croll, 5 years ago

Hmm... I thought I'd switched to using struct_edit everywhere, but it seems I only did so for adding *bonds*, not atoms. Will correct.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 13 May 2021 18:45
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4617: Specifier for picked atom may need to use serial number in some situations

#4617: Specifier for picked atom may need to use serial number in some situations
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  feedback
          Priority:  normal         |  Milestone:
         Component:  Command Line   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------

Comment (by Eric Pettersen):

 You need to assign unique serial numbers to atoms you add.  If you were
 using chimerax.atomic.struct_edit.add_atom that would be done
 automatically for you.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4617#comment:6>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:8 by Eric Pettersen, 5 years ago

Resolution:	→ fixed
Status:	feedback → closed

I'm going to close this on the presumption that once serial numbers are assigned, it will work.

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