selected_atoms not current

[Tristan Croll]

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.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
Some change since ChimeraX 1.1 has broken a few methods in ISOLDE (including some *very* old code) in a strange way. For example, when I try to start a simulation with atoms from more than one model selected (worked in ChimeraX 1.1, fails now with unchanged code). The culprit appears to be the `Isolde._get_main_sim_selection()` method at https://github.com/tristanic/isolde/blob/3bafd1bc006f9a7054938c270fba6387a918ae6d/isolde/src/isolde.py#L2918, which aggregates the atoms to keep/exclude by changing their `selected` property (I realise this could probably be done more neatly - but as I said, this is very old code from the early days of ISOLDE). At the start of the method it sets `selected=False` for all currently-selected atoms and re-sets it to True only for those atoms that are part of ISOLDE's currently-selected model. It then does some logic to expand the selection back and forth along each chain, and finally returns `selected_atoms(session)`. The problem that's new since ChimeraX 1.1 is that `selected_atoms(session)` still includes *all* atoms that were selected at the time `_get_main_sim_selection()` was called, including those for which `selected` has since been set to False. I can get around it easily enough, but the behaviour seems non-ideal. 

Log:
> 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.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> open 3io0 structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Resolution: 3.003  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,28,26, pixel 0.963, shown at
level 0.283, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,28,26, pixel 0.963, shown at
level -0.057,0.057, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 28,28,26, pixel 0.963,
shown at level 0.565, step 1, values float32  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.2/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 28,28,26, pixel 0.963,
shown at level 0.339, step 1, values float32  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #2  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for 3io0 (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 3io0 #1.2/A PRO 76  
Chain-final residues that are actual C termini: 3io0 #1.2/A PHE 304  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3io0 #1.2/A PHE 304  
198 hydrogen bonds  
Termini for 3io0 (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 3io0 #2/A PRO 76  
Chain-final residues that are actual C termini: 3io0 #2/A PHE 304  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3io0 #2/A PHE 304  
198 hydrogen bonds  
3384 hydrogens added  
  

> select #1,2

6702 atoms, 6746 bonds, 460 residues, 25 models selected  
Updating bulk solvent parameters...  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2719, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2753, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 968, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> ui tool show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select #1,2

6702 atoms, 6746 bonds, 460 residues, 25 models selected  




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        7.4G         42G        240M         13G         54G
	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: 2.9.0
    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: 2.1.4
    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: 1.12
    ChimeraX-AtomicLibrary: 3.0
    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: 2.5.1
    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: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103310726
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 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
    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.dev37
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 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: 1.1
    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
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    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
    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: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.1
    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: 4.4.2
    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

[pett]

Hi Tristan,

This is undoubtedly due to some newish code that tracks the order in which atoms are selected and returns them in that order. I *think* I know what the problem is. Will try to get to it today.

--Eric

[pett]

Hi Tristan,

Could you check that this change fixes your problem (and doesn't blow anything else up)? Thanks!

--Eric

diff --git a/src/bundles/atomic/src/changes.py b/src/bundles/atomic/src/changes.py
index 92b618f33..418f7ca4a 100644
--- a/src/bundles/atomic/src/changes.py
+++ b/src/bundles/atomic/src/changes.py
@@ -177,6 +177,7 @@ class Changes:

def selected_atoms(session=None):

global _full_sel, _ordered_sel

+ check_for_changes(session)

from .molarray import Atoms
return _ordered_sel if _ordered_sel is not None else (_full_sel if _full_sel is not None else Atoms())

[Tristan Croll]

Very tied up with some urgent work right now, but will do as soon as possible. Although, my bigger problem with that particular code was that using selected_atoms(session)​ was a silly way of doing things, when I could just do m.atoms[m.atoms.selecteds]​ and avoid any ambiguity while also being slightly more efficient...
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 26 April 2021 20:06
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4560: selected_atoms not current

#4560: selected_atoms not current
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  feedback
          Priority:  normal         |  Milestone:
         Component:  Core           |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Tristan,
         Could you check that this change fixes your problem (and doesn't
 blow anything else up)?  Thanks!

 --Eric

 diff --git a/src/bundles/atomic/src/changes.py
 b/src/bundles/atomic/src/changes.py
 index 92b618f33..418f7ca4a 100644
 --- a/src/bundles/atomic/src/changes.py
 +++ b/src/bundles/atomic/src/changes.py
 @@ -177,6 +177,7 @@ class Changes:

  def selected_atoms(session=None):
      global _full_sel, _ordered_sel
 +    check_for_changes(session)
      from .molarray import Atoms
      return _ordered_sel if _ordered_sel is not None else (_full_sel if
 _full_sel is not None else Atoms())

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4560#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Sure. I guess I'll commit the change for now so it gets into the 1.2 release candidate, but will back it out if your testing uncovers deleterious effects.

--Eric

[pett]

I guess I'll assume it worked. Feel free to reopen if it's still a problem.

[Tristan Croll]

Sorry for not following up. All seems to behave correctly now.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 09 June 2021 02:03
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4560: selected_atoms not current

#4560: selected_atoms not current
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Core           |    Version:
        Resolution:  fixed          |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

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


Comment:

 I guess I'll assume it worked.  Feel free to reopen if it's still a
 problem.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4560#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Good to hear!

--Eric