Opened 5 years ago

Closed 5 years ago

#3672 closed defect (fixed)

Deleting residue involved in sequence alignment: list indices must be integers or slices, not str

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
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-centos-7.8.2003-Core
ChimeraX Version: 1.1rc202008252015 (2020-08-25 20:15:37 UTC)
Description
First traceback in the log is mine (fixed). Second happens when deleting residues with an alignment open in the sequence viewer.

Log:
UCSF ChimeraX version: 1.1rc202008252015 (2020-08-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open hLHCGR_Gs_Nb35_initial10.pdb

Chain information for hLHCGR_Gs_Nb35_initial10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
R | No description available  
X | No description available  
Y | No description available  
  

> open hLHCGR_Gs_Nb35_j72_post_31.mrc

Opened hLHCGR_Gs_Nb35_j72_post_31.mrc, grid size 220,220,220, pixel 1, shown
at level 0.0166, step 1, values float32  

> clipper associate #2 toModel #1

Chain information for hLHCGR_Gs_Nb35_initial10.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/G | No description available  
1.2/N | No description available  
1.2/R | No description available  
1.2/X | No description available  
1.2/Y | No description available  
  

> set bgColor white

> isolde start

> set selectionWidth 4

Done loading forcefield  

> clipper set contourSensitivity 0.25

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> isolde stepto

> volume gaussian #1 bfactor 50

> clipper associate #2 toModel #1

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/cmd.py", line 118, in associate_volumes  
session.models.add([mgr.crystal_mgr])  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py",
line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model Data manager (hLHCGR_Gs_Nb35_initial10.pdb)
#1 to scene twice  
  
ValueError: Attempted to add model Data manager (hLHCGR_Gs_Nb35_initial10.pdb)
#1 to scene twice  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py",
line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  

> open
> /run/media/tic20/storage/structure_dump/collaboration/eric_xu/hLHGCR/sequences.fasta

Sequence 'Chain_G_Ggamma' differs in length from preceding sequences, and it
is therefore impossible to open these sequences as an alignment. If you want
to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.  

> open sequences.fasta alignment false

Summary of feedback from opening sequences.fasta  
---  
notes | Alignment identifier is sequences.fasta-1  
Alignment identifier is sequences.fasta-2  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain G to Chain_G_Ggamma with 0
mismatches  
Alignment identifier is sequences.fasta-3  
Alignment identifier is sequences.fasta-4  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain B to Chain_B_Gbeta with 0
mismatches  
Alignment identifier is sequences.fasta-5  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain N to Chain_N_Nb35 with 0
mismatches  
Alignment identifier is sequences.fasta-6  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain X to Chain_X_CGalpha with
0 mismatches  
Alignment identifier is sequences.fasta-7  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain Y to Chain_Y_CGbeta with 0
mismatches  
  
Opened 7 sequences from sequences.fasta  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

487 atoms, 487 bonds, 28 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1.2/A  

> select clear

> open
> /run/media/tic20/storage/structure_dump/collaboration/eric_xu/hLHGCR/chain_a.aln

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/eric_xu/hLHGCR/chain_a.aln  
---  
notes | Alignment identifier is chain_a.aln  
Associated hLHCGR_Gs_Nb35_initial10.pdb (1.2) chain A to
hLHCGR_Gs_Nb35_initial10.pdb|Chain=A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment chain_a.aln  
  
Opened 2 sequences from chain_a.aln  

> swapaa mousm sel GLY

Missing or invalid "residues" argument: invalid residues specifier  

> swapaa mousmode sel GLY

Missing or invalid "residues" argument: invalid residues specifier  

> usage swapaa

swapaa residues resType [angleSlop a number] [bfactor a number] [criteria
criteria] [density a density map specifier] [distSlop a number]
[hbondAllowance a number] [ignoreOtherModels true or false] [rotLib rotLib]
[log true or false] [preserve preserve] [relax true or false] [retain true or
false] [scoreMethod scoreMethod] [overlapCutoff a number]  
— Swap amino acid side chain(s)  
resType: a text string  
criteria: some an integer ≥ 0 or a text string  
rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode  
preserve: a number ≥ 0  
scoreMethod: one of num or sum

swapaa interactive residues resType [rotLib rotLib] [log true or false]  
— Show possible side-chain rotamers  
resType: a text string  
rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode

swapaa mousemode residues restype  
— Replace residue with specified amino acid  
restype: one of ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS,
MET, PHE, PRO, SER, THR, TRP, TYR, or VAL  

> swapaa mousemode sel GLY

> swapaa mousemode sel CYS

> swapaa mousemode sel THR

> swapaa mousemode sel LEU

> swapaa mousemode sel SER

> swapaa mousemode sel ALA

> swapaa mousemode sel ASP

> select clear

> swapaa mousemode sel ALA

> swapaa mousemode sel VAL

> swapaa mousemode sel ARG

> swapaa mousemode sel SER

> swapaa mousemode sel MET

> view sel

> swapaa mousemode sel ASP

> swapaa mousemode sel ASN

> swapaa mousemode sel SER

> view sel

> swapaa mousemode sel ASP

> view sel

> swapaa mousemode sel ASP

> delete sel

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 580, in _atomic_changes_done  
self._notify_observers(self.NOTE_MOD_ASSOC, (self.NOTE_MOD_ASSOC,
self._modified_mmaps))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
TypeError: list indices must be integers or slices, not str  
  
Error processing trigger "changes done":  
TypeError: list indices must be integers or slices, not str  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 580, in _atomic_changes_done  
self._notify_observers(self.NOTE_MOD_ASSOC, (self.NOTE_MOD_ASSOC,
self._modified_mmaps))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
TypeError: list indices must be integers or slices, not str  
  
Error processing trigger "changes done":  
TypeError: list indices must be integers or slices, not str  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 580, in _atomic_changes_done  
self._notify_observers(self.NOTE_MOD_ASSOC, (self.NOTE_MOD_ASSOC,
self._modified_mmaps))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
TypeError: list indices must be integers or slices, not str  
  
Error processing trigger "changes done":  
TypeError: list indices must be integers or slices, not str  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 450, in alignment_notification  
match_maps = [note_data[1]['match map']]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.51.06
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
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        4.9G         47G        177M        9.9G         57G
	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
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-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1rc202008252015
    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-ISOLDE: 1.0.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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-Phenix: 0.1
    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: 1.2.2
    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
    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: 0.16
    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
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.6
    psutil: 5.7.0
    ptyprocess: 0.6.0
    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
    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: 4.3.3
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Deleting residue involved in sequence alignment: list indices must be integers or slices, not str

Have to delete individual residues to reproduce. Deleting a whole chain works.

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Thanks for the report. Fixed in both develop and release branches.

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