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Opened 5 years ago
Closed 5 years ago
#4099 closed defect (fixed)
No matching residues in matchmaker sequence alignment
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
When displaying pairwise sequence alignment after using matchmaker, the aligned sequences do not have any matched residue regions and when closing the sequence window an error pops up saying "No statusbar messages will be shown due to inadequate OpenGL".
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui dockable false "Volume Viewer"
> ui dockable true "Volume Viewer"
> toolshed show
> ui tool show Updates
> ui tool show Updates
> interfaces ~solvent
No atoms specified
> graphics quality
Traceback (most recent call last):
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\graphics.py", line 167, in graphics_quality
dmin, dmax = min(div), max(div)
ValueError: min() arg is an empty sequence
ValueError: min() arg is an empty sequence
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\graphics.py", line 167, in graphics_quality
dmin, dmax = min(div), max(div)
See log for complete Python traceback.
> graphics quality 1
> graphics quality
Traceback (most recent call last):
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\graphics.py", line 167, in graphics_quality
dmin, dmax = min(div), max(div)
ValueError: min() arg is an empty sequence
ValueError: min() arg is an empty sequence
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\graphics.py", line 167, in graphics_quality
dmin, dmax = min(div), max(div)
See log for complete Python traceback.
> graphics quality 5
> ui tool show Updates
> open D:/Downloads/peclyases.cxc
> open 1jta
Summary of feedback from opening 1jta fetched from pdb
---
note | Fetching compressed mmCIF 1jta from
http://files.rcsb.org/download/1jta.cif
1jta title:
Crystal Structure of Pectate Lyase A (C2 form) [more info...]
Chain information for 1jta #1
---
Chain | Description
A | pectate lyase A
Non-standard residues in 1jta #1
---
SO4 — sulfate ion
> open 1bn8
Summary of feedback from opening 1bn8 fetched from pdb
---
notes | Fetching compressed mmCIF 1bn8 from
http://files.rcsb.org/download/1bn8.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
1bn8 title:
Bacillus subtilis pectate lyase [more info...]
Chain information for 1bn8 #2
---
Chain | Description
A | protein (pectate lyase)
Non-standard residues in 1bn8 #2
---
CA — calcium ion
> open 2pec
Summary of feedback from opening 2pec fetched from pdb
---
note | Fetching compressed mmCIF 2pec from
http://files.rcsb.org/download/2pec.cif
2pec title:
The refined three-dimensional structure of pectate lyase C from erwinia
chrysanthemi At 2.2 angstroms resolution: implications for an enzymatic
mechanism [more info...]
Chain information for 2pec #3
---
Chain | Description
A | pectate lyase C
> color #1 gold
> color #2 deep sky blue
> color #3 hot pink
> hide
> cartoon style xsection rectangle
> mmaker #2 to #1 show t
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1jta, chain A (#1) with 1bn8, chain A (#2), sequence alignment
score = 813.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 1jta #1/A, 1bn8 #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 273 pruned atom pairs is 0.843 angstroms; (across all 347 pairs:
2.376)
> mmaker #3 to #1 show t
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1jta, chain A (#1) with 2pec, chain A (#3), sequence alignment
score = 341.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 1jta #1/A, 2pec #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 148 pruned atom pairs is 0.961 angstroms; (across all 296 pairs:
8.794)
> set silhouettes true
> set bgColor white
> lighting gentle
executed peclyases.cxc
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 3/A
> sequence header 1 conservation setting initially_shown False
> sequence header 1 conservation setting initially_shown True
> sequence header 1 conservation setting initially_shown False
> sequence header 1 rmsd setting initially_shown True
No statusbar messages will be shown due to inadequate OpenGL
> graphics rate true
> graphics rate false
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
> ui tool show Matchmaker
OpenGL version: 3.3.0 NVIDIA 460.89
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro N (Build 19042)
Memory: 17,113,600,000
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 1700 Eight-Core Processor "
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: 2.1.3
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-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
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: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 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-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: 1.2.3
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
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
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+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
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
pywin32: 228
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: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (4)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → "graphics quality": min() arg is an empty sequence |
comment:2 by , 5 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
| Summary: | "graphics quality": min() arg is an empty sequence → No matching residues in matchmaker sequence alignment |
comment:3 by , 5 years ago
I eliminated the confusing error message "No statusbar messages will be shown due to inadequate OpenGL" which was really caused by a status message after the status line window was closed. Instead such late status messages will go to the log and info messages.
comment:4 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
When adding the code to show the RMSD header in the alignment, managed to punt the matching region. Fixed in the next daily build.
Note:
See TracTickets
for help on using tickets.
I fixed the error resulting from using the "graphics quality" command when no structures are open.
The reporter describes two different problems in the bug report.
1) When displaying pairwise sequence alignment after using matchmaker, the aligned sequences do not have any matched residue regions.
2) when closing the sequence window an error pops up saying "No statusbar messages will be shown due to inadequate OpenGL".
The second message is I believe because the sequence window has a status line and after it is closed some code attempts to output a status message to it. I will try to fix that error message to say something more sensible like "Tried to output status message "XYZ" but the status bar no longer exists"
For the first problem that matchmaker shows a sequence alignment with nothing aligned I am reassigning to Eric.