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#16698 closed defect (fixed)
Similar Structures: self.results is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Excellence/Downloads/query (2).pdb"
Summary of feedback from opening C:/Users/Excellence/Downloads/query (2).pdb
---
warning | Ignored bad PDB record found on line 1
PARENT N/A
Chain information for query (2).pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> select aromatic-ring
108 atoms, 114 bonds, 16 residues, 1 model selected
> undo
> select C
967 atoms, 742 bonds, 215 residues, 1 model selected
> undo
> color bfactor
1548 atoms, 215 residues, atom bfactor range 39.5 to 98.7
Alignment identifier is 1/A
> ui tool show H-Bonds
> hbonds reveal true
125 hydrogen bonds found
> color bfactor
1548 atoms, 215 residues, atom bfactor range 39.5 to 98.7
> interfaces ~solvent
0 buried areas:
> select ::name="ALA"
180 atoms, 151 bonds, 7 pseudobonds, 36 residues, 2 models selected
> select ::name="PRO"
105 atoms, 105 bonds, 15 residues, 1 model selected
> undo
[Repeated 1 time(s)]
> select backbone
860 atoms, 859 bonds, 84 pseudobonds, 215 residues, 2 models selected
> undo
> select ~sel & ##selected
Nothing selected
> ui tool show "Map Statistics"
> measure mapstats
> ui tool show "Altloc Explorer"
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> ui tool show "Model Panel"
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> open "C:/Users/Excellence/Downloads/query (1).pdb"
Summary of feedback from opening C:/Users/Excellence/Downloads/query (1).pdb
---
warning | Ignored bad PDB record found on line 1
PARENT N/A
Chain information for query (1).pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> hide #!1 models
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 2/A
> hbonds #2 reveal true
204 hydrogen bonds found
> color bfactor #2
1899 atoms, 249 residues, atom bfactor range 39.4 to 98.4
> ui tool show "Crystal Contacts"
QWindowsWindow::setGeometry: Unable to set geometry 1920x1005+0+35 (frame:
1942x1061-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 426x670 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=661,
y=1061)))
> color #2 bychain
> color bfactor #2
1899 atoms, 249 residues, atom bfactor range 39.4 to 98.4
> ui tool show H-Bonds
> hbonds reveal true
329 hydrogen bonds found
> open C:/Users/Excellence/Downloads/query3.pdb
Summary of feedback from opening C:/Users/Excellence/Downloads/query3.pdb
---
warning | Ignored bad PDB record found on line 1
PARENT N/A
Chain information for query3.pdb #4
---
Chain | Description
A | No description available
Computing secondary structure
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Alignment identifier is 4/A
QWindowsWindow::setGeometry: Unable to set geometry 1920x1109+0+35 (frame:
1942x1165-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x974+0+34 (frame: 1942x1030-11-11) margins: 11, 45,
11, 11 minimum size: 426x739 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=661,
y=1165)))
> show #1 models
> hide #1 models
> hide #2 models
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
> hbonds #4 reveal true
133 hydrogen bonds found
> color bfactor #4
1375 atoms, 193 residues, atom bfactor range 27.4 to 98
> select O
926 atoms, 14 pseudobonds, 657 residues, 4 models selected
> undo
> select ligand
Nothing selected
> select helix
1508 atoms, 1507 bonds, 51 pseudobonds, 204 residues, 4 models selected
> select coil
2558 atoms, 2598 bonds, 23 pseudobonds, 350 residues, 4 models selected
> select coil
2558 atoms, 2598 bonds, 23 pseudobonds, 350 residues, 4 models selected
> select strand
756 atoms, 756 bonds, 19 pseudobonds, 103 residues, 4 models selected
> undo
[Repeated 3 time(s)]
> show #2 models
> hide #2 models
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> hide #4 models
> show #1 models
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
> hide #1 models
> show #1 models
> select down
Nothing selected
> select down
Nothing selected
> show #4 models
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
> select #1/A:33-39,45-51,83-89,129-135,157-161
246 atoms, 247 bonds, 33 residues, 1 model selected
> select add #1
1548 atoms, 1584 bonds, 215 residues, 1 model selected
> color #1 #aa00ffff
> color #2 #aa0000ff
> undo
[Repeated 3 time(s)]
> hide #3 models
> hide #1 models
> color bfactor #4
1375 atoms, 193 residues, atom bfactor range 27.4 to 98
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 4/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
> select add #1
1548 atoms, 1584 bonds, 215 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #4
1375 atoms, 1398 bonds, 107 pseudobonds, 193 residues, 2 models selected
> select subtract #4
Nothing selected
> select ligand
Nothing selected
> hbonds #4 reveal true
133 hydrogen bonds found
> select ions
Nothing selected
> select H
Nothing selected
> nucleotides #4 ladder
> select ions
Nothing selected
> select sideonly
2194 atoms, 1661 bonds, 13 pseudobonds, 595 residues, 4 models selected
> undo
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
Cannot run BLAST without some kind of sequence.
[Repeated 1 time(s)]
> ui tool show H-Bonds
> hbonds reveal true
462 hydrogen bonds found
> ui tool show "Model Loops"
> modeller refine 4/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> modeller refine 4/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> ui tool show AlphaFold
Cannot run BLAST without some kind of sequence.
> select down
Nothing selected
> select down
Nothing selected
> alphafold search #1
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
> alphafold predict #1
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> alphafold search #1
[Repeated 2 time(s)]
> alphafold match #1
Fetching compressed AlphaFold A0A7W8BV96 from
https://alphafold.ebi.ac.uk/files/AF-A0A7W8BV96-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A7W8BV96 (chain
A)
AlphaFold prediction matching query (2).pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A7W8BV96 | A0A7W8BV96_9ACTN | 10.68 | 131 | 215 | 92
Opened 1 AlphaFold model
> alphafold match #1
1 AlphaFold model found using sequence similarity searches: A0A7W8BV96 (chain
A)
AlphaFold prediction matching query (2).pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A7W8BV96 | A0A7W8BV96_9ACTN | 10.68 | 131 | 215 | 92
Opened 1 AlphaFold model
> hide #6.1 models
> show #6.1 models
> hide #!6 models
> show #!6 models
> label ligand
> color #6 #55aa00ff models
> color #6 #0055ffff models
> color #6 springgreen models
> color #6 #0055ffff models
> color #3 #55ff7fff models
> color bfactor #4#5.1#6.1
3295 atoms, 455 residues, atom bfactor range 27.4 to 98.7
> hide #6.1 models
> hide #!6 models
> show #!6 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> show #3 models
> hide #3 models
> show #3 models
> color #5 #ff5500ff models
> color #5 #aa00ffff models
> hide #!6 models
> show #!6 models
Alignment identifier is 1/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
Alignment identifier is 1
> hide #3 models
> hide #!5 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> hide #!5 models
> show #!5 models
> show #5.1 models
> show #3 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> select clear
[Repeated 2 time(s)]
> label ligand
> hide #!6 models
> hide #5.1 models
> hide #!5 models
> hide #4 models
> show #4 models
> label ligand
[Repeated 1 time(s)]
> show target m
[Repeated 1 time(s)]
> hide target m
> show #4 models
> label ligand
> show #!6 models
> show #6.1 models
> hide #!6 models
> show #!6 models
> hide #6.1 models
> show #6.1 models
> select add #6
960 atoms, 983 bonds, 131 residues, 2 models selected
> select subtract #6
Nothing selected
> log metadata #6
No models had metadata
> log chains #6
Chain information for AlphaFold A0A7W8BV96_9ACTN chain A #6.1
---
Chain | Description | UniProt
A | Candicidin polyketide synthase FscB | A0A7W8BV96_9ACTN 1-1231
> show #3 models
> close #6.1
> ui mousemode right zoom
> show #1 models
> hide #3 models
> hide #4 models
> show #3 models
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
query (2).pdb #1/A VAL 215: phi -94.0, psi none trans
query (1).pdb #2/A ILE 249: phi -114.9, psi none trans
query3.pdb #4/A PRO 193: phi -120.6, psi none trans
Applying VAL rotamer (chi angles: 175.9) to query (2).pdb #1/A VAL 215
Applying ILE rotamer (chi angles: -63.8 170.1) to query (1).pdb #2/A ILE 249
Applying PRO rotamer (chi angles: 27.0 -34.6) to query3.pdb #4/A PRO 193
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for query (2).pdb (#1) chain A; guessing termini instead
Chain-initial residues that are actual N termini: query (2).pdb #1/A HIS 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: query (2).pdb #1/A VAL 215
127 hydrogen bonds
query (2).pdb #1/A VAL 215 is not terminus, removing H atom from 'C'
No usable SEQRES records for query (1).pdb (#2) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: query (1).pdb #2/A ALA 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: query (1).pdb #2/A ILE 249
178 hydrogen bonds
query (1).pdb #2/A ILE 249 is not terminus, removing H atom from 'C'
No usable SEQRES records for query3.pdb (#4) chain A; guessing termini instead
Chain-initial residues that are actual N termini: query3.pdb #4/A LEU 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: query3.pdb #4/A PRO 193
108 hydrogen bonds
query3.pdb #4/A PRO 193 is not terminus, removing H atom from 'C'
Termini for AlphaFold A0A7W8BV96_9ACTN chain A (#5.1) chain A determined from
SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: AlphaFold
A0A7W8BV96_9ACTN chain A #5.1/A HIS 1101
Chain-final residues that are actual C termini: AlphaFold A0A7W8BV96_9ACTN
chain A #5.1/A SER 1231
Chain-final residues that are not actual C termini:
69 hydrogen bonds
Adding 'H' to AlphaFold A0A7W8BV96_9ACTN chain A #5.1/A HIS 1101
5663 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> ui mousemode right windowing
[Repeated 1 time(s)]
> ui tool show "Similar Structures"
Must choose a chain in the similar structures panel before running search
Must run search first
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
AttributeError: 'NoneType' object has no attribute 'hits'
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
You must press the similar structures Search button before you can open
matching structures.
> ui windowfill toggle
[Repeated 1 time(s)]Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
AttributeError: 'NoneType' object has no attribute 'hits'
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #6 models
> show #6 models
> hide #6 models
> view #5.1 clip false
No displayed objects specified.
You must press the similar structures Search button before you can open
matching structures.
[Repeated 1 time(s)]Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
AttributeError: 'NoneType' object has no attribute 'hits'
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot
if r.query_chain is None:
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'query_chain'
AttributeError: 'NoneType' object has no attribute 'query_chain'
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot
if r.query_chain is None:
^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot
if r.query_chain is None:
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'query_chain'
AttributeError: 'NoneType' object has no attribute 'query_chain'
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 339, in _show_cluster_plot
if r.query_chain is None:
^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2125
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Latitude 3410
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 8,339,001,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (6)
comment:1 by , 9 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Similar Structures: self.results is None |
comment:2 by , 9 months ago
comment:3 by , 9 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Made Ligands and Clusters button show message in error panel saying to do a Search first.
comment:4 by , 6 months ago
I think this happened while opening the map file, since the map information had not made it into the log -- perhaps after the file itself had been opened but before the log's rate-limiting timer had gone off to actually put the info in the log.
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Pressing the Ligands or Clusters button on the Similar Structures GUI produces a traceback if no search has been done. The Sequences and Traces button raise a dialog saying that a search must first be done. The Ligands and Clusters button should do the same.