The following bug report has been submitted:
Platform: Linux-5.15.0-122-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/manu/5rlz_B.pdb
Chain information for 5rlz_B.pdb #1
---
Chain | Description
B | No description available
> ui tool show "Blast Protein"
> blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp1
Webservices job id: DDXWEF5NCHC0PMLR
> open pdb:5RL7
Summary of feedback from opening 5RL7 fetched from pdb
---
note | Fetching compressed mmCIF 5rl7 from
http://files.rcsb.org/download/5rl7.cif
5rl7 title:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase
in complex with Z364321922 [more info...]
Chain information for 5rl7 #2
---
Chain | Description | UniProt
A B | Helicase | R1AB_SARS2 1-601
Non-standard residues in 5rl7 #2
---
PO4 — phosphate ion
VVD — 5-(acetylamino)-2-fluorobenzoic acid
ZN — zinc ion
5rl7 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> matchmaker #2/A to #1/B
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 5rlz_B.pdb, chain B (#1) with 5rl7, chain A (#2), sequence
alignment score = 2891.5
RMSD between 491 pruned atom pairs is 0.950 angstroms; (across all 567 pairs:
1.674)
Alignment identifier is bp1 [1]
Associated 5rlz_B.pdb chain B to 5RL7_A with 0 mismatches
Associated 5rl7 chain B to 5RL7_A with 0 mismatches
Associated 5rl7 chain A to 5RL7_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]
> ui tool show "Modeller Comparative"
> modeller comparative "bp1 [1]:1" numModels 5 fast false multichain true
> hetPreserve true hydrogens true waterPreserve true
Cannot preserve water/het with more than one template per target; not
preserving
Webservices job id: Z0ZW8HVQ73IKMJW6
Modeller job (ID Z0ZW8HVQ73IKMJW6) finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 243, in get_file
content = self.chimerax_api.get_file(self.job_id, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info
return self.api_client.call_api(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 319, in call_api
return self.__call_api(resource_path, method,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 151, in __call_api
response_data = self.request(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/cxservices/api_client.py", line 341, in request
return self.rest_client.GET(url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 228, in GET
return self.request("GET", url,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/cxservices/rest.py",
line 222, in request
raise ApiException(http_resp=r)
cxservices.rest.ApiException: (400)
Reason: Bad Request
HTTP response headers: HTTPHeaderDict({'Date': 'Wed, 26 Feb 2025 17:48:40
GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=63072000;
includeSubdomains; preload', 'Content-Length': '60', 'vary': 'Accept',
'Connection': 'close', 'Content-Type': 'application/json'})
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file "}'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 586, in get_pdb_model
pdb_text = self.get_file(fname)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 245, in get_file
raise KeyError("%s: %s" % (filename, str(e)))
KeyError: '#1B.B99990001.pdb: (400)\nReason: Bad Request\nHTTP response
headers: HTTPHeaderDict({\'Date\': \'Wed, 26 Feb 2025 17:48:40 GMT\',
\'Server\': \'Apache\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'60\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file "}\'\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 665, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 591, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 400, in process_ok_models
model = get_pdb_model(pdb_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
RuntimeError: Could not find Modeller out PDB #1B.B99990001.pdb on server
RuntimeError: Could not find Modeller out PDB #1B.B99990001.pdb on server
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/modeller/common.py", line 588, in get_pdb_model
raise RuntimeError("Could not find Modeller out PDB %s on server" % fname)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 620 (KBL GT2)
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: HP
Model: HP Spectre x360 Convertible 13-ac0XX
OS: Linux Mint 21.1 Vera
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz
Cache Size: 4096 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 4.7Gi 5.1Gi 2.1Gi 5.6Gi 8.4Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 620 [8086:5916] (rev 02)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company HD Graphics 620 [103c:827e]
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Manuel,
--Eric