Opened 8 months ago

Closed 8 months ago

Last modified 8 months ago

#16972 closed defect (duplicate)

'#' character in sequence name of Modeller job

Reported by: mllanos@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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
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    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
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    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
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    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
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    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
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    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
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    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
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    sfftk-rw: 0.7.3
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    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
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    typing-extensions: 4.5.0
    tzdata: 2023.3
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    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 8 months ago

Component: UnassignedStructure Prediction
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submission'#' character in sequence name of Modeller job

comment:2 by Eric Pettersen, 8 months ago

Resolution: duplicate
Status: acceptedclosed

Hi Manuel,

Thanks for reporting this problem. It was fixed a little under a year ago, so if you upgrade to the latest ChimeraX production release then it won't happen again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by mllanos@…, 8 months ago

Thanks for your quick response it's working now!
manu
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, February 26, 2025 11:27 AM
To: Manuel Llanos <mllanos@scripps.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #16972: '#' character in sequence name of Modeller job

#16972: '#' character in sequence name of Modeller job
-------------------------------------------+--------------------
          Reporter:  mllanos@…             |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:  duplicate             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Changes (by pett):

 * resolution:   => duplicate
 * status:  accepted => closed

Comment:

 Hi Manuel,
         Thanks for reporting this problem.  It was fixed a little under a
 year ago, so if you upgrade to the latest ChimeraX production release then
 it won't happen again.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16972#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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