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#9164 closed defect (fixed)

ESMFold sequence search web service failed

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Structure Prediction	Version:
Keywords:		Cc:	Zach Pearson
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.19.0-43-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:
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  

> toolshed show

Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_Cytoscape-0.1-py3-none-any.whl  
Installing collected packages: ChimeraX-Cytoscape  
Attempting uninstall: ChimeraX-Cytoscape  
Found existing installation: ChimeraX-Cytoscape 0.1  
Uninstalling ChimeraX-Cytoscape-0.1:  
Successfully uninstalled ChimeraX-Cytoscape-0.1  
Successfully installed ChimeraX-Cytoscape-0.1  
\---  

Successfully installed ChimeraX-Cytoscape-0.1  
Installed ChimeraX-Cytoscape (0.1)  
Downloading bundle ChimeraX_PDBImages-1.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_PDBImages-1.1-py3-none-any.whl  
Installing collected packages: ChimeraX-PDBImages  
Attempting uninstall: ChimeraX-PDBImages  
Found existing installation: ChimeraX-PDBImages 1.1  
Uninstalling ChimeraX-PDBImages-1.1:  
Successfully uninstalled ChimeraX-PDBImages-1.1  
Successfully installed ChimeraX-PDBImages-1.1  
\---  

Successfully installed ChimeraX-PDBImages-1.1  
Installed ChimeraX-PDBImages (1.1)  
Downloading bundle ChimeraX_TugLigands-1.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_TugLigands-1.1-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.6.dev202303230000 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
TugLigands==1.1) (1.6.1)  
Installing collected packages: ChimeraX-TugLigands  
Successfully installed ChimeraX-TugLigands-1.1  
\---  

Successfully installed ChimeraX-TugLigands-1.1  
Installed ChimeraX-TugLigands (1.1)  
Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
chimerax-dockprep 1.1.1 requires ChimeraX-AddH~=2.2, but you have chimerax-
addh 2.1.3 which is incompatible.  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_AddH-2.1.3-py3-none-any.whl  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (2.12)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Hbonds~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (2.4)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (2.0.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (1.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-AddH==2.1.3) (1.43.10)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.7.2)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.0.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0.2)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (10.0.6)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.1.1)  
Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (2.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.16 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.28.4)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.10.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.5.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.16->ChimeraX-
Hbonds~=2.0->ChimeraX-AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.16->ChimeraX-
Hbonds~=2.0->ChimeraX-AddH==2.1.3) (1.2)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.16->ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.1.4)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.10.3)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.0.1)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.4)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Installing collected packages: ChimeraX-AddH  
Successfully installed ChimeraX-AddH-2.1.3  
\---  

Successfully installed ChimeraX-AddH-2.1.3  
Installed ChimeraX-AddH (2.1.3)  
Downloading bundle ChimeraX_DevelExtras-0.4.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_DevelExtras-0.4.2-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core~=1.4 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-DevelExtras==0.4.2)
(1.6.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-DevelExtras==0.4.2)
(1.28.4)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
DevelExtras==0.4.2) (1.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
DevelExtras==0.4.2) (1.1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
DevelExtras==0.4.2) (1.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI~=1.0->ChimeraX-DevelExtras==0.4.2) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI~=1.0->ChimeraX-DevelExtras==0.4.2) (1.3)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-DevelExtras==0.4.2) (1.0.1)  
Installing collected packages: ChimeraX-DevelExtras  
Successfully installed ChimeraX-DevelExtras-0.4.2  
\---  

Successfully installed ChimeraX-DevelExtras-0.4.2  
Installed ChimeraX-DevelExtras (0.4.2)  
Downloading bundle MolecularDynamicsViewer-1.4-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/MolecularDynamicsViewer-1.4-py3-none-any.whl  
Installing collected packages: MolecularDynamicsViewer  
Attempting uninstall: MolecularDynamicsViewer  
Found existing installation: MolecularDynamicsViewer 1.4  
Uninstalling MolecularDynamicsViewer-1.4:  
Successfully uninstalled MolecularDynamicsViewer-1.4  
Successfully installed MolecularDynamicsViewer-1.4  
\---  

Successfully installed MolecularDynamicsViewer-1.4  
Installed MolecularDynamicsViewer (1.4)  
Downloading bundle ChimeraX_StarMap-1.1.75-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /home/shabir/Downloads/ChimeraX_StarMap-1.1.75-py3-none-any.whl  
Requirement already satisfied: pyparsing in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-StarMap==1.1.75) (3.0.9)  
Collecting pyqtgraph  
Downloading pyqtgraph-0.13.3-py3-none-any.whl (960 kB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 961.0/961.0 kB 9.5 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-Core>=1.4 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-StarMap==1.1.75) (1.6.1)  
Requirement already satisfied: numpy>=1.20.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from pyqtgraph->ChimeraX-
StarMap==1.1.75) (1.23.5)  
Installing collected packages: pyqtgraph, ChimeraX-StarMap  
Successfully installed ChimeraX-StarMap-1.1.75 pyqtgraph-0.13.3  
\---  

Successfully installed ChimeraX-StarMap-1.1.75 pyqtgraph-0.13.3  
Installed ChimeraX-StarMap (1.1.75)  

> ui tool show ESMFold

> esmfold match
> MSPRPLRALLGAAAAALVSAAALAFPSQAAANDSPFYVNPNMSSAEWVRNNPNDPRTPVIRDRIASVPQGTWFAHHNPGQITGQVDALMSAAQAAGKIPILVVYNAPGRDCGNHSSGGAPSHSAYRSWIDEFAAGLKNRPAYIIVEPDLISLMSSCMQHVQQEVLETMAYAGKALKAGSSQARIYFDAGHSAWHSPAQMASWLQQADISNSAHGIATNTSNYRWTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNEWCDPSGRAIGTPSTTNTGDPMIDAFLWIKLPGEADGCIAGAGQFVPQAAYEMAIAAGGTNPNPNPNPTPTPTPTPTPPPGSSGACTATYTIANEWNDGFQATVTVTANQNITGWTVTWTFTDGQTITNAWNADVSTSGSSVTARNVGHNGTLSQGASTEFGFVGSKGNSNSVPTLTCAAS

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/alphafold/panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/alphafold/panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/esmfold/match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/esmfold/search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/esmfold/search.py", line 52, in _search_sequences_web  
raise SearchError('ESMFold sequence search web service failed (%s) "%s"\n\n%s'  
chimerax.esmfold.search.SearchError: ESMFold sequence search web service
failed (500) "Internal Server Error"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/esmfold_search_cgi.py  
  
chimerax.esmfold.search.SearchError: ESMFold sequence search web service
failed (500) "Internal Server Error"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/esmfold_search_cgi.py  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/esmfold/search.py", line 52, in _search_sequences_web  
raise SearchError('ESMFold sequence search web service failed (%s) "%s"\n\n%s'  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 525.105.17
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: pt_BR.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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: H110-D3A
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Pentium(R) CPU G4600 @ 3.60GHz
Cache Size: 3072 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.7Gi       3.3Gi       380Mi        79Mi       4.0Gi       4.0Gi
	Swap:          2.0Gi       865Mi       1.2Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GP104 [GeForce GTX 1070] [1043:85a0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    argcomplete: 3.0.5
    asttokens: 2.2.1
    attrs: 22.2.0
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    biopython: 1.81
    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: 2.1.3
    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-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-DevelExtras: 0.4.2
    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-ISOLDE: 1.6.0
    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-NIHPresets: 1.1.10
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.11
    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-RIBFIND: 0.2
    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-StarMap: 1.1.75
    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-TugLigands: 1.1
    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
    jsonschema: 4.17.3
    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
    MolecularDynamicsViewer: 1.4
    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
    pyqtgraph: 0.13.3
    pyrsistent: 0.19.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    regex: 2023.3.23
    requests: 2.28.2
    ribfind: 2.0.2
    scipy: 1.9.3
    Send2Trash: 1.8.0
    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

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Cc:	Zach Pearson added
Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ESMFold sequence search web service failed

comment:2 by Tom Goddard, 2 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Had to update esmfold kmer search cgi script to use /usr/bin/python3 instead of /usr/local/bin/python3 after server OS updated from CentOS 7 to Rocky 8.

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