error in running kvfinder

[vincent.chaptal@…]

Hi,

by typing the command "kvfinder #2" I got the following error message.

I tried to report the bug using the bug reporter but it couldn't reach 
internet so couldn't be sent (but internet connection is working)

perhaps a firewall issue? (but my firewall is configured correctly for 
chimeraX, but is it different for python?)

Thanks

Vincent

Chimera X version: 1.9 (2024-12-11 19:11:19 UTC)

Platform: macOS-14.6.1-arm64-arm-64bit

Could not install pyKVFinder module from PyPi repository: RuntimeError: 
WARNING: Retrying (Retry(total=4, connect=None, read=None, 
redirect=None, status=None)) after connection broken by 
'ProxyError('Your proxy appears to only use HTTP and not HTTPS, try 
changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=3, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=2, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=1, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=0, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ ERROR: Could not find a version 
that satisfies the requirement pyKVFinder (from versions: none) ERROR: 
No matching distribution found for pyKVFinder File 
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/python_utils.py", 
line 143, in run_logged_pip raise RuntimeError(s) See log for complete 
Python traceback.

Gathered information:

OpenGL version: 4.1 Metal - 88.1

OpenGL renderer: Apple M3 Pro

OpenGL vendor: Apple

Python: 3.11.4

Locale: UTF-8

Qt version: PyQt6 6.7.1, Qt 6.7.1

Qt runtime version: 6.7.3

Qt platform: cocoa

Hardware:

Hardware Overview:

Model Name: MacBook Pro

Model Identifier: Mac15,7

Model Number: Z1AJ00112FN/A

Chip: Apple M3 Pro

Total Number of Cores: 12 (6 performance and 6 efficiency)

Memory: 36 GB

System Firmware Version: 10151.140.19

OS Loader Version: 10151.140.19

Software:

System Software Overview:

System Version: macOS 14.6.1 (23G93)

Kernel Version: Darwin 23.6.0

Time since boot: 29 jours, 21 heures et 41 minutes

Graphics/Displays:

Apple M3 Pro:

Chipset Model: Apple M3 Pro

Type: GPU

Bus: Built-In

Total Number of Cores: 18

Vendor: Apple (0x106b)

Metal Support: Metal 3

Displays:

Color LCD:

Display Type: Built-in Liquid Retina XDR Display

Resolution: 3456 x 2234 Retina

Main Display: Yes

Mirror: Off

Online: Yes

Automatically Adjust Brightness: Yes

Connection Type: Internal

PL3480WQ:

Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)

UI Looks like: 3440 x 1440 @ 100.00Hz

Mirror: Off

Online: Yes

Rotation: Supported

Installed Packages:

alabaster: 1.0.0

anyio: 4.7.0

appdirs: 1.4.4

appnope: 0.1.4

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: 2023.11.17

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

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: 3.9.2

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: 1.26.4

openvr: 1.26.701

packaging: 23.2

ParmEd: 4.2.2

parso: 0.8.4

pep517: 0.13.1

pexpect: 4.9.0

pillow: 10.4.0

pip: 24.2

pkginfo: 1.11.1

platformdirs: 4.3.6

prompt_toolkit: 3.0.48

psutil: 6.0.0

ptyprocess: 0.7.0

pure_eval: 0.2.3

py-cpuinfo: 9.0.0

pycollada: 0.8

pydicom: 2.4.4

pyelftools: 0.31

Pygments: 2.18.0

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

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

tifffile: 2024.7.24

tinyarray: 1.2.4

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

-- 

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab

MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

http://mmsb.cnrs.fr/en/

[Eric Pettersen]

Hi Vincent,

What are your proxy settings in the "Web Access" section of the ChimeraX preferences?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[vincent.chaptal@…]

Hi Eric,

the settings for HTTP and HTTPS proxys are ftprox.ibcp.fr and port 3128.

Vincent

Le 20/12/2024 à 18:27, ChimeraX a écrit :
>
>
>
>
>

[Eric Pettersen]

They opening the Python shell tool (Tools→General→Shell) and type:

import os
os.environhttps_proxy = "​http://ftprox.ibcp.fr:3128"

Then see if that changes the KVFinder behavior

[Eric Pettersen]

They... → Try...

[vincent.chaptal@…]

Hi Eric,

sorry for not getting back to you sooner, I took a much needed full 
break, and am only re-starting now.
Trying what you described worked.

Best wishes for this new year!
Vincent

Le 23/12/2024 à 18:21, ChimeraX a écrit :
>
>
>

[Eric Pettersen]

Hi Vincent,

That's great! Starting with tomorrow's daily build the Web Access preference category will also allow you to specify the proxy-server protocol to use. If you could try that out (putting "http" in both protocol boxes) and let me know how it works, I would really appreciate it.

--Eric

[vincent.chaptal@…]

Hi Eric,

no problem to try it. I just saw this morning that the daily build dates 
from January 10, so I'll wait for today's release and will try it out 
tomorrow with the time difference.

Best
Vincent

Le 10/01/2025 à 20:56, ChimeraX a écrit :
>
>

[Eric Pettersen]

Yes, the non-Windows/flatpak builds haven't worked for the past few days. We're hoping they'll work tonight, but yes -- check the date.

--Eric

[vincent.chaptal@…]

Hi Eric,

I've tested it today on version version 1.10.dev202501140846 (2025-01-14)

It works!

I've placed "http" in both boxes, and the ftprox.ibcp.fr in the hosts 
boxes.

Best
Vincent

Le 10/01/2025 à 20:56, ChimeraX a écrit :
>
>

[Eric Pettersen]

That's great to hear! Thanks for checking it out.

--Eric