id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16558 Cannot 'pip install pyKVFinger' chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10.dev202412280203 (2024-12-28 02:03:40 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10.dev202412280203 (2024-12-28) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:/Users/taher/Desktop/4i23 prepared protein.cxs"" Log from Mon Jan 6 13:04:30 2025 Startup Messages --- warning | Your computer has Intel graphics driver 7810 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202412280203 (2024-12-28) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4i23 fromDatabase pdbe_bio format mmcif Summary of feedback from opening 4i23 fetched from pdbe_bio --- warning | Missing or incomplete sequence information. Inferred polymer connectivity. 4i23 bioassembly 1 title: Crystal structure of the wild-type EGFR kinase domain in complex with dacomitinib (soaked) [more info...] Chain information for 4i23 bioassembly 1 #1 --- Chain | Description A | Epidermal growth factor receptor Non-standard residues in 4i23 bioassembly 1 #1 --- 1C9 — (1C9) Computing secondary structure Opened 1 biological assemblies for 4i23 > select protein 2429 atoms, 2479 bonds, 3 pseudobonds, 304 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > save ""C:/Users/taher/Desktop/4i23 ligand.cxs"" > close session > open 4i23 format mmcif fromDatabase pdbe_bio Summary of feedback from opening 4i23 fetched from pdbe_bio --- warning | Missing or incomplete sequence information. Inferred polymer connectivity. 4i23 bioassembly 1 title: Crystal structure of the wild-type EGFR kinase domain in complex with dacomitinib (soaked) [more info...] Chain information for 4i23 bioassembly 1 #1 --- Chain | Description A | Epidermal growth factor receptor Non-standard residues in 4i23 bioassembly 1 #1 --- 1C9 — (1C9) Computing secondary structure Opened 1 biological assemblies for 4i23 > open 4i23 format mmcif fromDatabase pdbe_bio Summary of feedback from opening 4i23 fetched from pdbe_bio --- warning | Missing or incomplete sequence information. Inferred polymer connectivity. 4i23 bioassembly 1 title: Crystal structure of the wild-type EGFR kinase domain in complex with dacomitinib (soaked) [more info...] Chain information for 4i23 bioassembly 1 #2 --- Chain | Description A | Epidermal growth factor receptor Non-standard residues in 4i23 bioassembly 1 #2 --- 1C9 — (1C9) Opened 1 biological assemblies for 4i23 Computing secondary structure > select ligand 44 atoms, 48 bonds, 2 residues, 2 models selected > delete atoms sel > delete bonds sel > select #2/A 2429 atoms, 2479 bonds, 3 pseudobonds, 304 residues, 2 models selected > select clear > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 4858 atoms, 4958 bonds, 6 pseudobonds, 608 residues, 4 models selected > select ions Nothing selected > select solvent Nothing selected > 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 4i23 bioassembly 1 #1/A ILE 1018: phi -117.4, psi none trans 4i23 bioassembly 1 #2/A ILE 1018: phi -117.4, psi none trans Applying ILE rotamer (chi angles: 61.7 -80.0) to 4i23 bioassembly 1 #1/A ILE 1018 Applying ILE rotamer (chi angles: 61.7 -80.0) to 4i23 bioassembly 1 #2/A ILE 1018 Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for 4i23 bioassembly 1 (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: 4i23 bioassembly 1 #1/A SER 695 Chain-initial residues that are not actual N termini: 4i23 bioassembly 1 #1/A GLY 724, 4i23 bioassembly 1 #1/A ALA 750, 4i23 bioassembly 1 #1/A ASP 1006 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 4i23 bioassembly 1 #1/A ILE 1018, 4i23 bioassembly 1 #1/A SER 720, 4i23 bioassembly 1 #1/A LEU 747, 4i23 bioassembly 1 #1/A PRO 990 Adding 'H' to 4i23 bioassembly 1 #1/A GLY 724 Adding 'H' to 4i23 bioassembly 1 #1/A ALA 750 Adding 'H' to 4i23 bioassembly 1 #1/A ASP 1006 4i23 bioassembly 1 #1/A ILE 1018 is not terminus, removing H atom from 'C' No usable SEQRES records for 4i23 bioassembly 1 (#2) chain A; guessing termini instead Chain-initial residues that are actual N termini: 4i23 bioassembly 1 #2/A SER 695 Chain-initial residues that are not actual N termini: 4i23 bioassembly 1 #2/A GLY 724, 4i23 bioassembly 1 #2/A ALA 750, 4i23 bioassembly 1 #2/A ASP 1006 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 4i23 bioassembly 1 #2/A ILE 1018, 4i23 bioassembly 1 #2/A SER 720, 4i23 bioassembly 1 #2/A LEU 747, 4i23 bioassembly 1 #2/A PRO 990 Adding 'H' to 4i23 bioassembly 1 #2/A GLY 724 Adding 'H' to 4i23 bioassembly 1 #2/A ALA 750 Adding 'H' to 4i23 bioassembly 1 #2/A ASP 1006 4i23 bioassembly 1 #2/A ILE 1018 is not terminus, removing H atom from 'C' 4966 hydrogens added Closest equivalent command: addcharge standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Dock prep finished > select ligand Nothing selected > save ""C:/Users/taher/Desktop/4i23 prepared protein.cxs"" ——— End of log from Mon Jan 6 13:04:30 2025 ——— > view name session-start opened ChimeraX session > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pykvfinder/ ERROR: Could not find a version that satisfies the requirement pyKVFinder (from versions: none) ERROR: No matching distribution found for pyKVFinder File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > select protein 9824 atoms, 9924 bonds, 6 pseudobonds, 608 residues, 4 models selected > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1863, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: ERROR: Exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 438, in _error_catcher yield File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 561, in read data = self._fp_read(amt) if not fp_closed else b"""" ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 527, in _fp_read return self._fp.read(amt) if amt is not None else self._fp.read() ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\cachecontrol\filewrapper.py"", line 98, in read data: bytes = self.__fp.read(amt) ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py"", line 466, in read s = self.fp.read(amt) ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py"", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1278, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py"", line 1134, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 105, in _run_wrapper status = _inner_run() ^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\base_command.py"", line 96, in _inner_run return self.run(options, args) ^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\cli\req_command.py"", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\commands\install.py"", line 379, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\resolution\resolvelib\resolver.py"", line 179, in resolve self.factory.preparer.prepare_linked_requirements_more(reqs) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 554, in prepare_linked_requirements_more self._complete_partial_requirements( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\operations\prepare.py"", line 469, in _complete_partial_requirements for link, (filepath, _) in batch_download: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\download.py"", line 184, in __call__ for chunk in chunks: File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_internal\network\utils.py"", line 65, in response_chunks for chunk in response.raw.stream( File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 622, in stream data = self.read(amt=amt, decode_content=decode_content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 560, in read with self._error_catcher(): File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py"", line 155, in __exit__ self.gen.throw(typ, value, traceback) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\pip\\_vendor\urllib3\response.py"", line 449, in _error_catcher raise SSLError(e) pip._vendor.urllib3.exceptions.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac (_ssl.c:2576) File ""C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 3.3.0 - Build 26.20.100.7810 OpenGL renderer: Intel(R) UHD Graphics 620 OpenGL vendor: Intel Python: 3.11.4 Locale: en_IN.cp1252 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: windows Manufacturer: LENOVO Model: 81HN OS: Microsoft Windows 11 Enterprise (Build 26100) Memory: 7,981,445,120 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i3-8130U CPU @ 2.20GHz 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: 2024.12.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 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: 2.16.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.59 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: 1.0.2 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: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202412280203 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: 1.2.7 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: 1.5.1 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: 2.7.7 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-ProfileGrids: 1.0.1 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: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.15 ChimeraX-Shape: 1.1 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: 1.19.1 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: 2.5.1 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: 1.42.2 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 coverage: 7.6.10 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.11 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 iniconfig: 2.0.0 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: 1.4.8 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 OpenMM: 8.2.0 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 pluggy: 1.5.0 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 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: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 pytest: 8.3.4 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pywin32: 306 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.1 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: 2.3.0 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 }}} " defect closed normal Core fixed chimera-programmers all ChimeraX