Context Navigation

Trac Ticket Queries

In addition to reports, Trac provides support for custom ticket queries, which can be used to display tickets that meet specified criteria.

To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.

Filters

When you first go to the query page, the default filter will display tickets relevant to you:

If logged in then all open tickets, it will display open tickets assigned to you.
If not logged in but you have specified a name or email address in the preferences, then it will display all open tickets where your email (or name if email not defined) is in the CC list.
If not logged in and no name/email is defined in the preferences, then all open issues are displayed.

Current filters can be removed by clicking the button to the left with the minus sign on the label. New filters are added from the pulldown lists at the bottom corners of the filters box; 'And' conditions on the left, 'Or' conditions on the right. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an Or on the criteria.

You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.

After you have edited your filters, click the Update button to refresh your results.

Some shortcuts can be used to manipulate checkbox filters.

Clicking on a filter row label toggles all checkboxes.
Pressing the modifier key while clicking on a filter row label inverts the state of all checkboxes.
Pressing the modifier key while clicking on a checkbox selects the checkbox and deselects all other checkboxes in the filter.

The modifier key is platform and browser dependent. On Mac the modified key is Option/Alt or Command. On Linux the modifier key is Ctrl + Alt. Opera on Windows seems to use Ctrl + Alt, while Alt is effective for other Windows browsers.

Navigating Tickets

Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.

You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria , the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.

The query results can be refreshed and cleared of these status indicators by clicking the Update button again.

Saving Queries

Trac allows you to save the query as a named query accessible from the reports module. To save a query ensure that you have Updated the view and then click the Save query button displayed beneath the results. You can also save references to queries in Wiki content, as described below.

Note: one way to easily build queries like the ones below, you can build and test the queries in the Custom report module and when ready - click Save query. This will build the query string for you. All you need to do is remove the extra line breaks.

Note: you must have the REPORT_CREATE permission in order to save queries to the list of default reports. The Save query button will only appear if you are logged in as a user that has been granted this permission. If your account does not have permission to create reports, you can still use the methods below to save a query.

Using TracLinks

You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page.

[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]

Which is displayed as:

Active tickets against 1.0

This uses a very simple query language to specify the criteria, see Query Language.

Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character:

[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]

Which is displayed as:

Assigned tickets by owner

Customizing the table format

You can also customize the columns displayed in the table format (format=table) by using col=<field>. You can specify multiple fields and what order they are displayed in by placing pipes (|) between the columns:

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]

This is displayed as:

Results (1 - 3 of 13590)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19997	limitation	KVFinder on old MacOS	Eric Pettersen	chimerax-bug-report@…
#19995	can't reproduce	Crash in event loop	Eric Pettersen	anurag@…
#19988	duplicate	Crash on Mac waking from sleep	Tom Goddard	a.fasemire@…

1 2 3 4 5 6 7 8 9 10 11 →

Full rows

In table format you can also have full rows by using rows=<field>:

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]

This is displayed as:

Results (1 - 3 of 13590)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19997	limitation	KVFinder on old MacOS	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/noacastrosanchez/Desktop/Bwbg1_lactose_sample_0.cif Summary of feedback from opening /Users/noacastrosanchez/Desktop/Bwbg1_lactose_sample_0.cif --- warning \| Unable to fetch template for 'l01': will connect using distance criteria Chain information for Bwbg1_lactose_sample_0.cif #1 --- Chain \| Description A \| . Computing secondary structure > select ligand 23 atoms, 24 bonds, 1 residue, 1 model selected > save /Users/noacastrosanchez/Desktop/image1.png supersample 3 > style sel ball Changed 23 atom styles > ui tool show H-Bonds > hbonds sel reveal true 22 hydrogen bonds found > hbonds sel reveal true 22 hydrogen bonds found > save /Users/noacastrosanchez/Desktop/image2.png supersample 3 > save "/Users/noacastrosanchez/Desktop/Bioquímica /DOCENCIAS > INTERACTIVAS/PUENTES DE HIDRÓGENO.png" width 864 height 723 supersample 3 > save "/Users/noacastrosanchez/Desktop/Bioquímica /DOCENCIAS > INTERACTIVAS/PUENTES DE HIDRÓGENO LACTOSA.png" width 864 height 723 > supersample 3 > select clear > ui tool show "Show Sequence Viewer" > sequence chain /A Alignment identifier is 1/A > select > /A:25-27,30-42,54-57,68-70,72-81,99-102,105-109,120-136,138-140,142-144,157-159,161-182,208-217,245-257,300-314,316-321,331-333,391-393,436-438,457-459,499-502,530-533,538-540,567-571,576-580,587-589,644-648,667-669,686-688 1544 atoms, 1571 bonds, 181 residues, 1 model selected > select > /A:2-4,9-11,18-22,47-51,85-89,148-152,189-191,199-204,225-228,240-242,262-265,335-341,344-351,358-362,365-369,373-378,381-385,410-413,428-430,446-455,461-468,473-478,481-485,503-510,513-522,548-551,560-564,596-603,611-614,620-625,628-634,651-653,662-665,673-680,690-693 1584 atoms, 1596 bonds, 189 residues, 1 model selected > select > /A:2-4,9-11,18-22,47-51,85-89,148-152,189-191,199-204,225-228,240-242,262-265,335-341,344-351,358-362,365-369,373-378,381-385,410-413,428-430,446-455,461-468,473-478,481-485,503-510,513-522,548-551,560-564,596-603,611-614,620-625,628-634,651-653,662-665,673-680,690-693 1584 atoms, 1596 bonds, 189 residues, 1 model selected > select /A:52 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:50-52 26 atoms, 26 bonds, 3 residues, 1 model selected > select /A:52 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:52 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:192 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:192 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:192 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:192 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:288 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:288 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51,273-274 31 atoms, 31 bonds, 3 residues, 1 model selected > undo > select > /A:25-27,30-42,54-57,68-70,72-81,99-102,105-109,120-136,138-140,142-144,157-159,161-182,208-217,245-257,300-314,316-321,331-333,391-393,436-438,457-459,499-502,530-533,538-540,567-571,576-580,587-589,644-648,667-669,686-688 1544 atoms, 1571 bonds, 181 residues, 1 model selected > select /A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:276-278 23 atoms, 22 bonds, 3 residues, 1 model selected > select /A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:276-278 23 atoms, 22 bonds, 3 residues, 1 model selected > select /A:276-277 19 atoms, 18 bonds, 2 residues, 1 model selected > select /A:276-278 23 atoms, 22 bonds, 3 residues, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:51,288 24 atoms, 24 bonds, 2 residues, 1 model selected > select /A:51,191,288 30 atoms, 29 bonds, 3 residues, 1 model selected > select /A:51,156,191,288 39 atoms, 37 bonds, 4 residues, 1 model selected > select /A:51,96,156,191,288 44 atoms, 41 bonds, 5 residues, 1 model selected > select /A:51,96,156,191,227,288 53 atoms, 49 bonds, 6 residues, 1 model selected > select ~sel & ##selected 5597 atoms, 5782 bonds, 22 pseudobonds, 689 residues, 2 models selected > hide sel cartoons > hide sel atoms [Repeated 1 time(s)] > show sel atoms [Repeated 1 time(s)] > hide sel atoms > show sel cartoons > undo [Repeated 5 time(s)] > select clear > label #1 text "{0.name} {0.number}{0.insertion_code}" > save "/Users/noacastrosanchez/Desktop/Bioquímica /DOCENCIAS > INTERACTIVAS/ETIQUETADAsss.png" width 743 height 723 supersample 3 > preset "overall look" "publication 1 (silhouettes)" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > save "/Users/noacastrosanchez/Desktop/Bioquímica /DOCENCIAS > INTERACTIVAS/publication 1 foto.png" width 743 height 672 supersample 3 > show cartoons > hide cartoons > show cartoons > hide cartoons > ui tool show "Find Cavities" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- uzx0a670/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- uzx0a670/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- uzx0a670/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- uzx0a670/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- hzleeezt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- hzleeezt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- hzleeezt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- hzleeezt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-x5jhhmfc/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-x5jhhmfc/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-x5jhhmfc/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-x5jhhmfc/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > show cartoons > ui tool show "Find Cavities" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-f3z5yt74/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-f3z5yt74/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-f3z5yt74/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-f3z5yt74/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-p5kz6nq2/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-p5kz6nq2/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-p5kz6nq2/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build- env-p5kz6nq2/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > select clear > ui tool show "Find Cavities" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- gakl9wsx/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- gakl9wsx/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1939, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- gakl9wsx/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/1w/754mftkx2q75gl2gk26dhd6c0000gn/T/pip-build-env- gakl9wsx/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD82Y/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 2 días, 1 hora y 3 minutos Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0
#19995	can't reproduce	Crash in event loop	Eric Pettersen	anurag@…
Description	The following bug report has been submitted: Platform: Windows-10-10.0.26200 ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Windows fatal exception: code 0x8001010d Current thread 0x00004afc (most recent call first): File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Windows fatal exception: code 0x80000003 Thread 0x00000690 (most recent call first): File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 324 in wait File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 622 in wait File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1392 in run File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00004afc (most recent call first): File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9hdk 9hdk title: Structure of s.c.Osh6 in complex with Ist2 732-756 and POPS [more info...] Chain information for 9hdk #1 --- Chain \| Description \| UniProt A \| Oxysterol-binding protein homolog 6 \| OSH6_YEAST 31-448 C \| Increased sodium tolerance protein 2 \| IST2_YEAST 732-756 Non-standard residues in 9hdk #1 --- P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) > set bgColor white > color byhetero > color bychain > select /C 164 atoms, 150 bonds, 36 residues, 1 model selected > color sel #9f8cffff > color sel #9e8bffff > color sel #9189ffff > color sel #8789ffff > color sel #858bffff > color sel #858dffff > color sel #8394ffff > color sel #839affff > color sel #829fffff > color sel #82a8ffff > color sel #81adffff > color sel #80b3ffff > color sel #7eb8ffff > color sel #7dcbffff > color sel #7dd8ffff > color sel #7ce9ffff > color sel #7ceeffff > color sel #7bf4ffff > color sel #7bfdffff > color sel #7bffffff > color sel #7bfffbff > color sel #7bfff4ff > color sel #7bfff0ff > color sel #7bffebff > color sel #7cffe9ff > color sel #7cffe5ff > color sel #7cffe3ff > color sel #7cffdeff > color sel #7cffdaff > color sel #7dffdaff > color sel #7dffcdff > color sel #80ffc6ff > color sel #81ffb3ff > color sel #82ffa5ff > color sel #83ff98ff > color sel #85ff89ff > color sel #87ff85ff > color sel #8cff86ff > color sel #8eff86ff > color sel #8fff87ff > color sel #93ff87ff > color sel #96ff8aff > color sel #98ff8cff > color sel #96ff8eff > color sel #92ff90ff > color sel #93ff9aff > color sel #94ffa6ff > color sel #97ffb4ff > color sel #99ffc2ff > color sel #9dffd3ff > color sel #a0ffdfff > color sel #a4ffedff > color sel #a7fff9ff > color sel #aafeffff > color sel #acf7ffff > color sel #b0f1ffff > color sel #b4e7ffff > color sel #b8e3ffff > color sel #b9deffff > color sel #bcdfffff > color sel #bddaffff > color sel #c0d8ffff > color sel #c1d9ffff > color sel #c2d5ffff > color sel #c5d4ffff > color sel #c6d3ffff > color sel #c9d5ffff > color sel #cad4ffff > color sel #cfd5ffff > color sel #d2d7ffff > color sel #d4d7ffff > color sel #d7d9ffff > color sel #dbddffff > color sel #dcddffff > color sel #e0e0ffff > color sel #e2e2ffff > color sel #e4e4ffff > color sel #e7e6ffff > color sel #e8e7ffff > color sel #eae9ffff > color sel #ebeaffff > color sel #ecebffff > color sel #efeeffff > color sel #eeedffff > color sel #ebe9ffff > color sel #e7e4ffff > color sel #e5e1ffff > color sel #e1dbffff > color sel #ded4ffff > color sel #decfffff > color sel #dccaffff > color sel #ddc4ffff > color sel #e3bcffff > color sel #eab4ffff > color sel #ffaaffff > color sel #ffa4f0ff > color sel #ffa0e2ff > color sel #ff9dd8ff > color sel #ff98c6ff > color sel #ff95bfff > color sel #ff92b8ff > color sel #ff8fa9ff > color sel #ff8ca1ff > color sel #ff868cff > color sel #ff8385ff > color sel #ff8183ff > color sel #ff8082ff > color sel #ff7e80ff > color sel #ff7c7eff > color sel #ff797bff > color sel #ff787aff > color sel #ff7779ff > color sel #ff7476ff > color sel #ff7375ff > color sel #ff7072ff > color sel #ff6e70ff > color sel #ff6b6dff > color sel #ff6973ff > color sel #ff667aff > color sel #ff6385ff > color sel #ff638dff > color sel #ff6198ff > color sel #ff5ea4ff > color sel #ff5da6ff > color sel #ff5dabff > color sel #ff5cabff > color sel #ff5cb0ff > color sel #ff5aafff > color sel #ff5ab2ff > color sel #ff57b6ff > color sel #ff55bbff > color sel #ff53baff > color sel #ff52baff > color sel #ff50bcff > color sel #ff4ec1ff > color sel #ff4bc0ff > color sel #ff4ac6ff > color sel #ff47c8ff > color sel #ff47ceff > color sel #ff46d4ff > color sel #ff43d3ff > color sel #ff43d6ff > color sel #ff42dcff > color sel #ff41dcff > color sel #ff41dfff > color sel #ff40dfff > color sel #ff3edfff > color sel #ff3de5ff > color sel #ff3ce5ff > color sel #ff3aebff > color sel #ff39ebff > color sel #ff37f5ff > color sel #ff35f5ff > color sel #ff35fcff > color sel #f134ffff > color sel #e134ffff > color sel #b534ffff > color sel #a034ffff > color sel #8934ffff > color sel #6734ffff > color sel #5735ffff > color sel #3e37ffff > color sel #3737ffff > color sel #385cffff > color sel #3974ffff > color sel #3a93ffff > color sel #3cb1ffff > color sel #3dd5ffff > color sel #3efff9ff > color sel #3effd5ff > color sel #3effafff > color sel #3eff95ff > color sel #3eff75ff > color sel #3eff4eff > color sel #48ff3eff > color sel #58ff3eff > color sel #5aff3dff > color sel #67ff3dff > color sel #70ff3cff > color sel #76ff3cff > color sel #7aff3cff > color sel #80ff3cff > color sel #87ff3cff > color sel #8aff3cff > color sel #90ff3cff > color sel #94ff3cff > color sel #9aff3cff > color sel #a1ff3cff > color sel #a4ff3cff > color sel #abff3cff > color sel #b1ff3cff > color sel #b4ff3cff > color sel #bbff3cff > color sel #c5ff3cff > color sel #cbff3cff > color sel #d2ff3cff > color sel #d5ff3cff > color sel #dbff3cff > color sel #dfff3cff > color sel #e5ff3aff > color sel #ebff3aff > color sel #efff39ff > color sel #f5ff38ff > color sel #f5ff37ff > color sel #fcff37ff > color sel #ffff35ff > color sel #fff835ff > color sel #fff834ff > color sel #fff134ff > color sel #fff133ff > color sel #ffee33ff > color sel #ffee31ff > color sel #ffe731ff > color sel #ffd52fff > color sel #ffc32cff > color sel #ffbf2bff > color sel #ffb82bff > color sel #ffb12aff > color sel #ffad2aff > color sel #ffad29ff > color sel #ffa629ff > color sel #ffa527ff > color sel #ff9a26ff > color sel #ff9225ff > color sel #ff7e22ff > color sel #ff7a21ff > color sel #ff6a20ff > color sel #ff6720ff > color sel #ff5f20ff > color sel #ff5820ff > color sel #ff5420ff > color sel #ff4d20ff > color sel #ff4520ff > color sel #ff4120ff > color sel #ff3b21ff > color sel #ff3422ff > color sel #ff3223ff > color sel #ff2a23ff > color sel #ff2525ff > color sel #ff2626ff > color sel #ff2929ff > color sel #ff2b2bff > color sel #ff3030ff > color sel #ff3a3aff > color sel #ff4545ff > color sel #ff4e4eff > color sel #ff5353ff > color sel #ff5959ff > color sel #ff6363ff > color sel #ff6e6eff > color sel #ff7777ff > color sel #ff8585ff > color sel #ff9292ff > color sel #ffaca1ff > color sel #ffbcabff > color sel #ffc4b0ff > color sel #ffceb8ff > color sel #ffd8c1ff > color sel #ffe1c9ff > color sel #ffe9d2ff > color sel #ffebd5ff > color sel #fff0dcff > color sel #fff2ddff > color sel #fff4e1ff > color sel #fff5e2ff > color sel #fff7e6ff > color sel #fff8e6ff > color sel #fff8e7ff > color sel #fff9eaff > color sel #fffaedff > color sel #fffbeeff > color sel #fffbf0ff > color sel #fffcf2ff > color sel #fffcf3ff > color sel #fffdf4ff > color sel #fffef4ff > color sel #fffff4ff > color sel #fefff4ff > color sel #fcfff2ff > color sel #fafff2ff > color sel #f7fff2ff > color sel #f4fff2ff > color sel #f2fff5ff > color sel #f2fff7ff > color sel #f2fff9ff > color sel #f2fffbff > color sel #f2fffcff > color sel #f2fffeff > color sel #f2feffff > color sel #f2fdffff > color sel #f2fcffff > color sel #f2faffff > color sel #f2f9ffff > color sel #f2f6ffff > color sel #f2f4ffff > color sel #f2f2ffff > color sel #f3f2ffff > color sel #f4f2ffff > color sel #f5f2ffff > color sel #f6f2ffff > color sel #f7f2ffff > color sel #f8f2ffff > color sel #f9f2ffff > color sel #faf0ffff > color sel #fbf0ffff > color sel #fdefffff > color sel #ffeeffff > color sel #ffeefdff > color sel #ffeefcff > color sel #ffeefbff > color sel #ffedfaff > color sel #ffebf9ff > color sel #ffebf7ff > color sel #ffeaf7ff > color sel #ffe6f5ff > color sel #ffdbecff > color sel #ffcbdfff > color sel #ffc6d8ff > color sel #ffb3c3ff > color sel #ffa6b9ff > color sel #ff9eb3ff > color sel #ff93aaff > color sel #ff8ba6ff > color sel #ff81a3ff > color sel #ff7ba5ff > color sel #ff74a5ff > color sel #ff6ea8ff > color sel #ff66a8ff > color sel #ff62a9ff > color sel #ff61a8ff > color sel #ff60adff > color sel #ff5eacff > color sel #ff5eb1ff > color sel #ff60bfff > color sel #ff62c8ff > color sel #ff66e3ff > color sel #ff6af0ff > color sel #ff6bfdff > color sel #ff6bffff > color sel #fa6cffff > color sel #f36effff > color sel #ee6effff > color sel #e96effff > color sel #db6effff > color sel #c96bffff > color sel #bc6affff > color sel #ac69ffff > color sel #a467ffff > color sel #9f67ffff > color sel #9a67ffff > color sel #9966ffff > color sel #9166ffff > color sel #8c66ffff > color sel #8c65ffff > color sel #7d63ffff > color sel #7462ffff > color sel #6661ffff > color sel #6068ffff > color sel #5e69ffff > color sel #5e6effff > color sel #5d73ffff > color sel #5c74ffff > color sel #5c7affff > color sel #5a78ffff > color sel #5473ffff > color sel #4b66ffff > color sel #435cffff > color sel #3e51ffff > color sel #3a47ffff > color sel #3946ffff > color sel #3845ffff > color sel #3744ffff > color sel #3542ffff > color sel #3442ffff > color sel #3341ffff > color sel #333dffff > color sel #313bffff > color sel #303affff > color sel #2f39ffff > color sel #2e38ffff > color sel #2c37ffff > color sel #2b36ffff > color sel #2934ffff > color sel #2732ffff > color sel #2631ffff > color sel #2530ffff > color sel #232effff > color sel #222dffff > color sel #212cffff > color sel #202bffff > color sel #1e29ffff > color sel #1d28ffff > color sel #1d2cffff > color sel #1c2bffff > color sel #1a29ffff > color sel #1928ffff > color sel #1930ffff > color sel #182fffff > color sel #1837ffff > color sel #1736ffff > color sel #1534ffff > color sel #1538ffff > color sel #1437ffff > color sel #1336ffff > color sel #133effff > color sel #113dffff > color sel #103cffff > color sel #0f3bffff > color sel #0e3affff > color sel #0e32ffff > color sel #0f33ffff > color sel #113dffff > color sel #184effff > color sel #1d61ffff > color sel #2277ffff > color sel #2785ffff > color sel #2b91ffff > color sel #2f9effff > color sel #31a6ffff > color sel #33a7ffff > color sel #33adffff > color sel #33b1ffff > color sel #34b1ffff > color sel #34bfffff > color sel #34c9ffff > color sel #34f5ffff > color sel #35ffe7ff > color sel #35ffd7ff > color sel #35ffd3ff > color sel #37ffc6ff > color sel #37ffc3ff > color sel #38ffc3ff > color sel #38ffc7ff > color sel #38ffcdff > color sel #38ffd4ff > color sel #38ffd7ff > color sel #39ffd7ff > color sel #39ffdeff > color sel #39ffe1ff > color sel #39ffe8ff > color sel #3affe8ff > color sel #3dffe8ff > color sel #3effe8ff > color sel #40ffe9ff > color sel #45ffe9ff > color sel #4cffe4ff > color sel #57ffe6ff > color sel #5cffe4ff > color sel #63ffe5ff > color sel #6affe1ff > color sel #6effe2ff > color sel #74ffe1ff > color sel #7dffe3ff > color sel #82ffe0ff > color sel #87ffe1ff > color sel #8affe2ff > color sel #8bffe2ff > color sel #8cffe2ff > color sel #8effe3ff > color sel #8fffe3ff > select clear > lighting soft > graphics silhouettes true > graphics silhouettes false > cartoon style xsection rectangle modeHelix default > graphics silhouettes true > cartoon style coil xsection oval > cartoon style xsection barbell modeHelix default > select ligand 53 atoms, 52 bonds, 1 residue, 1 model selected > color sel purple > select clear > cartoon style modeHelix tube sides 20 > cartoon style xsection oval modeHelix default > select /A 3617 atoms, 3413 bonds, 690 residues, 1 model selected > color sel dark gray > select clear > select /C 164 atoms, 150 bonds, 36 residues, 1 model selected > color sel purple > ui tool show "Color Actions" > color sel medium purple > select clear > lighting soft > graphics silhouettes false > lighting shadows true intensity 0.5 > graphics silhouettes true > lighting soft > lighting full > graphics silhouettes false > graphics silhouettes true > lighting soft > select ligand 53 atoms, 52 bonds, 1 residue, 1 model selected > color sel purple > select clear > select /C 164 atoms, 150 bonds, 36 residues, 1 model selected > ui tool show "Color Actions" > color sel medium purple > color sel #af7961ff > color sel #4b4b4bff > color sel #505050ff > color sel #171717ff > color sel #1e1e1eff > color sel #c885b6ff > color sel #a477c8ff > color sel #8e73c8ff > color sel #7f6cc8ff > color sel #6a67c8ff > color sel #6567c8ff > color sel #6469c8ff > color sel #6368c8ff > color sel #6267c7ff > color sel #6065c3ff > color sel #5e63bfff > color sel #585db3ff > color sel #5559acff > color sel #5458aaff > color sel #4e529eff > color sel #4c509aff > color sel #4d519cff > color sel #4c509aff > color sel #4b4f98ff > color sel #424686ff > color sel #3a3d75ff > color sel #313464ff > color sel #2a2d56ff > color sel #282a50ff > color sel #242548ff > color sel #1f203eff > color sel #1d1f3bff > color sel #1d1e3aff > color sel #222344ff > color sel #232547ff > color sel #2c2f5aff > color sel #2e305dff > color sel #303261ff > color sel #333567ff > color sel #34376aff > color sel #35386bff > color sel #36396dff > color sel #373a6fff > color sel #373a70ff > color sel #383b71ff > color sel #393c73ff > color sel #393c74ff > color sel #3a3d75ff > color sel #3b3e78ff > color sel #3c3f79ff > color sel #3c3f7aff > color sel #3d407cff > color sel #3e417dff > color sel #3f427fff > color sel #404381ff > color sel #414584ff > color sel #434687ff > color sel #434788ff > color sel #44488aff > color sel #45488bff > select clear > select sequence k145 Nothing selected > view > select /C 164 atoms, 150 bonds, 36 residues, 1 model selected > view sel > view > select clear > save C:\Users\Admin/Desktop\image26.png supersample 3 > show surfaces > select /C 164 atoms, 150 bonds, 36 residues, 1 model selected > color (#!1 & sel) dark gray > select clear > color #1 #aa557fff > color #1 #aa55ffff > color #1 #ff55ffff > color #1 #ff557fff > color #1 #aa557fff > graphics silhouettes false > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting soft > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > graphics silhouettes true > graphics silhouettes false > color #1 #6a3faaff > color #1 #aa1f9eff > color #1 #aa1977ff > color #1 #aa007fff > color #1 #aa00ffff > color #1 #aa557fff > view orient > color purple > color #1 #ca00caff > color #1 #f900f9ff > color #1 #aa007fff > color #1 #ff00bfff > color #1 magenta > color #1 #ff55ffff > graphics silhouettes true > graphics silhouettes false > lighting full > lighting soft > color #1 #ed89ffff > color #1 #e978ffff > color #1 #cb8bffff > view orient > save C:\Users\Admin/Desktop\image27.png supersample 3 > hide surfaces > show atoms > hide atoms > select ligand 53 atoms, 52 bonds, 1 residue, 1 model selected > show sel atoms > select clear > lighting soft > graphics silhouettes true > save C:\Users\Admin/Desktop\image28.png supersample 3 > show surfaces > hide surfaces > show surfaces > graphics silhouettes false > transparency 70 > save C:\Users\Admin/Desktop\image29.png supersample 3 > hide surfaces > graphics silhouettes true > save C:\Users\Admin/Desktop\image30.png supersample 3 > select ligand 53 atoms, 52 bonds, 1 residue, 1 model selected > color sel purple > select clear > open 9hdh 9hdh title: Structure of s.c.Osh6 in complex with Ist2 732-761 and POPS [more info...] Chain information for 9hdh #2 --- Chain \| Description \| UniProt A \| Oxysterol-binding protein homolog 6 \| OSH6_YEAST 31-448 C \| Increased sodium tolerance protein 2 \| IST2_YEAST 732-761 Non-standard residues in 9hdh #2 --- P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) > hide #!1 models > color #2 #c780ebff > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > color (#2 & sel) purple > select clear > save C:\Users\Admin/Desktop\image31.png supersample 3 > ui tool show "Side View" > view > color #2 #9e66bcff > color #2 #c27de7ff > save C:\Users\Admin/Desktop\image32.png supersample 3 > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > color (#2 & sel) purple > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > view sel > view > select clear > save C:\Users\Admin/Desktop\image33.png supersample 3 > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > view sel > save C:\Users\Admin/Desktop\image34.png supersample 3 > select clear > save C:\Users\Admin/Desktop\image35.png supersample 3 > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > view sel > surface (#2 & sel) > select clear > transparency #2 60 > select clear > color sel yellow > select clear > color sel yellow > color sel byhetero > select #2/A:501@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select #2/A:501@CA 1 atom, 1 residue, 1 model selected > select #2/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #2/A:67 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select clear Drag select of 9hdh_A SES surface, 543 of 13738 triangles, 4 atoms, 4 residues, 3 bonds > select clear > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:501@C34 1 atom, 1 residue, 1 model selected > select clear > select #2/A:86 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:79 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:160 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select clear Drag select of 9hdh_A SES surface, 152 of 13738 triangles, 2 atoms, 1 residues > select clear > select #2/A:501@O18 1 atom, 1 residue, 1 model selected > select clear > select #2/A:129 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #2/A:67@CA 1 atom, 1 residue, 1 model selected > color sel byhetero > select #2/A:64@CA 1 atom, 1 residue, 1 model selected > color sel byhetero > select #2/A:79 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #2/A:79 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero Drag select of 1 residues, 1 bonds > select clear > select #2/A:164@CA 1 atom, 1 residue, 1 model selected > select clear Drag select of 4 residues > select clear > select #2/A:164 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:127 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select #2/A:126@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:126 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:501@C21 1 atom, 1 residue, 1 model selected > select clear > select #2/A:126 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #2/A:127@N 1 atom, 1 residue, 1 model selected > select #2/A:127@N 1 atom, 1 residue, 1 model selected > select #2/A:127@N 1 atom, 1 residue, 1 model selected > select #2/A:127@N 1 atom, 1 residue, 1 model selected > select clear > select #2/A:127@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:127@CD 1 atom, 1 residue, 1 model selected > select #2/A:127@CD 1 atom, 1 residue, 1 model selected > select clear > select #2/A:127@N 1 atom, 1 residue, 1 model selected > select clear > select #2/A:127 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select #2/A:501@C33 1 atom, 1 residue, 1 model selected > select clear > graphics silhouettes false > select #2/A:192 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > graphics silhouettes true > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > hide sel & #!2 surfaces > color sel & #!2 byhetero > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > show sel & #!2 surfaces > select clear > select #2/A:112 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #2/A 3619 atoms, 3413 bonds, 692 residues, 1 model selected > surface (#!2 & sel) > select add #2 3847 atoms, 3627 bonds, 737 residues, 4 models selected > select subtract #2 2 models selected > select add #1 3781 atoms, 3563 bonds, 726 residues, 1 model selected > select subtract #1 2 models selected > select add #2 3847 atoms, 3627 bonds, 737 residues, 2 models selected > graphics silhouettes false > transparency (#!2 & sel) 80 > select clear > cartoon hide #2 > hide #!2 surfaces > lighting soft > graphics silhouettes true > label #2 text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > select #2/A:183@O 1 atom, 1 residue, 1 model selected > select #2/A:183@O 1 atom, 1 residue, 1 model selected > select #2/A:183@N 1 atom, 1 residue, 1 model selected > select clear > select #2/A:183@OG 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select #2/A:183@CA 1 atom, 1 residue, 1 model selected > select #2/A:183@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:183@N 1 atom, 1 residue, 1 model selected > select clear > select #2/A:183@OG 1 atom, 1 residue, 1 model selected > select #2/A:183@OG 1 atom, 1 residue, 1 model selected > select #2/A:183@O 1 atom, 1 residue, 1 model selected > select #2/A:183@O 1 atom, 1 residue, 1 model selected > select clear > select #2/A:183@CA 1 atom, 1 residue, 1 model selected > select #2/A:183@CA 1 atom, 1 residue, 1 model selected > select #2/A:65@OG1 1 atom, 1 residue, 1 model selected > select #2/A:65@CA 1 atom, 1 residue, 1 model selected > select clear > select #2/A:65@CB 1 atom, 1 residue, 1 model selected > select #2/A:65@OG1 1 atom, 1 residue, 1 model selected > select #2/A:65@CG2 1 atom, 1 residue, 1 model selected > select #2/A:65@CB 1 atom, 1 residue, 1 model selected > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > surface (#!2 & sel) > set bgColor black > set bgColor transparent > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Admin/Desktop\movie11.mp4 Movie saved to C:\Users\Admin/Desktop\movie11.mp4 > select clear > view orient > view > set bgColor white > set bgColor #ffffff00 > view orient > save C:\Users\Admin/Desktop\image36.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Admin/Desktop\movie12.mp4 Movie saved to C:\Users\Admin/Desktop\movie12.mp4 > set bgColor black > set bgColor transparent > show #!2 cartoons > ~label #2 residues > set bgColor white > set bgColor #ffffff00 > view orient > save C:\Users\Admin/Desktop\image37.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Admin/Desktop\movie13.mp4 Movie saved to C:\Users\Admin/Desktop\movie13.mp4 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Admin/Desktop\movie14.mp4 C:\Program Files\ChimeraX 1.10.dev202501142332\bin\ffmpeg.exe -r 25 -i C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm -vf crop=floor(in_w/2)2:floor(in_h/2)2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt yuv420p -crf 20 C:\Users\Admin/Desktop\movie14.mp4 stdout: stderr: ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers built with gcc 6.3.0 (GCC) configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable- fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable- libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable- libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable- libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable- libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable- lzma --enable-zlib libavutil 55. 34.101 / 55. 34.101 libavcodec 57. 64.101 / 57. 64.101 libavformat 57. 56.101 / 57. 56.101 libavdevice 57. 1.100 / 57. 1.100 libavfilter 6. 65.100 / 6. 65.100 libswscale 4. 2.100 / 4. 2.100 libswresample 2. 3.100 / 2. 3.100 libpostproc 54. 1.100 / 54. 1.100 Input #0, image2, from 'C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm': Duration: 00:00:07.20, start: 0.000000, bitrate: N/A Stream #0:0: Video: ppm, rgb24, 1116x491, 25 fps, 25 tbr, 25 tbn, 25 tbc [libx264 @ 0000000001055760] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 AVX2 LZCNT BMI2 [libx264 @ 0000000001055760] profile High, level 3.1 [libx264 @ 0000000001055760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 Output #0, mp4, to 'C:\Users\Admin/Desktop\movie14.mp4': Metadata: encoder : Lavf57.56.101 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1116x490, q=-1--1, 25 fps, 12800 tbn, 25 tbc Metadata: encoder : Lavc57.64.101 libx264 Side data: cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 Stream mapping: Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) Press [q] to stop, [?] for help frame= 58 fps=0.0 q=25.0 size= 159kB time=00:00:00.20 bitrate=6511.4kbits/s speed=0.368x frame= 101 fps= 96 q=25.0 size= 910kB time=00:00:01.92 bitrate=3882.6kbits/s speed=1.83x frame= 145 fps= 93 q=25.0 size= 1657kB time=00:00:03.68 bitrate=3687.7kbits/s speed=2.37x frame= 180 fps= 77 q=-1.0 Lsize= 3112kB time=00:00:07.08 bitrate=3600.2kbits/s speed=3.04x video:3109kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.095030% [libx264 @ 0000000001055760] frame I:1 Avg QP: 8.08 size: 28439 [libx264 @ 0000000001055760] frame P:45 Avg QP:21.44 size: 23225 [libx264 @ 0000000001055760] frame B:134 Avg QP:26.40 size: 15738 [libx264 @ 0000000001055760] consecutive B-frames: 0.6% 0.0% 1.7% 97.8% [libx264 @ 0000000001055760] mb I I16..4: 84.9% 0.0% 15.1% [libx264 @ 0000000001055760] mb P I16..4: 0.5% 0.7% 6.4% P16..4: 2.2% 3.4% 4.6% 0.0% 0.0% skip:82.1% [libx264 @ 0000000001055760] mb B I16..4: 0.1% 0.1% 1.2% B16..8: 3.6% 4.2% 7.8% direct: 0.6% skip:82.4% L0:42.7% L1:38.3% BI:19.0% [libx264 @ 0000000001055760] 8x8 transform intra:7.2% inter:2.3% [libx264 @ 0000000001055760] coded y,uvDC,uvAC intra: 69.6% 74.6% 73.7% inter: 7.4% 5.3% 4.0% [libx264 @ 0000000001055760] i16 v,h,dc,p: 87% 7% 6% 0% [libx264 @ 0000000001055760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 5% 7% 85% 1% 0% 0% 0% 0% 0% [libx264 @ 0000000001055760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 11% 21% 7% 10% 10% 11% 9% 8% [libx264 @ 0000000001055760] i8c dc,h,v,p: 66% 12% 13% 9% [libx264 @ 0000000001055760] Weighted P-Frames: Y:2.2% UV:0.0% [libx264 @ 0000000001055760] ref P L0: 53.3% 10.7% 22.0% 13.7% 0.3% [libx264 @ 0000000001055760] ref B L0: 82.9% 13.3% 3.7% [libx264 @ 0000000001055760] ref B L1: 93.6% 6.4% [libx264 @ 0000000001055760] kb/s:3536.13 Exiting normally, received signal 15. An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: \----------------------------- Exit value: 3221225786 Error message: stdout: stderr: ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers built with gcc 6.3.0 (GCC) configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable- fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable- libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable- libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable- libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable- libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable- lzma --enable-zlib libavutil 55. 34.101 / 55. 34.101 libavcodec 57. 64.101 / 57. 64.101 libavformat 57. 56.101 / 57. 56.101 libavdevice 57. 1.100 / 57. 1.100 libavfilter 6. 65.100 / 6. 65.100 libswscale 4. 2.100 / 4. 2.100 libswresample 2. 3.100 / 2. 3.100 libpostproc 54. 1.100 / 54. 1.100 Input #0, image2, from 'C:\Users\Admin\AppData\Local\Temp\chimovie_Dng2-%05d.ppm': Duration: 00:00:07.20, start: 0.000000, bitrate: N/A Stream #0:0: Video: ppm, rgb24, 1116x491, 25 fps, 25 tbr, 25 tbn, 25 tbc [libx264 @ 0000000001055760] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 AVX2 LZCNT BMI2 [libx264 @ 0000000001055760] profile High, level 3.1 [libx264 @ 0000000001055760] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00 Output #0, mp4, to 'C:\Users\Admin/Desktop\movie14.mp4': Metadata: encoder : Lavf57.56.101 Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1116x490, q=-1--1, 25 fps, 12800 tbn, 25 tbc Metadata: encoder : Lavc57.64.101 libx264 Side data: cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1 Stream mapping: Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264)) Press [q] to stop, [?] for help frame= 58 fps=0.0 q=25.0 size= 159kB time=00:00:00.20 bitrate=6511.4kbits/s speed=0.368x frame= 101 fps= 96 q=25.0 size= 910kB time=00:00:01.92 bitrate=3882.6kbits/s speed=1.83x frame= 145 fps= 93 q=25.0 size= 1657kB time=00:00:03.68 bitrate=3687.7kbits/s speed=2.37x frame= 180 fps= 77 q=-1.0 Lsize= 3112kB time=00:00:07.08 bitrate=3600.2kbits/s speed=3.04x video:3109kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.095030% [libx264 @ 0000000001055760] frame I:1 Avg QP: 8.08 size: 28439 [libx264 @ 0000000001055760] frame P:45 Avg QP:21.44 size: 23225 [libx264 @ 0000000001055760] frame B:134 Avg QP:26.40 size: 15738 [libx264 @ 0000000001055760] consecutive B-frames: 0.6% 0.0% 1.7% 97.8% [libx264 @ 0000000001055760] mb I I16..4: 84.9% 0.0% 15.1% [libx264 @ 0000000001055760] mb P I16..4: 0.5% 0.7% 6.4% P16..4: 2.2% 3.4% 4.6% 0.0% 0.0% skip:82.1% [libx264 @ 0000000001055760] mb B I16..4: 0.1% 0.1% 1.2% B16..8: 3.6% 4.2% 7.8% direct: 0.6% skip:82.4% L0:42.7% L1:38.3% BI:19.0% [libx264 @ 0000000001055760] 8x8 transform intra:7.2% inter:2.3% [libx264 @ 0000000001055760] coded y,uvDC,uvAC intra: 69.6% 74.6% 73.7% inter: 7.4% 5.3% 4.0% [libx264 @ 0000000001055760] i16 v,h,dc,p: 87% 7% 6% 0% [libx264 @ 0000000001055760] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 5% 7% 85% 1% 0% 0% 0% 0% 0% [libx264 @ 0000000001055760] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 11% 21% 7% 10% 10% 11% 9% 8% [libx264 @ 0000000001055760] i8c dc,h,v,p: 66% 12% 13% 9% [libx264 @ 0000000001055760] Weighted P-Frames: Y:2.2% UV:0.0% [libx264 @ 0000000001055760] ref P L0: 53.3% 10.7% 22.0% 13.7% 0.3% [libx264 @ 0000000001055760] ref B L0: 82.9% 13.3% 3.7% [libx264 @ 0000000001055760] ref B L1: 93.6% 6.4% [libx264 @ 0000000001055760] kb/s:3536.13 Exiting normally, received signal 15. \----------------------------- > ui tool show "Selection Inspector" > volume planes z style image imageMode "full region" No volumes specified > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > view sel > select clear > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Admin/Desktop\movie14.mp4 Movie saved to C:\Users\Admin/Desktop\movie14.mp4 > save "C:/Users/Admin/Downloads/cndntng gn.png" width 1116 height 491 > supersample 3 > color #2 #c37ee8ff > view orient > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > hide sel & #!2 surfaces > color (#!2 & sel) purple > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > show sel & #!2 surfaces > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > view sel > select clear > select ligand 106 atoms, 104 bonds, 2 residues, 2 models selected > hide sel & #!2 surfaces > select clear > close #1 > color #2 #00aa7fff > color #2 #50a9aaff > color #2 #2ba8aaff > color #2 #3ae2e5ff > color #2 #32c1c3ff > select clear > color #2 #be1fc3ff > color #2 #aa007fff > color #2 #ff00bfff > color byhetero > color bychain > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > style sel stick Changed 228 atom styles > show sel atoms > color sel byhetero > select ::name="HOH" 309 atoms, 309 residues, 1 model selected > hide sel atoms > color #2 #edeee7ff > color #2 #c6c7c1ff > color #2 #b8b9b3ff > color #2 #a7a8a3ff > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > ui tool show "Color Actions" > color sel medium purple > select clear > color #2 #b7b8b2ff > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > color #2 #aa007fff > select clear > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > select clear > select /A 3619 atoms, 3413 bonds, 692 residues, 1 model selected > color (#!2 & sel) dark gray > select clear > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > ui tool show "Color Actions" > color sel light blue > color sel dark violet > select clear > view orient > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > view sel > color sel byhetero > select clear > view orient > select /C 228 atoms, 214 bonds, 45 residues, 1 model selected > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > set bgColor white > set bgColor gray > set bgColor #80808000 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > save C:\Users\Admin/Desktop\image38.png supersample 3 > ~label #2 residues > ui tool show "Show Sequence Viewer" > sequence chain /A Alignment identifier is 2/A > ui tool show "Show Sequence Viewer" > sequence chain /C Alignment identifier is 2/C > select /C:732 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:732 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select > /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437 1124 atoms, 1139 bonds, 136 residues, 1 model selected > select /A:391 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:391 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select /A:420 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:420 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select /A:405 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:405 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select > /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437 1124 atoms, 1139 bonds, 136 residues, 1 model selected > select /A:408 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:408 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select /A:404 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:404 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select > /A:39-56,70-72,79-86,89-98,101-116,169-171,319-323,327-341,343-369,399-411,420-437 1124 atoms, 1139 bonds, 136 residues, 1 model selected > select /A:170 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:170 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select /A:145 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:145 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > hide atoms > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > undo > hide cartoons > undo > save C:\Users\Admin/Desktop\image39.png supersample 3 > hide cartoons Drag select of 177 atoms, 168 bonds Drag select of 169 atoms, 161 bonds > hide target m > undo > hide sel atoms ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 - Build 31.0.101.5522 OpenGL renderer: Intel(R) UHD Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_IN.cp1252 Qt version: PyQt6 6.8.0, Qt 6.8.1 Qt runtime version: 6.8.1 Qt platform: windows Manufacturer: LENOVO Model: 82KA OS: Microsoft Windows 11 Pro (Build 26200) Memory: 4,084,523,008 MaxProcessMemory: 137,438,953,344 CPU: 4 11th Gen Intel(R) Core(TM) i3-1115G4 @ 3.00GHz OSLanguage: en-GB Installed Packages: alabaster: 1.0.0 anyio: 4.8.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.2.0 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: 1.60 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.dev202501142332 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-NIHPresets: 1.2.8 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: 1.6.3 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: 1.43 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: 3.1.5 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 pickleshare: 0.7.5 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: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.0 PyQt6-Qt6: 6.8.1 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.1 PyQt6_sip: 13.9.1 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
#19988	duplicate	Crash on Mac waking from sleep	Tom Goddard	a.fasemire@…
Description	The following bug report has been submitted: Platform: macOS-15.7.4-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000031c8fb000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000000031b8ef000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000000031a8e3000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x00000003198d7000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x00000003188cb000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x00000003178bf000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x00000003168b3000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x00000003158a7000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000000031489b000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000000031388f000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000000312883000 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Current thread 0x00000001fd0fe240 (most recent call first): File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54) 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"procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"1285D59A-DC79-5D40-B366-2F3C3C4E451C","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "31E19731-CFC0-05F8-DC37-45557C23533F", "appleIntelligenceStatus" : {"state":"restricted","reasons":["siriAssetIsNotReady","assetIsNotReady"]}, "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "codeSigningAuxiliaryInfo" : 0, "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="}, "bootSessionUUID" : "EC65655E-BA96-4622-B5B0-4D24C1466F0D", "wakeTime" : 7023, "sleepWakeUUID" : "72A578B2-C187-41DB-9942-6578E7EC83F4", "sip" : "enabled", "vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4303109783\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1007c4000-1007c8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX", "exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40923}, "vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4303109783\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1007c4000-1007c8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX", "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 0, "threads" : 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"arch" : "arm64e", "base" : 6719025152, "CFBundleShortVersionString" : "6.9", "CFBundleIdentifier" : "com.apple.Foundation", "size" : 14587328, "uuid" : "7c9aba87-468a-3830-86e2-6ac8f8105acd", "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation", "name" : "Foundation", "CFBundleVersion" : "3603.1.405" }, { "source" : "P", "arch" : "arm64e", "base" : 6691389440, "size" : 342164, "uuid" : "e6f30eb4-facf-3381-ae46-10e556f1fc39", "path" : "\/usr\/lib\/libobjc.A.dylib", "name" : "libobjc.A.dylib" } ], "sharedCache" : { "base" : 6690897920, "size" : 5039783936, "uuid" : "06500f56-f17f-34b5-bbbb-ca9b1caea316" }, "vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=3.6G written=79.8M(2%) resident=2168K(0%) swapped_out=77.7M(2%) unallocated=3.5G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 368K 20 \nColorSync 624K 33 \nCoreAnimation 1872K 112 \nCoreGraphics 48K 3 \nCoreServices 9616K 2 \nCoreUI image data 4656K 33 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 97 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 363.3M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 323.6M 221 \nVM_ALLOCATE (reserved) 96.0M 3 reserved VM address space (unallocated)\n__AUTH 5517K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 34.9M 1112 \n__DATA_CONST 37.5M 1130 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 654.1M 181 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2397K 1 \n__TEXT 1.3G 1148 \n__TEXT (graphics) 1696K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 5936K 48 \nmapped file 280.2M 62 \npage table in kernel 2168K 1 \nshared memory 3152K 21 \n=========== ======= ======= \nTOTAL 6.1G 6326 \nTOTAL, minus reserved VM space 6.0G 6326 \n", "legacyInfo" : { "threadTriggered" : { "name" : "CrBrowserMain", "queue" : "com.apple.main-thread" } }, "logWritingSignature" : "bfdf5344846e316b6e81bdca7905296f7f169039", "trialInfo" : { "rollouts" : [ { "rolloutId" : "63f9578e238e7b23a1f3030a", "factorPackIds" : { }, "deploymentId" : 240000005 }, { "rolloutId" : "65a8173205d942272410674b", "factorPackIds" : { "SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION" : "65d39fa4cb0e2417d11ce5f6" }, "deploymentId" : 240000001 } ], "experiments" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_0.pdb" > format pdb Chain information for model_0.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure > set bgColor white > color byattribute a:bfactor 7847 atoms, 487 residues, atom bfactor range 0.245 to 2.81 > worm bfactor 487 residues, residue bfactor range 0.245 to 2.81 > graphics silhouettes true > lighting intensity 0.7 > lighting intensity 0.9 > lighting intensity 1.5 > lighting intensity 1.2 > worm bfactor 487 residues, residue bfactor range 0.245 to 2.81 > worm bfactor min:0.2 max:0.7 487 residues, residue bfactor range 0.245 to 2.81 > ui tool show "Side View" > cd "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/flexible_mode/new_worms" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact map/1IRA/CABSflex_Video/wiki_tutorial/flexible_mode/new_worms > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > set bgColor white > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_1.pdb" Chain information for model_1.pdb #2 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_2.pdb" Chain information for model_2.pdb #3 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_3.pdb" Chain information for model_3.pdb #4 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_4.pdb" Chain information for model_4.pdb #5 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_5.pdb" Chain information for model_5.pdb #6 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_6.pdb" Chain information for model_6.pdb #7 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_7.pdb" Chain information for model_7.pdb #8 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_8.pdb" Chain information for model_8.pdb #9 --- Chain \| Description A \| No description available > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_9.pdb" Chain information for model_9.pdb #10 --- Chain \| Description A \| No description available Computing secondary structure > worm bfactor min:0.2 max:0.7 4870 residues, residue bfactor range 0.245 to 2.81 > color byattribute a:bfactor 78470 atoms, 4870 residues, atom bfactor range 0.245 to 2.81 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > close > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1C9S_flexible/1C9S_flexible_with_rmsf/model_0.pdb" Chain information for model_0.pdb #1 --- Chain \| Description A D F H I K \| No description available B E \| No description available C \| No description available G \| No description available J \| No description available > show atoms > hide atoms > show cartoons Computing secondary structure > color byattribute a:bfactor 11824 atoms, 756 residues, atom bfactor range 0.07 to 1.05 > worm bfactor 756 residues, residue bfactor range 0.07 to 1.05 > worm bfactor min:0.2 max:0.7 756 residues, residue bfactor range 0.07 to 1.05 > worm bfactor min:0.2 max:0.9 756 residues, residue bfactor range 0.07 to 1.05 > save 19CS_worm.png width 2000 supersample 4 > lighting simple > lighting intensity 1.2 > lighting intensity 1.5 > save 19CS_worm.png width 2000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > lighting depthCue false > lighting depthCue true > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > save 19CS_worm.png width 2000 supersample 4 > close > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1g0y_flexible/1g0y_flexible_with_rmsf/model_0.pdb" Chain information for model_0.pdb #1 --- Chain \| Description R \| No description available Computing secondary structure > color byattribute a:bfactor 4982 atoms, 310 residues, atom bfactor range 0.18 to 1.39 > worm bfactor min:0.2 max:0.9 310 residues, residue bfactor range 0.18 to 1.39 > worm bfactor min:0.2 max:0.7 310 residues, residue bfactor range 0.18 to 1.39 > worm bfactor min:0.2 max:0.9 310 residues, residue bfactor range 0.18 to 1.39 > save 1GOY_worm.png width 2000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > close > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1IJZ_flexible/1IJZ_flexible_with_rmsf/model_0.pdb" Chain information for model_0.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure > color byattribute a:bfactor 1770 atoms, 113 residues, atom bfactor range 0.473 to 1.74 > worm bfactor min:0.2 max:0.9 113 residues, residue bfactor range 0.473 to 1.74 > worm bfactor min:0.2 max:0.7 113 residues, residue bfactor range 0.473 to 1.74 > worm bfactor min:0.2 max:0.8 113 residues, residue bfactor range 0.473 to 1.74 > save 1IJZ_worm.png width 2000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > close > open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact > map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_0.pdb" Chain information for model_0.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure > color byattribute a:bfactor 7847 atoms, 487 residues, atom bfactor range 0.245 to 2.81 > worm bfactor min:0.2 max:0.9 487 residues, residue bfactor range 0.245 to 2.81 > worm bfactor min:0.2 max:0.7 487 residues, residue bfactor range 0.245 to 2.81 > worm bfactor min:0.2 max:0.8 487 residues, residue bfactor range 0.245 to 2.81 > save 1EOV_worm.png width 2000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Air Model Identifier: Mac15,12 Model Number: MXCV3ZE/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.4 (24G517) Kernel Version: Darwin 24.6.0 Time since boot: 14 days, 14 hours, 32 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal P24h-2L: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz 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 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 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-Clipper: 0.24.0 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-ISOLDE: 1.9 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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 MolecularDynamicsViewer: 1.6 more-itertools: 10.3.0 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 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 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 platformdirs: 4.2.2 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 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2

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Query Language

query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).

The available operators are:

`=`	the field content exactly matches one of the values
`~=`	the field content contains one or more of the values
`^=`	the field content starts with one of the values
`$=`	the field content ends with one of the values

All of these operators can also be negated:

`!=`	the field content matches none of the values
`!~=`	the field content does not contain any of the values
`!^=`	the field content does not start with any of the values
`!$=`	the field content does not end with any of the values

The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.

`created=2007-01-01..2008-01-01`	query tickets created in 2007
`created=lastmonth..thismonth`	query tickets created during the previous month
`modified=1weekago..`	query tickets that have been modified in the last week
`modified=..30daysago`	query tickets that have been inactive for the last 30 days

See also: TracTickets, TracReports, TracGuide, TicketQuery

Last modified 9 years ago Last modified on Jan 4, 2017, 10:45:36 AM

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Query Language

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