![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Trac Ticket Queries
Table of Contents
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:
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:
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 13968)
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 13968)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20481 | duplicate | Multiple consecutive Find Cavities: dead models | ||
| Description |
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\alexa\Desktop\SCIENCE\Research\HU_AF-Q8DPT3-F1-model_v6.pdb
> format pdb
HU_AF-Q8DPT3-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for DNA-binding protein hu (Q8DPT3) [more
info...]
Chain information for HU_AF-Q8DPT3-F1-model_v6.pdb #1
---
Chain | Description | UniProt
A | DNA-binding protein hu | Q8DPT3_STRR6 1-91
Computing secondary structure
> close session
> help help:quickstart
> open "C:/Users/alexa/Desktop/SCIENCE/Research/AF-Q8DPI9-F1-Topo I R6.pdb"
AF-Q8DPI9-F1-Topo I R6.pdb title:
Alphafold monomer V2.0 prediction for DNA topoisomerase 1 (Q8DPI9) [more
info...]
Chain information for AF-Q8DPI9-F1-Topo I R6.pdb #1
---
Chain | Description | UniProt
A | DNA topoisomerase 1 | Q8DPI9_STRR6 1-701
Computing secondary structure
> set bgColor black
> ui tool show "Find Cavities"
> kvfinder
33 cavities found for AF-Q8DPI9-F1-Topo I R6.pdb #1
AF-Q8DPI9-F1-Topo I R6.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.18 | | 610.85 | 607.48 | 2828 | 7.25 | 1.65
1.1.9 | | 182.52 | 116.62 | 845 | 2.55 | 0.77
1.1.27 | | 57.89 | 80.22 | 268 | 0 | 0
1.1.16 | | 57.46 | 87.69 | 266 | 0 | 0
1.1.25 | | 55.94 | 75.17 | 259 | 3.84 | 1.55
1.1.1 | | 50.98 | 60.95 | 236 | 3 | 1.03
1.1.12 | | 47.3 | 50.09 | 219 | 2.16 | 0.68
1.1.23 | | 46.66 | 37.25 | 216 | 1.8 | 0.53
1.1.31 | | 46.22 | 43.26 | 214 | 2.4 | 0.65
1.1.30 | | 31.97 | 42.35 | 148 | 1.8 | 0.6
1.1.4 | | 30.24 | 28.47 | 140 | 1.2 | 0.3
1.1.14 | | 29.59 | 31.66 | 137 | 1.8 | 0.42
1.1.29 | | 28.3 | 55.47 | 131 | 0 | 0
1.1.7 | | 26.57 | 27.12 | 123 | 1.04 | 0.25
1.1.11 | | 22.9 | 39.3 | 106 | 0 | 0
1.1.20 | | 21.6 | 36.41 | 100 | 1.34 | 0.35
1.1.22 | | 21.17 | 31.4 | 98 | 1.8 | 0.7
1.1.24 | | 20.74 | 41.19 | 96 | 0 | 0
1.1.33 | | 18.58 | 23.63 | 86 | 1.2 | 0.35
1.1.3 | | 17.93 | 27.46 | 83 | 1.99 | 0.71
1.1.26 | | 16.42 | 26.54 | 76 | 1.34 | 0.5
1.1.32 | | 15.98 | 25.52 | 74 | 1.2 | 0.31
1.1.13 | | 15.55 | 21.45 | 72 | 1.04 | 0.34
1.1.6 | | 12.96 | 20.59 | 60 | 1.2 | 0.26
1.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.8 | | 12.1 | 21.1 | 56 | 1.34 | 0.39
1.1.21 | | 10.15 | 16.62 | 47 | 1.34 | 0.42
1.1.19 | | 7.99 | 9.21 | 37 | 0.6 | 0.15
1.1.10 | | 7.56 | 12.55 | 35 | 0.6 | 0.07
1.1.15 | | 7.34 | 16.14 | 34 | 0.6 | 0.11
1.1.2 | | 5.62 | 12.58 | 26 | 0.85 | 0.3
1.1.28 | | 5.4 | 14.2 | 25 | 0.85 | 0.33
> kvfinder
33 cavities found for AF-Q8DPI9-F1-Topo I R6.pdb #1
AF-Q8DPI9-F1-Topo I R6.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.18 | | 610.85 | 607.48 | 2828 | 7.25 | 1.65
1.1.9 | | 182.52 | 116.62 | 845 | 2.55 | 0.77
1.1.27 | | 57.89 | 80.22 | 268 | 0 | 0
1.1.16 | | 57.46 | 87.69 | 266 | 0 | 0
1.1.25 | | 55.94 | 75.17 | 259 | 3.84 | 1.55
1.1.1 | | 50.98 | 60.95 | 236 | 3 | 1.03
1.1.12 | | 47.3 | 50.09 | 219 | 2.16 | 0.68
1.1.23 | | 46.66 | 37.25 | 216 | 1.8 | 0.53
1.1.31 | | 46.22 | 43.26 | 214 | 2.4 | 0.65
1.1.30 | | 31.97 | 42.35 | 148 | 1.8 | 0.6
1.1.4 | | 30.24 | 28.47 | 140 | 1.2 | 0.3
1.1.14 | | 29.59 | 31.66 | 137 | 1.8 | 0.42
1.1.29 | | 28.3 | 55.47 | 131 | 0 | 0
1.1.7 | | 26.57 | 27.12 | 123 | 1.04 | 0.25
1.1.11 | | 22.9 | 39.3 | 106 | 0 | 0
1.1.20 | | 21.6 | 36.41 | 100 | 1.34 | 0.35
1.1.22 | | 21.17 | 31.4 | 98 | 1.8 | 0.7
1.1.24 | | 20.74 | 41.19 | 96 | 0 | 0
1.1.33 | | 18.58 | 23.63 | 86 | 1.2 | 0.35
1.1.3 | | 17.93 | 27.46 | 83 | 1.99 | 0.71
1.1.26 | | 16.42 | 26.54 | 76 | 1.34 | 0.5
1.1.32 | | 15.98 | 25.52 | 74 | 1.2 | 0.31
1.1.13 | | 15.55 | 21.45 | 72 | 1.04 | 0.34
1.1.6 | | 12.96 | 20.59 | 60 | 1.2 | 0.26
1.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.8 | | 12.1 | 21.1 | 56 | 1.34 | 0.39
1.1.21 | | 10.15 | 16.62 | 47 | 1.34 | 0.42
1.1.19 | | 7.99 | 9.21 | 37 | 0.6 | 0.15
1.1.10 | | 7.56 | 12.55 | 35 | 0.6 | 0.07
1.1.15 | | 7.34 | 16.14 | 34 | 0.6 | 0.11
1.1.2 | | 5.62 | 12.58 | 26 | 0.85 | 0.3
1.1.28 | | 5.4 | 14.2 | 25 | 0.85 | 0.33
> kvfinder
33 cavities found for AF-Q8DPI9-F1-Topo I R6.pdb #1
AF-Q8DPI9-F1-Topo I R6.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.18 | | 610.85 | 607.48 | 2828 | 7.25 | 1.65
1.1.9 | | 182.52 | 116.62 | 845 | 2.55 | 0.77
1.1.27 | | 57.89 | 80.22 | 268 | 0 | 0
1.1.16 | | 57.46 | 87.69 | 266 | 0 | 0
1.1.25 | | 55.94 | 75.17 | 259 | 3.84 | 1.55
1.1.1 | | 50.98 | 60.95 | 236 | 3 | 1.03
1.1.12 | | 47.3 | 50.09 | 219 | 2.16 | 0.68
1.1.23 | | 46.66 | 37.25 | 216 | 1.8 | 0.53
1.1.31 | | 46.22 | 43.26 | 214 | 2.4 | 0.65
1.1.30 | | 31.97 | 42.35 | 148 | 1.8 | 0.6
1.1.4 | | 30.24 | 28.47 | 140 | 1.2 | 0.3
1.1.14 | | 29.59 | 31.66 | 137 | 1.8 | 0.42
1.1.29 | | 28.3 | 55.47 | 131 | 0 | 0
1.1.7 | | 26.57 | 27.12 | 123 | 1.04 | 0.25
1.1.11 | | 22.9 | 39.3 | 106 | 0 | 0
1.1.20 | | 21.6 | 36.41 | 100 | 1.34 | 0.35
1.1.22 | | 21.17 | 31.4 | 98 | 1.8 | 0.7
1.1.24 | | 20.74 | 41.19 | 96 | 0 | 0
1.1.33 | | 18.58 | 23.63 | 86 | 1.2 | 0.35
1.1.3 | | 17.93 | 27.46 | 83 | 1.99 | 0.71
1.1.26 | | 16.42 | 26.54 | 76 | 1.34 | 0.5
1.1.32 | | 15.98 | 25.52 | 74 | 1.2 | 0.31
1.1.13 | | 15.55 | 21.45 | 72 | 1.04 | 0.34
1.1.6 | | 12.96 | 20.59 | 60 | 1.2 | 0.26
1.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.8 | | 12.1 | 21.1 | 56 | 1.34 | 0.39
1.1.21 | | 10.15 | 16.62 | 47 | 1.34 | 0.42
1.1.19 | | 7.99 | 9.21 | 37 | 0.6 | 0.15
1.1.10 | | 7.56 | 12.55 | 35 | 0.6 | 0.07
1.1.15 | | 7.34 | 16.14 | 34 | 0.6 | 0.11
1.1.2 | | 5.62 | 12.58 | 26 | 0.85 | 0.3
1.1.28 | | 5.4 | 14.2 | 25 | 0.85 | 0.33
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 34, in data
val = col.display_value(item)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 886, in display_value
val = self.value(instance)
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 903, in value
return self.data_fetch(instance)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 201, in color_func
if s.display and s.atoms.displays.any():
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 529, in _get_display
return Model.display.fget(self)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 Core Profile Context 25.8.1.250617
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: pt_PT.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: LENOVO
Model: 82R4
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 14,870,306,816
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics
OSLanguage: pt-PT
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2025.6.15
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
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: 2.5.1
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: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.2.6
numpy: 1.26.4
nvidia-cuda-cupti-cu12: 12.9.79
nvidia-cuda-nvcc-cu12: 12.9.86
nvidia-cuda-nvrtc-cu12: 12.9.86
nvidia-cuda-runtime-cu12: 12.9.79
nvidia-cufft-cu12: 11.4.1.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.9.2
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.15.0
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
|
|||
| #20479 | limitation | KVFinder on old MacOS | ||
| Description |
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.12rc202606082314 (2026-06-08 23:14:43 UTC)
Description
tools: find cavity does not work
Log:
UCSF ChimeraX version: 1.12rc202606082314 (2026-06-08)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/henryyao/Desktop/MDSimulation/Pa_PASB4dock.pdb
Summary of feedback from opening
/Users/henryyao/Desktop/MDSimulation/Pa_PASB4dock.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK GENERATED BY TRJCONV
Pa_PASB4dock.pdb title:
Protein t= 1638000.00000 [more info...]
Chain information for Pa_PASB4dock.pdb #1
---
Chain | Description
A | No description available
> open /Users/henryyao/Desktop/MDSimulation/S215321r.pdb
> 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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
alp1jeq_/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
alp1jeq_/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
alp1jeq_/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
alp1jeq_/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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.
> hide #2 models
> 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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
iw_osh40/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
iw_osh40/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
iw_osh40/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
iw_osh40/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
twyprori/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
twyprori/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
twyprori/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
twyprori/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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 #2 models
> 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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-5f6m14zs/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-5f6m14zs/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-5f6m14zs/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-5f6m14zs/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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 Toolbar
> 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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-s720nq90/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-s720nq90/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-s720nq90/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-
env-s720nq90/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
ar3me3qg/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
ar3me3qg/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
ar3me3qg/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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/xd/ftyftsfj2z346y67hvqr5m780000gn/T/pip-build-env-
ar3me3qg/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12-rc2026.06.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12-rc2026.06.09.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-1.12-rc2026.06.09.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 - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 2 days, 17 hours, 22 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
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:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.2
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202606082314
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: 1.2.2
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: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
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: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
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: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
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: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.4.4
stack-data: 0.6.3
starlette: 1.2.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.1
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
|
|||
| #20478 | duplicate | glClear: invalid framebuffer operation on statusbar expose | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.1-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:
You can double click a model's Name or ID in the model panel to edit those
fields
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/yoji_PMG5/Downloads/fold_2026_06_09_14_49-2/fold_2026_06_09_14_49_model_0.cif
Summary of feedback from opening
/Users/yoji_PMG5/Downloads/fold_2026_06_09_14_49-2/fold_2026_06_09_14_49_model_0.cif
---
note | Fetching CCD FAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FAD/FAD.cif
Chain information for fold_2026_06_09_14_49_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> save /Users/yoji_PMG5/Desktop/AF3_human_MAO-A_with_FAD.pdb relModel #1
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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 218, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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 218, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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 218, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
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/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
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/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Error processing trigger "mouse hover":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
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/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
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/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
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/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Error processing trigger "mouse hover":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.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: Mac mini
Model Identifier: Mac16,10
Model Number: MU9E3J/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5.1 (25F80)
Kernel Version: Darwin 25.5.0
Time since boot: 6日 1時間 34分
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL S2722QC:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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
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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
Note:
See TracWiki
for help on using the wiki.
