wiki:TracQuery

Version 2 (modified by trac, 9 years ago) ( diff )

--

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.

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.

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

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

Which is displayed as:

Active tickets against 1.0

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

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

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

Which is displayed as:

Assigned tickets by owner

Customizing the table format

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

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

This is displayed as:

Results (1 - 3 of 13830)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20311 can't reproduce Match→Align associating to alignment: numpy error Eric Pettersen chimerax-bug-report@…
#20310 duplicate Crash deleting a QDockWidget involving QWindowContainer::parentWasChanged Tom Goddard chimerax-bug-report@…
#20309 can't reproduce UnicodeDecodeError reading PDB file Eric Pettersen chimerax-bug-report@…
1 2 3 4 5 6 7 8 9 10 11 →

Full rows

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

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

This is displayed as:

Results (1 - 3 of 13830)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20311 can't reproduce Match→Align associating to alignment: numpy error Eric Pettersen chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        macOS-14.8.3-x86_64-i386-64bit
ChimeraX Version: 1.12rc202605070126 (2026-05-07 01:26:37 UTC)
Description
ui tool show Match→Align
msa3d #2/A#3/A
Match→Align cutoff: 5.0, in column if within cutoff of: any 82 residue pairs aligned 110 fully populated columns 
Pairwise RMSDs across all fully populated columns
Model
2
3
2
0.000
28.811
3
28.811
0.000
Overall RMSD: 28.811 Sequence lengths: 110 522 SDM (cutoff 5.0): -247.145 Q-score: 0.002 Alignment identifier is MA-1 Showing conservation header ("seq_clustal_conservation" residue attribute) for alignment MA-1 Traceback (most recent call last):   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/tool.py", line 259, in match_align     run(self.session, "msa3d " + ' '.join(args))   File "/Applications/ChimeraX-1.12-rc2026.05.07.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-rc2026.05.07.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-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/cmd.py", line 225, in make_alignment     alignment.associate(orig, seq=aligned, silent=True)   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 386, in associate     do_assoc()   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 305, in do_assoc     self.prematched_assoc_structure(best_match_map, best_errors, reassoc)   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 742, in prematched_assoc_structure     self._set_residue_attributes(match_maps=[match_map])   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 1071, in _set_residue_attributes     values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 1071, in <listcomp>     values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))]                       ^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 691, in most_common     chars, counts = self.column_counts()[col_index]                     ^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 485, in column_counts     data = numpy.array([list(seq.characters) for seq in self._seqs])            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs])

Log:
UCSF ChimeraX version: 1.12rc202605070126 (2026-05-07)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

Log from Sun Jan 25 11:55:12 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

Log from Sun Jan 25 11:18:21 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs" format session

Log from Tue Jan 20 17:12:49 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs" format session

Log from Tue Jan 20 16:53:43 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

Log from Tue Jan 20 16:01:25 2026

> set bgColor light grey

> ui tool show "command line interface"

UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif format mmcif

6His-860_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 6His-860_0.cif #1  
---  
Chain | Description  
A | Entity A  
  
Color 6His-860_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> close session

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"
> format mmcif

850His_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 850His_0.cif #1  
---  
Chain | Description  
A | Entity A  
  
Color 850His_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"
> format mmcif

850His_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 850His_0.cif #2  
---  
Chain | Description  
A | Entity A  
  
Color 850His_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif

6His-860_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 6His-860_0.cif #3  
---  
Chain | Description  
A | Entity A  
  
Color 6His-860_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> ui tool show Matchmaker

> close #1

> ui tool show Matchmaker

> matchmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3),
sequence alignment score = 152.3  
RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs:
14.240)  
  

> ui tool show Matchmaker

> matchmaker #3 to #2 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3),
sequence alignment score = 152.3  
Alignment identifier is 1  
Showing conservation header ("seq_clustal_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 850His_0.cif #2/A,
6His-860_0.cif #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs:
14.240)  
  

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

——— End of log from Tue Jan 20 16:01:25 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #c0c0c0ff

[Repeated 1 time(s)]

> color sel #c0c0c0fa

> color sel #c0c0c0e5

> color sel #c0c0c0d5

> color sel #c0c0c0cf

> color sel #c0c0c0cc

> color sel #c0c0c0c7

> color sel #c0c0c0b8

> set bgColor white

> color sel #c0c0c0b6

> color sel #c0c0c0ac

> color sel #c0c0c0a9

> color sel #c0c0c09b

> color sel #c0c0c099

> color sel #c0c0c094

> color sel #c0c0c092

> color sel #c0c0c091

> color sel #c0c0c08f

> color sel #c0c0c08b

> color sel #c0c0c08a

> color sel #c0c0c088

> color sel #c0c0c081

> color sel #c0c0c079

> color sel #c0c0c072

> color sel #c0c0c071

> color sel #c0c0c0ff

> color sel #ebebebff

> color sel #d6d6d6ff

> color sel #ebebebff

> color sel #d6d6d6ff

> select clear

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #d6d6d6ff

> color sel #d6d6d6f7

> color sel #d6d6d6ec

> color sel #d6d6d6ea

> color sel #d6d6d6cb

> color sel #d6d6d6b1

> color sel #d6d6d6a9

> color sel #d6d6d694

> color sel #d6d6d686

> color sel #d6d6d67d

> color sel #d6d6d67b

> color sel #d6d6d678

> color sel #d6d6d66e

> color sel #d6d6d661

> color sel #d6d6d65a

[Repeated 1 time(s)]

> color sel #d6d6d66a

> color sel #d6d6d672

> color sel #d6d6d67e

> color sel #d6d6d687

> color sel #d6d6d693

> color sel #d6d6d695

> color sel #d6d6d697

> color sel #d6d6d698

> color sel #d6d6d656

> color sel #d6d6d615

> color sel #d6d6d604

> color sel #d6d6d600

> color sel #d6d6d611

> color sel #d6d6d635

> color sel #d6d6d646

> color sel #d6d6d64a

> color sel #d6d6d663

> color sel #d6d6d677

[Repeated 1 time(s)]

> color sel #d6d6d663

> color sel #d6d6d60a

> color sel #d6d6d600

> color sel #d6d6d60a

> color sel #d6d6d62c

> color sel #d6d6d632

> color sel #d6d6d631

> color sel #d6d6d62c

> color sel #d6d6d628

> color sel #d6d6d626

[Repeated 1 time(s)]

> color sel #d6d6d625

> color sel #d6d6d626

> color sel #d6d6d628

> color sel #d6d6d629

> color sel #d6d6d62a

> color sel #d6d6d62e

> color sel #d6d6d630

> color sel #d6d6d632

> color sel #d6d6d633

> color sel #d6d6d634

> color sel #d6d6d636

[Repeated 1 time(s)]

> select clear

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

[Repeated 1 time(s)]

——— End of log from Tue Jan 20 16:53:43 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #a9a9a942

> color sel #a9a9a944

> color sel #a9a9a947

> color sel #a9a9a948

> color sel #a9a9a949

> color sel #a9a9a94b

> color sel #a9a9a94c

> color sel #a9a9a94d

> color sel #a9a9a94f

> color sel #a9a9a950

> color sel #a9a9a952

> color sel #a9a9a953

> color sel #a9a9a954

> color sel #a9a9a955

> color sel #a9a9a956

> color sel #a9a9a958

[Repeated 1 time(s)]

> color sel #a9a9a959

[Repeated 1 time(s)]

> color sel #a9a9a95b

> color sel #a9a9a95c

> color sel #a9a9a95d

[Repeated 1 time(s)]

> color sel #a9a9a95e

> select clear

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

——— End of log from Tue Jan 20 17:12:49 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> "select #3/a:1-177,259-525"

Unknown command: "select #3/a:1-177,259-525"  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:1-525

3959 atoms, 4022 bonds, 522 residues, 1 model selected  

> color sel #ebebebff

> select clear

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:181-260

586 atoms, 593 bonds, 80 residues, 1 model selected  

> color sel #dda0ddff

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/6His-860"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His/6His-860  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

——— End of log from Sun Jan 25 11:18:21 2026 ———

> view name session-start

opened ChimeraX session  

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

> save /Users/frankseeber/Desktop/model_1.tif width 1800 transparentBackground
> true

[Repeated 3 time(s)]

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

——— End of log from Sun Jan 25 11:55:12 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  

> ui tool show Match→Align

> msa3d #2/A#3/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
82 residue pairs aligned  
110 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 2 | 3  
2 | 0.000 | 28.811  
3 | 28.811 | 0.000  
  
Overall RMSD: 28.811  
Sequence lengths: 110 522  
SDM (cutoff 5.0): -247.145  
Q-score: 0.002  
Alignment identifier is MA-1  
Showing conservation header ("seq_clustal_conservation" residue attribute) for
alignment MA-1  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align  
run(self.session, "msa3d " + ' '.join(args))  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.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-rc2026.05.07.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-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 225, in make_alignment  
alignment.associate(orig, seq=aligned, silent=True)  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 386, in associate  
do_assoc()  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 305, in do_assoc  
self.prematched_assoc_structure(best_match_map, best_errors, reassoc)  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 742, in
prematched_assoc_structure  
self._set_residue_attributes(match_maps=[match_map])  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 1071, in
_set_residue_attributes  
values = [100.0 * self.most_common(col)[1] / num_seqs for col in
range(len(self._seqs[0]))]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 1071, in <listcomp>  
values = [100.0 * self.most_common(col)[1] / num_seqs for col in
range(len(self._seqs[0]))]  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 691, in most_common  
chars, counts = self.column_counts()[col_index]  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 485, in column_counts  
data = numpy.array([list(seq.characters) for seq in self._seqs])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: setting an array element with a sequence. The requested array has
an inhomogeneous shape after 1 dimensions. The detected shape was (2,) +
inhomogeneous part.  
  
ValueError: setting an array element with a sequence. The requested array has
an inhomogeneous shape after 1 dimensions. The detected shape was (2,) +
inhomogeneous part.  
  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 485, in column_counts  
data = numpy.array([list(seq.characters) for seq in self._seqs])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-22.5.15
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2094.80.5.0.0 (iBridge: 23.16.13120.0.0,0)
      OS Loader Version: 580.140.1~106

Software:

    System Software Overview:

      System Version: macOS 14.8.3 (23J220)
      Kernel Version: Darwin 23.6.0
      Time since boot: 4 Tage, 4 Stunden und 42 Minuten

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2421E:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2S6N6H3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        DELL U2421E:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: BPTJBH3     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    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: 4.1.2
    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: 1.12rc202605070126
    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: 1.2.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    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: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    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: 1.50.6
    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: 8.3.3
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    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: 3.13
    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: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.20.0
    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: 8.4.0
    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: 4.9.6
    plotly: 6.7.0
    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: 2.13.4
    pydantic-settings: 2.14.0
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.17.1
    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: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    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: 0.0.27
    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: 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: 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: 3.4.2
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.6.3
    uvicorn: 0.46.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.23.0
#20310 duplicate Crash deleting a QDockWidget involving QWindowContainer::parentWasChanged Tom Goddard chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603022002 (2026-03-02 20:02:06 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2026-05-06 15:03:29.00 -0400","app_version":"1.12.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.12.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.4.1 (25E253)","roots_installed":0,"name":"ChimeraX","incident_id":"AE75646E-D3E8-4004-AC9A-915A65808715"}
{
  "uptime" : 22000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,9",
  "coalitionID" : 8141,
  "osVersion" : {
    "train" : "macOS 26.4.1",
    "build" : "25E253",
    "releaseType" : "User"
  },
  "captureTime" : "2026-05-06 15:03:25.3194 -0400",
  "codeSigningMonitor" : 2,
  "incident" : "AE75646E-D3E8-4004-AC9A-915A65808715",
  "pid" : 21214,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procLaunch" : "2026-05-06 15:01:58.1219 -0400",
  "procStartAbsTime" : 533950411714,
  "procExitAbsTime" : 536043083136,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"219FFBC8-1D68-5608-88AE-D84A1054BCD2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C250A671-49D3-4DBF-46B0-E9CD373356D3",
  "appleIntelligenceStatus" : {"state":"available"},
  "developerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "0E811BAB-7BB0-4531-9EBB-74A559199332",
  "wakeTime" : 3456,
  "sleepWakeUUID" : "535F901D-64AA-4D3D-AF7D-CCADCE65534E",
  "sip" : "enabled",
  "vmRegionInfo" : "0x8 is not in any region.  Bytes before following region: 4304617464
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      __TEXT                      100934000-100938000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":21214},
  "vmregioninfo" : "0x8 is not in any region.  Bytes before following region: 4304617464
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      __TEXT                      100934000-100938000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PySide6\/QtOpenGL.abi3.so",
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
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    "size" : 131072,
    "uuid" : "63b5bd02-9626-3588-a39c-88d4f882312b",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    "name" : "_elementpath.cpython-311-darwin.so"
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    "arch" : "arm64e",
    "base" : 6659387392,
    "size" : 250512,
    "uuid" : "51565b39-f595-3e96-a217-fef29815057a",
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    "uuid" : "e7a73008-0c09-31e3-9dd9-0c61652f0e85",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
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    "size" : 528120,
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    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
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    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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CoreGraphics                        80K        5 
CoreServices                       816K        3 
CoreUI image data                 1568K       19 
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MALLOC                           225.6M       78 
MALLOC guard page                 3632K        4 
Memory Tag 22                     64.0M        1 
OpenGL GLSL                        256K        3 
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Stack                            187.5M       29 
Stack Guard                       56.0M        1 
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VM_ALLOCATE (reserved)           416.0M        1         reserved VM address space (unallocated)
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__LINKEDIT                       608.2M      138 
__OBJC_RO                         79.1M        1 
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__TEXT                             1.5G     1188 
__TPRO_CONST                       128K        2 
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mapped file                      302.4M       47 
page table in kernel              1138K        1 
shared memory                     1520K       24 
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TOTAL, minus reserved VM space     3.4G     6624 
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Log:
UCSF ChimeraX version: 1.12.dev202603022002 (2026-03-02)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open "/Users/tj4488/Library/Mobile
> Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA
> project/4_NC_reviewer comments/3_experiments/3.4_Chimera X analysis/2_iadDE
> compare to 7YLS.cxs"

Log from Tue Mar 3 19:47:08 2026UCSF ChimeraX version: 1.12.dev202603022002
(2026-03-02)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tj4488/Library/Mobile
> Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA
> project/2_items/2_Protein and crystal
> structure/2_iadDE/1.3_structure/1.2_model1c_refine_001.pdb"

Summary of feedback from opening /Users/tj4488/Library/Mobile
Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA
project/2_items/2_Protein and crystal
structure/2_iadDE/1.3_structure/1.2_model1c_refine_001.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2022-10-18 Time 14:28:29 EDT -0400 (1666117709.28 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : jc12-4-fast_dp-truncated-unique.mtz  
  
36 messages similar to the above omitted  
  
Chain information for 1.2_model1c_refine_001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> open "/Users/tj4488/Library/Mobile
> Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA
> project/2_items/2_Protein and crystal
> structure/2_iadDE/1.3_structure/2.1_model1h_refmac1_expanded.pdb"

2.1_model1h_refmac1_expanded.pdb title:  
\--- [more info...]  
  
Chain information for 2.1_model1h_refmac1_expanded.pdb #2  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
  
Non-standard residues in 2.1_model1h_refmac1_expanded.pdb #2  
---  
EDO — (EDO)  
FES — (FES)  
ZN — (ZN)  
  
315 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open "/Users/tj4488/Library/Mobile
> Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA
> project/2_items/2_Protein and crystal
> structure/2_iadDE/1.3_structure/2.2_model1h_refmac1.pdb"

2.2_model1h_refmac1.pdb title:  
\--- [more info...]  
  
Chain information for 2.2_model1h_refmac1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in 2.2_model1h_refmac1.pdb #3  
---  
EDO — (EDO)  
FES — (FES)  
ZN — (ZN)  
  
105 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hide #!1 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> close #1

> close #2

> open 7YLS.pdb

No such file/path: 7YLS.pdb  

> open /Users/tj4488/Desktop/7YLS.cif

Summary of feedback from opening /Users/tj4488/Desktop/7YLS.cif  
---  
notes | Fetching CCD ACT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif  
Fetching CCD FE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif  
Fetching CCD FES from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FES/FES.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
  
7YLS.cif title:  
Structure of a bacteria protein complex [more info...]  
  
Chain information for 7YLS.cif #1  
---  
Chain | Description | UniProt  
A | Aromatic-ring-hydroxylating dioxygenase beta subunit | C5CSP7_VARPS 1-162  
B | Rieske (2Fe-2S) domain protein | C5CSP6_VARPS 1-437  
  
Non-standard residues in 7YLS.cif #1  
---  
ACT — acetate ion  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
4807 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3),
sequence alignment score = 2230.9  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> cartoon

> color cyan #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color orange #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 40 #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> cartoon

> color cyan #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> cartoon

> color cyan #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color orange #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 40 #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> cartoon

[Repeated 1 time(s)]

> color cyan cartoons #1

Expected ',' or a keyword  

> color orange cartoons #3

Expected ',' or a keyword  

> cartoon

> hide atoms

> color cyan #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color orange #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 40 #3 target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> rmsd #3 to #1 perResidue true

Expected a keyword  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3),
sequence alignment score = 2230.9  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> rmsd #3 to #1

Number of atoms from first atom spec (5625) differs from number in second
(9866)  

> select add #1

9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected  

> select add #3

15491 atoms, 14432 bonds, 18 pseudobonds, 2502 residues, 4 models selected  

> select subtract #3

9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected  

> select subtract #1

Nothing selected  

> color cyan #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> cartoon

> color cyan models #1

Expected ',' or a keyword  

> toolshed show

> show target ab

> color #1 #00c8b3ff

> color #3 #f2a350ff

> transparency 50

> ui tool show Matchmaker

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3),
sequence alignment score = 2230.9  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> morph #1 #2

Require at least 2 structures for morph  

> morph #1 #3

Computed 51 frame morph #2  

> coordset #2 1,51

> distance #1@ca #3@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1188 atoms and 0
measurable objects  

> transparency 50 #3

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> movie record

> movie encode /Users/tj4488/Desktop/movie1.mp4 framerate 25.0

Movie saved to /Users/tj4488/Desktop/movie1.mp4  
  

> show #2 target ab

> select add #2

844 atoms, 838 bonds, 4 pseudobonds, 135 residues, 2 models selected  

> close #2

No visible models!  

> show #!1 models

> show #!3 models

> transparency cartoons 50 #3

Missing or invalid "percent" argument: Expected a number  

> transparency #3 50 target c

> ui tool show Matchmaker

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3),
sequence alignment score = 2230.9  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> show #!1 target m

> view #1 clip false

> select add #1

9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected  

> select add #3

15491 atoms, 14432 bonds, 18 pseudobonds, 2502 residues, 4 models selected  

> transparency (#!1,3 & sel) 70

> select subtract #3

9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected  

> select subtract #1

Nothing selected  

> rmsd #1 to #3 perResidue true

Expected a keyword  

> rmsd #1 to #3 perResidue

Expected a keyword  

> align #1 toAtoms #3

Unequal number of atoms to pair, 9866 and 5625  

> matchmaker #1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2.2_model1h_refmac1.pdb, chain A (#3) with 7YLS.cif, chain B (#1),
sequence alignment score = 2230.9  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> help matchmaker

> mmaker #3/A to #1/B showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3),
sequence alignment score = 2230.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 7YLS.cif #1/B,
2.2_model1h_refmac1.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs:
0.924)  
  

> select #1/B:234

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/B:234-240

104 atoms, 105 bonds, 7 residues, 1 model selected  

> select #1/B:234 #3/A:234

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/B:226

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:226-300

1155 atoms, 1175 bonds, 75 residues, 1 model selected  

> hide atoms

> show cartoons

> select #3/A:234

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:234-240

57 atoms, 58 bonds, 7 residues, 1 model selected  

> select #1/B:245 #3/A:245

23 atoms, 21 bonds, 2 residues, 2 models selected  

> mmaker #3/B to #1/A showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7YLS.cif, chain A (#1) with 2.2_model1h_refmac1.pdb, chain B (#3),
sequence alignment score = 839.4  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 7YLS.cif #1/A,
2.2_model1h_refmac1.pdb #3/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 158 pruned atom pairs is 0.190 angstroms; (across all 158 pairs:
0.190)  
  

> select #1/B:280 #3/A:280

22 atoms, 21 bonds, 2 residues, 2 models selected  

> select #1/B:280

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #1/B:280-292

186 atoms, 189 bonds, 13 residues, 1 model selected  

> save "/Users/tj4488/Desktop/iadDE compare to 7YLS.cxs"

——— End of log from Tue Mar 3 19:47:08 2026 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,9
      Model Number: Z1AF001AGLL/A
      Chip: Apple M3 Max
      Total Number of Cores: 16 (12 Performance and 4 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.101.7
      OS Loader Version: 18000.101.7

Software:

    System Software Overview:

      System Version: macOS 26.4.1 (25E253)
      Kernel Version: Darwin 25.4.0
      Time since boot: 2 hours, 49 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    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: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.1
    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: 3.6.2
    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: 1.64.1
    ChimeraX-AtomicLibrary: 14.2.3
    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: 2.3
    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: 1.12.dev202603022002
    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
    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: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    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: 0.2.0
    ChimeraX-MDcrds: 2.18
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.5
    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: 2.7.12
    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: 1.5.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8
    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: 2.17.5
    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: 2.5.2
    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: 1.50.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    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: 7.13.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    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: 7.1.0
    ipython: 9.9.0
    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: 8.8.0
    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: 6.7.1
    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: 0.8.6
    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: 4.9.2
    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: 2.13.1
    pydantic_core: 2.41.5
    pydata-sphinx-theme: 0.16.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.0
    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
    PySide6: 6.10.1
    PySide6_Addons: 6.10.1
    PySide6_Essentials: 6.10.1
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.22
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.1
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    shiboken6: 6.10.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    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: 3.3.2
    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: 0.41.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.23.0
#20309 can't reproduce UnicodeDecodeError reading PDB file Eric Pettersen chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.12rc202605110632 (2026-05-11 06:32:03 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.12rc202605110632 (2026-05-11)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

[Repeated 1 time(s)]

> open C:/Users/yves/Downloads/AF-E9B373-F1-model_v6.pdb

AF-E9B373-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for tubulin--tyrosine ligase (E9B373) [more
info...]  
  
Chain information for AF-E9B373-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | tubulin--tyrosine ligase | E9B373_LEIMU 1-495  
  
Computing secondary structure  

> open C:/Users/yves/Downloads/AF-0000000065716909-model_v1TbTTL.pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 233, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 546, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 517, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\\__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\pdb.py", line 91, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> hide #1 models

> show #1 models

> open "C:/Users/yves/Downloads/AF-Q8NG68-F1-model_v6 Human TTL.pdb"

AF-Q8NG68-F1-model_v6 Human TTL.pdb title:  
Alphafold monomer V2.0 prediction for tubulin--tyrosine ligase (Q8NG68) [more
info...]  
  
Chain information for AF-Q8NG68-F1-model_v6 Human TTL.pdb #2  
---  
Chain | Description | UniProt  
A | tubulin--tyrosine ligase | TTL_HUMAN 1-377  
  
Computing secondary structure  

> open C:/Users/yves/Downloads/AF-0000000065716909-model_v1TbTTL.pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 233, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 546, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 517, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\\__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\pdb.py", line 91, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "C:/Users/yves/Downloads/AF-0000000065716909-model_v1 TbTTL.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 233, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 546, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 517, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\\__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\pdb.py", line 91, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open C:/Users/yves/Downloads/AF-0000000065716909-model_v1.pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 233, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 546, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 517, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\\__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\pdb\pdb.py", line 91, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8854
OpenGL renderer: Intel(R) HD Graphics 630
OpenGL vendor: Intel

Python: 3.11.9
Locale: fr_FR.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Microsoft Windows 10 Professionnel (Build 19045.6466)
Memory: 8,446,840,832
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7500 CPU @ 3.40GHz
OSLanguage: fr-FR

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.2.0
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.4.22
    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: 1.12rc202605110632
    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: 1.2.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    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: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    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: 1.50.6
    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: 8.3.3
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.14.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    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: 3.14
    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: 2.21.0
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    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: 0.17.1
    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: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    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: 0.0.28
    pywin32: 311
    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
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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

Note: See TracWiki for help on using the wiki.