wiki:TracQuery

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 13251)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#19461 worksforme Crash deleting atoms/bonds Eric Pettersen chimerax-bug-report@…
#19460 can't reproduce H-Bonds: More than 2 coplanar positions specified Eric Pettersen shabir.najmudin@…
#19459 can't reproduce Crash in event loop 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 13251)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#19461 worksforme Crash deleting atoms/bonds Eric Pettersen chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202509040038 (2025-09-04 00:38:56 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x00007d94 (most recent call first):
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\threading.py", line 331 in wait
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\threading.py", line 629 in wait
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\threading.py", line 1399 in run
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\threading.py", line 1002 in _bootstrap

Current thread 0x00007780 (most recent call first):
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "C:\Users\chem-wolf7086\AppData\Local\Programs\ChimeraX 1.11.dev202509040038\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202509040038 (2025-09-04)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QDxgiVSyncService: DXGI Factory is no longer Current  

> open 2vsm fromDatabase pdb format mmcif

2vsm title:  
Nipah virus attachment glycoprotein in complex with human cell surface
receptor ephrinB2 [more info...]  
  
Chain information for 2vsm #1  
---  
Chain | Description | UniProt  
A | HEMAGGLUTININ-NEURAMINIDASE | HN_NIPAV 188-602  
B | EPHRIN-B2 | EFNB2_HUMAN 31-168  
  
Non-standard residues in 2vsm #1  
---  
IPA — isopropyl alcohol (2-propanol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
134 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open 7ty0 fromDatabase pdb format mmcif

7ty0 title:  
Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3
neutralizing antibody Fab fragment (local refinement of the stalk region)
[more info...]  
  
Chain information for 7ty0 #2  
---  
Chain | Description | UniProt  
A B C D | Glycoprotein G | GLYCP_NIPAV 70-601  
J K | Igh protein | I6L985_MOUSE 1-443  
N O | nAH Fab light chain |   
  
Non-standard residues in 7ty0 #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 7tzx fromDatabase pdb format mmcif

7tzx title:  
The crystal structure of WT CYP199A4 bound to 4-chloromethylbenzoic acid [more
info...]  
  
Chain information for 7tzx #3  
---  
Chain | Description | UniProt  
A | Cytochrome P450 | Q2IU02_RHOP2 0-409  
  
Non-standard residues in 7tzx #3  
---  
CL — chloride ion  
HEM — protoporphyrin IX containing Fe (HEME)  
L3C — 4-(chloromethyl)benzoic acid  
  
41 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close #3

> open 7txz fromDatabase pdb format mmcif

7txz title:  
Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3
neutralizing antibody Fab fragment (local refinement of the distal region)
[more info...]  
  
Chain information for 7txz #3  
---  
Chain | Description | UniProt  
A B C D | Glycoprotein G | GLYCP_NIPAV 70-601  
E H | nAH1.3 Fab heavy chain |   
F L | nAH1.3 Fab light chain |   
  
Non-standard residues in 7txz #3  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select #2/J#2/K

1361 atoms, 1395 bonds, 9 pseudobonds, 202 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/N#2/O

1309 atoms, 1342 bonds, 6 pseudobonds, 202 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #3/E#3/H

1756 atoms, 1804 bonds, 234 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/F#3/L

1640 atoms, 1682 bonds, 221 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show cartoons

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #3/D

Alignment identifier is 3/D  

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #2/B

Alignment identifier is 2/B  

> sequence chain #2/C

Alignment identifier is 2/C  

> sequence chain #2/D

Alignment identifier is 2/D  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #3/B

Alignment identifier is 3/B  

> sequence chain #3/C

Alignment identifier is 3/C  

> select clear

> select #3/C:146

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #3/C:142-146

26 atoms, 25 bonds, 5 residues, 1 model selected  

> select #3/C:133-146

71 atoms, 70 bonds, 14 residues, 1 model selected  

> select #3/C:146

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #3/C:137-146

51 atoms, 50 bonds, 10 residues, 1 model selected  

> select clear

> select #3/B:219-220

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/B:219-222

31 atoms, 31 bonds, 4 residues, 1 model selected  

> select
> #3/B:159-161,179-180,201-203,215-225,228-237,244-257,263-271,279-287,290-297,314-320,332-336,340-341,347-350,356-358,361-371,407-417,426-430,442-447,450-455,465-471,476-479,512-515,520-526,535-541,544-550,558-568,571-580,591-596

1555 atoms, 1570 bonds, 192 residues, 1 model selected  

> select #3/C

205 atoms, 209 bonds, 34 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/D

3422 atoms, 3512 bonds, 4 pseudobonds, 488 residues, 2 models selected  

> select #3/D

212 atoms, 216 bonds, 34 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #3/A:131-139

45 atoms, 44 bonds, 9 residues, 1 model selected  

> select #3/A:174-175

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #3/A:174-211

272 atoms, 275 bonds, 38 residues, 1 model selected  

> select #3/A:211

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:209-211

16 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A:174

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:174

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:138

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:138-139

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #3/A:172

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:169-172

39 atoms, 39 bonds, 4 residues, 1 model selected  

> select clear

> select #3/A:131-172

282 atoms, 289 bonds, 42 residues, 1 model selected  

> select #3/A:131

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:131-171

271 atoms, 278 bonds, 41 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #3/B:132-171

271 atoms, 278 bonds, 40 residues, 1 model selected  

> select #3/B:132

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/B:132-164

206 atoms, 209 bonds, 33 residues, 1 model selected  

> select #3/B:163

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

> select #3/B:162-163

13 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/B:162-163

13 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/B:132-163

198 atoms, 201 bonds, 32 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #3/A:172-173

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:172-173

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:208

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

> select #3/A:205-208

34 atoms, 35 bonds, 4 residues, 1 model selected  

> select clear

> select #3/A:172

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:172

11 atoms, 10 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.11.dev202509040038 (2025-09-04)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 31.0.101.5085
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_GB.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex SFF Plus 7010
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500
OSLanguage: en-GB

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.7.2
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.16
    ChimeraX-AtomicLibrary: 14.1.23
    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.dev202509040038
    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: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    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-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    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: 1.0.1
    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: 1.15.1
    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: 1.3.1
    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: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.1
    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: 2.17.2
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.3.2
    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
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.6
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.16
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.59.2
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    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: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.1
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.1
    PyQt6_sip: 13.10.2
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.0.2
    qtconsole: 5.6.1
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    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
    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
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    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
#19460 can't reproduce H-Bonds: More than 2 coplanar positions specified Eric Pettersen shabir.najmudin@…
Description 
The following bug report has been submitted:
Platform:        Linux-5.5.8-1.el8.elrepo.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.3rc202111090815 (2021-11-09 08:15:14 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3rc202111090815 (2021-11-09)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/shabir/Topos_CTD/ATPase_CTD/RealSpaceRefine_8/SpTopoIV_ATPase_CTD_X-
> cryoEM_RSR24_rsr_007-coot-0_real_space_refined_008.pdb format pdb

Chain information for SpTopoIV_ATPase_CTD_X-
cryoEM_RSR24_rsr_007-coot-0_real_space_refined_008.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
D | No description available  
  

> close

> open /home/shabir/Topo_EM_figs/T14mer_B-DNA.pdb
> /home/shabir/Topo_EM_figs/E26mer_B-DNA.pdb
> /home/shabir/Topo_EM_figs/side_J484_rsr7.pdb
> /home/shabir/Topo_EM_figs/front_J479_rsr9.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5pq_on_4i3h-rev.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5p_2xflexCTDs_model.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5pq_on_4i3h.pdb
> /home/shabir/Topo_EM_figs/pinwheel_J238_Zflip_rsr26.pdb

Summary of feedback from opening /home/shabir/Topo_EM_figs/front_J479_rsr9.pdb  
---  
warnings | Cannot find LINK/SSBOND residue K (1 )  
Cannot find LINK/SSBOND residue K (1 )  
Cannot find LINK/SSBOND residue K (1 )  
  
Chain information for T14mer_B-DNA.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Chain information for E26mer_B-DNA.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for side_J484_rsr7.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  
Chain information for front_J479_rsr9.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  
Chain information for SpTopoIV_8qmb5j5pq_on_4i3h-rev.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
Q | No description available  
  
Chain information for SpTopoIV_8qmb5j5p_2xflexCTDs_model.pdb #6  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  
Chain information for SpTopoIV_8qmb5j5pq_on_4i3h.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
Q | No description available  
  
Chain information for pinwheel_J238_Zflip_rsr26.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> color bynucleotide

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> hide #1 models

> hide #2 models

> open /home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb

Summary of feedback from opening
/home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 AA1 2 GLN A
18 VAL A 19 0  
Start residue of secondary structure not found: SHEET 2 AA1 2 ALA B 105 GLY B
106 -1  
Start residue of secondary structure not found: SHEET 1 AA2 3 LYS A 155 PRO A
156 0  
Start residue of secondary structure not found: SHEET 2 AA2 3 ALA A 144 GLU A
151 -1  
Start residue of secondary structure not found: SHEET 3 AA2 3 LYS A 161 THR A
165 -1  
69 messages similar to the above omitted  
  
Chain information for T14merA_pinwheel_5J5Q.pdb #9  
---  
Chain | Description  
E F | No description available  
  

> color #5,7-9#!3-4,6 bynucleotide

> hide #!3 models

> color #5,7-9#!4,6 bynucleotide

> select #9

603 atoms, 673 bonds, 29 residues, 1 model selected  

> hide #!4 models

> hide #5 models

> hide #!6 models

> hide #7 models

> hide #8 models

> show sel surfaces

> ~select #9

2 models selected  

> show #8 models

> select #9

603 atoms, 673 bonds, 29 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,-3.0993,0,1,0,-4.6498,0,0,1,-7.3089

> view matrix models #9,1,0,0,-5.2235,0,1,0,-6.0613,0,0,1,-6.1341

> view matrix models #9,1,0,0,-6.3816,0,1,0,-6.1306,0,0,1,-7.8567

> view matrix models #9,1,0,0,-2.9224,0,1,0,-22.22,0,0,1,-0.21635

> view matrix models #9,1,0,0,-1.8316,0,1,0,-22.573,0,0,1,-0.033346

> view matrix models #9,1,0,0,-1.9487,0,1,0,-23.809,0,0,1,-0.81871

> view matrix models #9,1,0,0,-2.0034,0,1,0,-23.645,0,0,1,-0.32886

> view matrix models #9,1,0,0,-3.0617,0,1,0,-23.635,0,0,1,0.14824

> view matrix models #9,1,0,0,-2.7272,0,1,0,-26.233,0,0,1,2.4442

> view matrix models #9,1,0,0,-1.3285,0,1,0,-25.35,0,0,1,-0.22106

> view matrix models #9,1,0,0,-2.6177,0,1,0,-25.301,0,0,1,-1.0128

> view matrix models #9,1,0,0,-2.4201,0,1,0,-25.366,0,0,1,-0.53708

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.9986,0.003658,0.052837,-14.464,-0.0057742,0.99918,0.039956,-33.095,-0.052647,-0.040205,0.9978,15.379

> view matrix models
> #9,0.98934,0.096137,0.1094,-40.703,-0.10879,0.98724,0.11631,-30.806,-0.096826,-0.12697,0.98717,39.438

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.98934,0.096137,0.1094,-39.1,-0.10879,0.98724,0.11631,-30.75,-0.096826,-0.12697,0.98717,42.508

> view matrix models
> #9,0.98934,0.096137,0.1094,-43.187,-0.10879,0.98724,0.11631,-29.912,-0.096826,-0.12697,0.98717,42.162

> view matrix models
> #9,0.98934,0.096137,0.1094,-43.175,-0.10879,0.98724,0.11631,-29.75,-0.096826,-0.12697,0.98717,42.719

> view matrix models
> #9,0.98934,0.096137,0.1094,-42.882,-0.10879,0.98724,0.11631,-29.592,-0.096826,-0.12697,0.98717,42.873

> ~select #9

2 models selected  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> ui tool show "Build Structure"

> build start nucleic T56mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGA type dna form B

Chain information for T56mer_BDNA #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> build start nucleic T72mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGATGACGATTGCATTACG
> type dna form B

Chain information for T72mer_BDNA #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> save /home/shabir/Topos_CTD/T56mer_BDNA.pdb models #10

> save /home/shabir/Topos_CTD/T72mer_BDNA.pdb models #11

> open /home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb

Summary of feedback from opening
/home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 AA1 2 GLN A
18 VAL A 19 0  
Start residue of secondary structure not found: SHEET 2 AA1 2 ALA B 105 GLY B
106 -1  
Start residue of secondary structure not found: SHEET 1 AA2 3 LYS A 155 PRO A
156 0  
Start residue of secondary structure not found: SHEET 2 AA2 3 ALA A 144 GLU A
151 -1  
Start residue of secondary structure not found: SHEET 3 AA2 3 LYS A 161 THR A
165 -1  
69 messages similar to the above omitted  
  
Chain information for T14merA_pinwheel_5J5Q.pdb #12  
---  
Chain | Description  
E F | No description available  
  

> hide #!9 models

> show #!9 models

> show #1 models

> coulombic #1,8,10-12#!9

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
T14mer_B-DNA.pdb #1/B C 13  
T14mer_B-DNA.pdb #1/B C 13  
T14mer_B-DNA.pdb #1/B G 13  
T14mer_B-DNA.pdb #1/B A 13  
T14mer_B-DNA.pdb #1/B A 13  
T14mer_B-DNA.pdb #1/B A 13  
T14mer_B-DNA.pdb #1/B A 13  
T14mer_B-DNA.pdb #1/B A 13  
T14mer_B-DNA.pdb #1/B G 13  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 4  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 20  
pinwheel_J238_Zflip_rsr26.pdb #8/C MET 90  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 154  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 160  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 167  
pinwheel_J238_Zflip_rsr26.pdb #8/C SER 168  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 205  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 225  
pinwheel_J238_Zflip_rsr26.pdb #8/C ASP 238  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 240  
pinwheel_J238_Zflip_rsr26.pdb #8/C ASN 253  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLN 256  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 296  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 311  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 313  
pinwheel_J238_Zflip_rsr26.pdb #8/C ARG 353  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 370  
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 390  
pinwheel_J238_Zflip_rsr26.pdb #8/C ARG 393  
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 394  
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 20  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 154  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 161  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 167  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 169  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 205  
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 225  
pinwheel_J238_Zflip_rsr26.pdb #8/D ASP 238  
pinwheel_J238_Zflip_rsr26.pdb #8/D ASP 265  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 296  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 311  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 313  
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 370  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 384  
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 390  
pinwheel_J238_Zflip_rsr26.pdb #8/D ARG 393  
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 394  
pinwheel_J238_Zflip_rsr26.pdb #8/D ARG 396  
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 398  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B A 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B G 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B C 56  
T56mer_BDNA #10/B A 56  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B G 72  
T72mer_BDNA #11/B C 72  
T72mer_BDNA #11/B A 72  
T72mer_BDNA #11/B A 72  

Deleting 5' phosphates from: copy of pinwheel_J238_Zflip_rsr26.pdb #/F DA 1,
copy of pinwheel_J238_Zflip_rsr26.pdb #/H DG 1  
Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 5 time(s)]Coulombic values for T14mer_B-DNA.pdb_A SES surface #1.1:
minimum, -13.70, mean -9.23, maximum -1.20  
Coulombic values for T14mer_B-DNA.pdb_B SES surface #1.2: minimum, -14.76,
mean -10.13, maximum -1.83  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_A SES surface #8.1:
minimum, -21.83, mean -2.08, maximum 16.59  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_B SES surface #8.2:
minimum, -18.74, mean -1.45, maximum 14.32  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_C SES surface #8.3:
minimum, -21.76, mean -2.30, maximum 17.54  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_D SES surface #8.4:
minimum, -21.65, mean -2.29, maximum 16.87  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_E SES surface #8.5:
minimum, -18.12, mean -8.12, maximum -0.35  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_F SES surface #8.6:
minimum, -17.92, mean -8.92, maximum -1.64  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_G SES surface #8.7:
minimum, -18.45, mean -8.13, maximum -0.25  
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_H SES surface #8.8:
minimum, -24.22, mean -9.01, maximum -0.72  
Coulombic values for T56mer_BDNA_A SES surface #10.1: minimum, -15.64, mean
-11.45, maximum -1.73  
Coulombic values for T56mer_BDNA_B SES surface #10.2: minimum, -17.54, mean
-12.81, maximum -1.84  
Coulombic values for T72mer_BDNA_A SES surface #11.1: minimum, -16.08, mean
-11.67, maximum -1.13  
Coulombic values for T72mer_BDNA_B SES surface #11.2: minimum, -17.71, mean
-13.05, maximum -2.59  
Coulombic values for T14merA_pinwheel_5J5Q.pdb_E SES surface #12.1: minimum,
-17.38, mean -9.00, maximum -0.81  
Coulombic values for T14merA_pinwheel_5J5Q.pdb_F SES surface #12.2: minimum,
-16.15, mean -8.94, maximum -0.31  
Coulombic values for T14merA_pinwheel_5J5Q.pdb_E SES surface #9.1: minimum,
-17.38, mean -9.00, maximum -0.81  
Coulombic values for T14merA_pinwheel_5J5Q.pdb_F SES surface #9.2: minimum,
-16.15, mean -8.94, maximum -0.31  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!11 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!9 models

> hide #!10 models

> color #!1,8,12 bynucleotide

[Repeated 1 time(s)]

> hide #!12 models

> show #!12 models

> hide #!1 models

> show #!9 models

> hide #!9 models

> show #!9 models

> color #!8-9,12 bynucleotide

[Repeated 1 time(s)]

> nucleotides #!8-9,12 atoms

> style nucleic & #!8-9,12 stick

Changed 2108 atom styles  

> build start nucleic T88mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGATGACGATTGCATTACGATGCATATATATATGC
> type dna form B

Chain information for T88mer_BDNA #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #13

3643 atoms, 4086 bonds, 178 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #13,1,0,0,0.55824,0,1,0,-0.11646,0,0,1,6.5459

> view matrix models #13,1,0,0,-1.9729,0,1,0,1.5698,0,0,1,9.1859

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.75963,0.15233,0.63226,-93.156,-0.1701,0.98488,-0.032919,37.452,-0.62771,-0.082543,0.77406,163.43

> view matrix models
> #13,0.75106,0.18482,0.63384,-97.315,-0.20122,0.97842,-0.046866,45.942,-0.62882,-0.09234,0.77205,165.55

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.75106,0.18482,0.63384,-96.682,-0.20122,0.97842,-0.046866,45.671,-0.62882,-0.09234,0.77205,165.51

> view matrix models
> #13,0.75106,0.18482,0.63384,-100.39,-0.20122,0.97842,-0.046866,46.72,-0.62882,-0.09234,0.77205,164.69

> ~select #13

Nothing selected  

> ui tool show "Build Structure"

> toolshed show

Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl  
Bundle installation canceled  
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl  

> hide #!8 models

> hide #!9 models

> hide #!12 models

> hide #13 models

> open /home/shabir/Topos_CTD/Marks_model_CTD-coot-0.pdb
> /home/shabir/Topos_CTD/Marks_model_T14-72mer_G-E18mer-coot-1.pdb

Chain information for Marks_model_CTD-coot-0.pdb #14  
---  
Chain | Description  
A | No description available  
  
Chain information for Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J L | No description available  
M | No description available  
N | No description available  
P | No description available  
Q | No description available  
  

> coulombic #14-15

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 4  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 20  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C MET 90  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 154  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 160  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 167  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C SER 168  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 205  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 225  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASP 238  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 240  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASN 253  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLN 256  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 296  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 311  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 313  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 353  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 370  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 390  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 393  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 394  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 20  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 154  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 161  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 167  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 169  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 205  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 225  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 238  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 265  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 296  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 311  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 313  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 370  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 384  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 390  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 393  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 394  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 396  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 398  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 9  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 10  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 11  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 12  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 13  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 14  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 15  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 16  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 17  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 18  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 2  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 3  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 4  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 5  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 6  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 7  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 8  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 9  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 10  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 11  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 12  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q G 72  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q A 72  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q C 72  

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 80, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 46 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 46 were given  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> select #14

2598 atoms, 2638 bonds, 326 residues, 1 model selected  

> select #15

25776 atoms, 27744 bonds, 2816 residues, 1 model selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 4  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 20  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C MET 90  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 154  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 160  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 167  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C SER 168  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 205  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 225  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASP 238  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 240  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASN 253  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLN 256  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 296  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 311  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 313  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 353  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 370  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 390  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 393  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 394  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 20  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 154  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 161  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 167  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 169  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 205  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 225  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 238  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 265  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 296  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 311  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 313  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 370  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 384  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 390  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 393  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 394  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 396  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 398  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 9  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 10  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 11  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 12  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 13  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 14  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 15  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 16  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 17  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 18  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 2  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 3  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 4  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 5  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 6  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 7  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 8  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 9  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 10  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 11  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 12  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q G 72  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q A 72  
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q C 72  

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 80, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> select #14

2598 atoms, 2638 bonds, 326 residues, 1 model selected  

> ~select #15

2598 atoms, 2638 bonds, 326 residues, 1 model selected  




OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Stream 8 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           78Gi        32Gi        27Gi       4.2Gi        18Gi        41Gi
	Swap:         7.9Gi          0B       7.9Gi

Graphics:
	09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:3081]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    argcomplete: 3.6.0
    attrs: 25.3.0
    Babel: 2.9.1
    backcall: 0.2.0
    basis-set-exchange: 0.11
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.5
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111090815
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    flake8: 4.0.1
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jsonschema: 4.23.0
    jsonschema-specifications: 2024.10.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    mccabe: 0.6.1
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.2
    mypy: 0.910
    mypy-extensions: 0.4.3
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.2
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 22.1.2
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycodestyle: 2.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    pydocstyle: 6.1.1
    pyflakes: 2.4.0
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    referencing: 0.36.2
    regex: 2024.11.6
    requests: 2.26.0
    rpds-py: 0.23.1
    scipy: 1.7.1
    Send2Trash: 1.8.0
    SEQCROW: 1.6.3
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    toml: 0.10.2
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.12.2
    Unidecode: 1.3.8
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
#19459 can't reproduce Crash in event loop Eric Pettersen chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.11rc202511271917 (2025-11-27 19:17:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2025-11-30 22:45:05.00 -0800","app_version":"1.11.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.1 (25B78)","roots_installed":0,"name":"ChimeraX","incident_id":"B2CA14EB-7698-402A-9DBC-9698EB412661"}
{
  "uptime" : 140000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1702308178,
  "deployVersion" : 210,
  "modelCode" : "Mac16,7",
  "coalitionID" : 20852,
  "osVersion" : {
    "train" : "macOS 26.1",
    "build" : "25B78",
    "releaseType" : "User"
  },
  "captureTime" : "2025-11-30 22:44:54.2595 -0800",
  "codeSigningMonitor" : 2,
  "incident" : "B2CA14EB-7698-402A-9DBC-9698EB412661",
  "pid" : 26932,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-11-30 22:43:52.5888 -0800",
  "procStartAbsTime" : 3593408908362,
  "procExitAbsTime" : 3594888852285,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.11-rc2025.11.30.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"0F07621F-DE67-5336-BC81-97BFBCB83A26","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "48233B07-BC40-2EBC-954C-03CC166DA1A2",
  "appleIntelligenceStatus" : {"reasons":["notOptedIn","assetIsNotReady"],"state":"unavailable"},
  "developerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "A17784BE-D59B-4BF6-B6FD-40DBDB915835",
  "wakeTime" : 8346,
  "sleepWakeUUID" : "3FB00192-5472-4303-B073-AB69C57205F5",
  "sip" : "enabled",
  "vmRegionInfo" : "0x8 is not in any region.  Bytes before following region: 4299816952
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      __TEXT                      1004a0000-1004a4000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.11-rc2025.11.30.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":26932},
  "vmregioninfo" : "0x8 is not in any region.  Bytes before following region: 4299816952
      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      __TEXT                      1004a0000-1004a4000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.11-rc2025.11.30.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{

"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":35644029592},{"value":79},{"value":102},{"value":3461016349298363840},{"value":18446726482597246976},{"value":17418542726984877680},{"value":17418542730086950640},{"value":14757395258967641293},{"value":4294967286},{"value":35644029522},{"value":0},{"value":52},{"value":4294967280},{"value":328},{"value":8498582496},{"value":0},{"value":11},{"value":259},{"value":8475533664					,"symbolLocation":224,"symbol":    "_main_thread"},{"value":2},{"value":1},{"value":4323591736					,"symbolLocation":0,"symbol":    "faulthandler_handlers"},{"value":35656075680},{"value":35581074576},{"value":0},{"value":35692734648}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6653319304},"cpsr":{"value":1073741824},"fp":{"value":35644029664},"sp":{"value":35644029632},"esr":{"value":1442840704,"description":"(Syscall)"},"pc":{"value":6653081008,"matchesCrashFrame":1},"far":{"value":0}},"id":8788383,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[


{"imageOffset":38320,"symbol":    "__pthread_kill"					,"symbolLocation":8,"imageIndex":120},
{"imageOffset":26760,"symbol":    "pthread_kill"					,"symbolLocation":296,"imageIndex":121},
{"imageOffset":269616,"symbol":    "raise"					,"symbolLocation":32,"imageIndex":122},
{"imageOffset":2447420,"symbol":    "faulthandler_fatal_error"					,"symbolLocation":392,"imageIndex":1},
{"imageOffset":14148,"symbol":    "_sigtramp"					,"symbolLocation":56,"imageIndex":123},
{"imageOffset":707632,"imageIndex":50},
{"imageOffset":1323652,"imageIndex":50},
{"imageOffset":1323692,"imageIndex":50},
{"imageOffset":1360060,"imageIndex":50},
{"imageOffset":1610732,"imageIndex":50},
{"imageOffset":1626520,"imageIndex":50},
{"imageOffset":1382680,"imageIndex":50},
{"imageOffset":1389692,"symbol":    "QDockWidget::event(QEvent*)"					,"symbolLocation":348,"imageIndex":50},
{"imageOffset":1164488,"symbol":    "sipQDockWidget::event(QEvent*)"					,"symbolLocation":224,"imageIndex":49},
{"imageOffset":55148,"symbol":    "QApplicationPrivate::notify_helper(QObject*, QEvent*)"					,"symbolLocation":332,"imageIndex":50},
{"imageOffset":63720,"symbol":    "QApplication::notify(QObject*, QEvent*)"					,"symbolLocation":5032,"imageIndex":50},
{"imageOffset":1420288,"symbol":    "sipQApplication::notify(QObject*, QEvent*)"					,"symbolLocation":248,"imageIndex":49},
{"imageOffset":621068,"symbol":    "QCoreApplication::sendSpontaneousEvent(QObject*, QEvent*)"					,"symbolLocation":176,"imageIndex":46},
{"imageOffset":56772,"symbol":    "QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool)"					,"symbolLocation":892,"imageIndex":50},
{"imageOffset":461776,"imageIndex":50},
{"imageOffset":458364,"imageIndex":50},
{"imageOffset":55148,"symbol":    "QApplicationPrivate::notify_helper(QObject*, QEvent*)"					,"symbolLocation":332,"imageIndex":50},
{"imageOffset":59204,"symbol":    "QApplication::notify(QObject*, QEvent*)"					,"symbolLocation":516,"imageIndex":50},
{"imageOffset":1420288,"symbol":    "sipQApplication::notify(QObject*, QEvent*)"					,"symbolLocation":248,"imageIndex":49},
{"imageOffset":621068,"symbol":    "QCoreApplication::sendSpontaneousEvent(QObject*, QEvent*)"					,"symbolLocation":176,"imageIndex":46},
{"imageOffset":575440,"symbol":    "QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*)"					,"symbolLocation":1924,"imageIndex":51},
{"imageOffset":975780,"symbol":    "QWindowSystemInterface::sendWindowSystemEvents(QFlags)"					,"symbolLocation":408,"imageIndex":51},
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Log:
UCSF ChimeraX version: 1.11rc202511271917 (2025-11-27)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kedarsharma14/Desktop/Alpha_7_Maps/Phenix/17mer_Ecto/MapSharpeningCryoEM_13/cryosparc_P217_J2617_010_volume_map_sharpened.ccp4

Opened cryosparc_P217_J2617_010_volume_map_sharpened.ccp4 as #1, grid size
600,600,600, pixel 0.533, shown at level 1.47, step 4, values float32  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
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: MacBook Pro
      Model Identifier: Mac16,7
      Model Number: MX2X3LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 13822.41.1
      OS Loader Version: 13822.41.1

Software:

    System Software Overview:

      System Version: macOS 26.1 (25B78)
      Kernel Version: Darwin 25.1.0
      Time since boot: 7 days, 19 hours, 18 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    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: 3.11.1
    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: 3.6.1
    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: 1.11rc202511271917
    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: 1.7.2
    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: 2.7.11
    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: 1.4.1
    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: 7.12.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.0
    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: 4.25.1
    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: 4.5.0
    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: 2.12.5
    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: 3.2.5
    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: 9.0.1
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.20
    pytz: 2025.2
    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-py: 3.1.0
    rpds-py: 0.29.0
    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
    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: 3.0.3
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    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.