Context Navigation

Trac Ticket Queries

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

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

Filters

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

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

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

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

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

Some shortcuts can be used to manipulate checkbox filters.

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

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

Navigating Tickets

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

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

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

Saving Queries

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

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

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

Using TracLinks

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

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

Which is displayed as:

Active tickets against 1.0

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

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

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

Which is displayed as:

Assigned tickets by owner

Customizing the table format

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

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

This is displayed as:

Results (1 - 3 of 13862)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20356	fixed	Table deleted during timer interval	Eric Pettersen	chimerax-bug-report@…
#20355	can't reproduce	Crash during startup	Eric Pettersen	chimerax-bug-report@…
#20352	duplicate	Drag/drop receiving QKeyEvent	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 13862)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20356	fixed	Table deleted during timer interval	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs Log from Wed May 20 01:32:16 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs Log from Wed May 6 14:49:12 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs Log from Mon May 4 20:49:57 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/bxest1.pdbqt Chain information for bxest1.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure Opened bxest1.pdbqt containing 1 structures (2426 atoms, 2476 bonds) > close > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst2/bxest2.pdbqt Chain information for bxest2.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure Opened bxest2.pdbqt containing 1 structures (1679 atoms, 1701 bonds) > show surfaces > hide surfaces > close #1 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst3/bxest3.pdbqt Chain information for bxest3.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure Opened bxest3.pdbqt containing 1 structures (2592 atoms, 2644 bonds) > close > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst4/bxest4.pdbqt Chain information for bxest4.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure Opened bxest4.pdbqt containing 1 structures (1786 atoms, 1821 bonds) > close #1 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/bxest1.pdbqt Chain information for bxest1.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure Opened bxest1.pdbqt containing 1 structures (2426 atoms, 2476 bonds) > set bgColor white > set bgColor #ffffff00 > lighting simple > lighting soft > color #1 grey > show surfaces > color #1 #919191ff > color #1 grey > hide surfaces > select :222,192,93,94,117,24 57 atoms, 55 bonds, 6 residues, 1 model selected > show sel atoms > color select byatom Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byatom > addh Summary of feedback from adding hydrogens to bxest1.pdb #1 --- notes \| No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ILE 248 Chain-final residues that are not actual C termini: 233 hydrogen bonds 1533 hydrogens added > color byatom > ui mousemode right select > select clear > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed1.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed1.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.751 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.139 Ignored bad PDB record found on line 4 REMARK INTER: -18.872 Ignored bad PDB record found on line 5 REMARK INTRA: -3.267 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.267 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed1.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > hbonds #2.1-20 restrict #!1 & (main\|ligand) twoColors true reveal true 22 hydrogen bonds found 4 strict hydrogen bonds found > close #3 > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed2.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed2.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.274 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.142 Ignored bad PDB record found on line 4 REMARK INTER: -16.013 Ignored bad PDB record found on line 5 REMARK INTRA: -6.129 Ignored bad PDB record found on line 6 REMARK UNBOUND: -6.129 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed2.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.668 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.211 Ignored bad PDB record found on line 4 REMARK INTER: -18.711 Ignored bad PDB record found on line 5 REMARK INTRA: -3.500 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.500 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.668 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.211 Ignored bad PDB record found on line 4 REMARK INTER: -18.711 Ignored bad PDB record found on line 5 REMARK INTRA: -3.500 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.500 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #3 > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed3_11.pdb > models #2.11 Computing secondary structure > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed3_11.pdb > hide #!2 models > show #!2 models > close #3 > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed4.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed4.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.690 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -21.611 Ignored bad PDB record found on line 4 REMARK INTER: -18.754 Ignored bad PDB record found on line 5 REMARK INTRA: -2.857 Ignored bad PDB record found on line 6 REMARK UNBOUND: -2.857 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed4.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > hide #!2 target m > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed5.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed5.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.811 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -21.886 Ignored bad PDB record found on line 4 REMARK INTER: -18.988 Ignored bad PDB record found on line 5 REMARK INTRA: -2.898 Ignored bad PDB record found on line 6 REMARK UNBOUND: -2.898 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed5.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #2 > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed5_2.pdb > models #3.2 Computing secondary structure > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/Bxest1/Seed5_16.pdb > models #3.16 Computing secondary structure > close #3 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed3_11.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed5_2.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/Seed5_16.pdb > hide #2 models > hide #3 models > hide #4 models > show #!1 surfaces > select :93 11 atoms, 10 bonds, 1 residue, 1 model selected > color select redd Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color select red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel red > select clear > select :94,24 39 atoms, 38 bonds, 2 residues, 1 model selected > color sel orange > select clear > show #2 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #3 models > hide #3 models > hide #2 models > show #2 models > show #4 models > hide #4 models > show #4 models > hide #2,4#!1 surfaces > hide #4 models > close #3-4 > select add #2 59 atoms, 62 bonds, 1 residue, 1 model selected > select up 4018 atoms, 4071 bonds, 249 residues, 2 models selected > select down 59 atoms, 62 bonds, 1 residue, 2 models selected > color byatom > color #2 #a1a1a1ff > color #2 #00f900ff > color byatom > color #2 #00fdffff > select clear > show surfaces > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 4018 atom styles > style sphere Changed 4018 atom styles > style ball Changed 4018 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > undo > hide surfaces > show surfaces > nucleotides atoms > style nucleic stick Changed 0 atom styles > select add #2 59 atoms, 62 bonds, 1 residue, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 59 atom styles > select clear > select add #1 3959 atoms, 4009 bonds, 248 residues, 1 model selected > color byatom > select subtract #1 1 model selected > select add #1 3959 atoms, 4009 bonds, 248 residues, 1 model selected > select subtract #1 1 model selected > select add #1 3959 atoms, 4009 bonds, 248 residues, 1 model selected > select add #2 4018 atoms, 4071 bonds, 249 residues, 3 models selected > select subtract #2 3959 atoms, 4009 bonds, 248 residues, 2 models selected > select add #2 4018 atoms, 4071 bonds, 249 residues, 3 models selected > select subtract #1 59 atoms, 62 bonds, 1 residue, 2 models selected > select subtract #2 Nothing selected > color byatom > hide surfaces > show surfaces > color #1 #919191ff > color #1 grey > select :93 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select :94,24 39 atoms, 38 bonds, 2 residues, 1 model selected > color sel orange > select clear > color #2 #a1a1a1ff > color #2 #00fdffff > color #2 #00f900ff > color #2 #ff2600ff > color #2 #942192ff > color #2 white > color #2 #0433ffff > color #2 #00fdffff > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat [Repeated 1 time(s)] > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > graphics silhouettes false > lighting flat [Repeated 2 time(s)] > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting soft > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > select :194 17 atoms, 16 bonds, 1 residue, 1 model selected > select :194,129 24 atoms, 22 bonds, 2 residues, 1 model selected > transparency sel 20 > transparency sel 90 > transparency sel 70 > show sel atoms > style sel stick Changed 24 atom styles > transparency sel 70 [Repeated 1 time(s)] > select clear > select :194,129 24 atoms, 22 bonds, 2 residues, 1 model selected > hide sel atoms > hide sel cartoons > show sel cartoons > show sel atoms > hide sel atoms > select #1/A:231@OE1 1 atom, 1 residue, 1 model selected > select clear > style stick Changed 4018 atom styles > hide atoms > select add #2 59 atoms, 62 bonds, 1 residue, 1 model selected > show sel atoms > select clear > ui mousemode right translate > ui mousemode right "translate selected models" > ui mousemode right translate > select :194,129,121 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 70 > select :194,129,121,125 62 atoms, 58 bonds, 4 residues, 1 model selected > select :194,129,121,125,193 79 atoms, 76 bonds, 5 residues, 1 model selected > transparency sel 70 > transparency sel 60 > ui mousemode right select > select clear > select :194,129,121,125,193 79 atoms, 76 bonds, 5 residues, 1 model selected > show sel atoms > hide sel atoms > select :194,129,121,125,193,194 79 atoms, 76 bonds, 5 residues, 1 model selected > transparency sel 60 > select :194,129,121,125,193,194,222 96 atoms, 93 bonds, 6 residues, 1 model selected > transparency sel 60 > transparency sel 0 > select :194,129,121,194,222 63 atoms, 60 bonds, 4 residues, 1 model selected > transparency sel 60 > transparency sel 0 > select :194,129,121,194 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 60 > ui mousemode right select > select clear > undo > select ~sel & ##selected 3913 atoms, 3966 bonds, 245 residues, 1 model selected > select down 3913 atoms, 3966 bonds, 245 residues, 2 models selected > select ~sel & ##selected 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 0 > select :194,129194 17 atoms, 16 bonds, 1 residue, 1 model selected > select :194,129,194 24 atoms, 22 bonds, 2 residues, 1 model selected > transparency sel 60 > select :194,129,121,194 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 60 > select clear > ui mousemode right select > select clear > select :194,129,121,194 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 0 > select clear > select #1/A:129@CA 1 atom, 1 residue, 1 model selected > select #1/A:129@HA3 1 atom, 1 residue, 1 model selected > select #1/A:129@CA 1 atom, 1 residue, 1 model selected > select add #1/A:129@HA3 2 atoms, 1 residue, 2 models selected > select add #1/A:24@CD1 3 atoms, 2 residues, 2 models selected > select subtract #1/A:24@CD1 2 atoms, 1 residue, 2 models selected > select add #1/A:24@CD1 3 atoms, 2 residues, 2 models selected > select subtract #1/A:24@CD1 2 atoms, 1 residue, 2 models selected > select add #1/A:194@HE1 3 atoms, 2 residues, 2 models selected > select add #1/A:194@CE 4 atoms, 2 residues, 2 models selected > select add #1/A:194@SD 5 atoms, 2 residues, 2 models selected > select add #1/A:194@CG 6 atoms, 2 residues, 2 models selected > select subtract #1/A:194@CG 5 atoms, 2 residues, 2 models selected > transparency sel 60 > select add #1/A:129@HA2 6 atoms, 2 residues, 2 models selected > select add #1/A:194@HE2 7 atoms, 2 residues, 2 models selected > select add #1/A:194@HE3 8 atoms, 2 residues, 2 models selected > select add #1/A:23@CA 9 atoms, 3 residues, 2 models selected > select subtract #1/A:23@CA 8 atoms, 2 residues, 2 models selected > select subtract #1/A:194@HE3 7 atoms, 2 residues, 2 models selected > select subtract #1/A:194@CE 6 atoms, 2 residues, 2 models selected > select add #1/A:194@CE 7 atoms, 2 residues, 2 models selected > transparency sel 60 > select :194,129,121,194 46 atoms, 43 bonds, 3 residues, 1 model selected > transparency sel 60 > transparency sel 50 > select clear > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs > includeMaps true ——— End of log from Mon May 4 20:49:57 2026 ——— > view name session-start opened ChimeraX session > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed2-4.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed3-11.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed3-15.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed4-7.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed4-13.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-1.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-2.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-5.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-7.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed5-17.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-5.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-10.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-13.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed6-15.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed7-1.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-2.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-3.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-5.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-7.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-15.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed8-16.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed9-15.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed9-16.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-1.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-3.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-11.pdb > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked/Seed10-18.pdb > hide surfaces > show surfaces > hide #2 models > hide #!1 models > hide #3 models > show #!1 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > hide #13 models > hide #12 models > hide #14 models > hide #15 models > hide #16 models > hide #17 models > hide #18 models > hide #20 models > hide #19 models > hide #21 models > hide #22 models > hide #23 models > hide #24 models > hide #25 models > hide #26 models > hide #27 models > hide #28 models > show #28 models > show #27 models > hide #28 models > hide #27 models > show #26 models > hide #26 models > show #25 models > hide #25 models > show #24 models > hide #24 models > show #23 models > hide #23 models > show #23 models > hide #23 models > show #24 models > show #22 models > hide #22 models > show #22 models > show #21 models > hide #21 models > show #21 models > hide #21 models > show #20 models > hide #20 models > show #19 models > hide #19 models > show #18 models > hide #18 models > show #17 models > hide #17 models > show #16 models > hide #16 models > show #15 models > show #14 models > hide #14 models > show #14 models > hide #14 models > show #13 models > hide #13 models > show #12 models > hide #12 models > show #11 models > hide #11 models > show #10 models > hide #10 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #7 models > hide #7 models > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > hide #4 models > show #3 models > show #2 models > hide #2 models > hide #3,15,22,24#!1 surfaces > close #4-28 > close #2 > addh Summary of feedback from adding hydrogens to multiple structures --- notes \| No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248 Chain-final residues that are not actual C termini: 233 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 38 hydrogens added > hbonds reveal true 233 hydrogen bonds found > show surfaces > close #3 > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/docked_MHET4_rigid_seed3.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.668 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.211 Ignored bad PDB record found on line 4 REMARK INTER: -18.711 Ignored bad PDB record found on line 5 REMARK INTRA: -3.500 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.500 955 messages similar to the above omitted Opened docked_MHET4_rigid_seed3.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > addh Summary of feedback from adding hydrogens to multiple structures --- notes \| No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248 Chain-final residues that are not actual C termini: 233 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 760 hydrogens added > hbonds #2.1-20 restrict #!1 & (main\|ligand) twoColors true reveal true 19 hydrogen bonds found 8 strict hydrogen bonds found > hide #2.11#!1 surfaces > show #2.11#!1 atoms [Repeated 1 time(s)] > hbonds #2.11#!1 reveal true 252 hydrogen bonds found > hide #2.11#!1 atoms > show #2.11#!1 atoms > show #2.11#!1 surfaces > hide #2.3#!1 surfaces > select add #1 3959 atoms, 4009 bonds, 233 pseudobonds, 248 residues, 2 models selected > hide sel atoms > select add #2 5899 atoms, 6009 bonds, 233 pseudobonds, 268 residues, 24 models selected > select subtract #1 1940 atoms, 2000 bonds, 20 residues, 22 models selected > select subtract #2 Nothing selected > hbonds #2.1-20 restrict #!1 & (main\|ligand) twoColors true reveal true 19 hydrogen bonds found 8 strict hydrogen bonds found > ui mousemode right select > select #2.11/?:1@@serial_number=19 1 atom, 1 residue, 1 model selected > select add #1/A:93@HG 2 atoms, 1 bond, 2 residues, 2 models selected > select subtract #1/A:93@HG 1 atom, 1 residue, 2 models selected > select #1/A:93@HG 1 atom, 1 residue, 1 model selected > select add #2.11/?:1@@serial_number=19 2 atoms, 2 residues, 3 models selected > bond sel Created 0 bonds > bond sel Created 0 bonds > bond sel Created 0 bonds > select #2.11/?:1@@serial_number=20 1 atom, 1 residue, 1 model selected > select #1/A:93 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:120 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel surfaces > select clear > show #2.11#!1 surfaces > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs > hbonds 252 hydrogen bonds found > hide #2.11#!1 surfaces > hide #3 models > show #3 models > hide #3 models > show #3 models > addh Summary of feedback from adding hydrogens to multiple structures --- notes \| No usable SEQRES records for bxest1.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: bxest1.pdb #1/A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: bxest1.pdb #1/A ILE 248 Chain-final residues that are not actual C termini: 233 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds 0 hydrogens added > show #2.11#!1 surfaces > ui tool show ViewDock > ui tool show H-Bonds > hbonds reveal true 252 hydrogen bonds found > hide #2.11#!1 atoms > show #2.11#!1 atoms > close #3 > hide #2.11#!1 surfaces > hide #2.11#!1 atoms > select add #2 1940 atoms, 2000 bonds, 20 residues, 21 models selected > show sel & #2.11 atoms > select clear > select :79,10 33 atoms, 31 bonds, 2 residues, 1 model selected > select #1/A:93 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #1/A:94 30 atoms, 28 bonds, 2 residues, 2 models selected > select add #1/A:24 50 atoms, 48 bonds, 3 residues, 2 models selected > show sel atoms > select clear > show #2.11#!1 surfaces > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs ——— End of log from Wed May 6 14:49:12 2026 ——— > view name session-start opened ChimeraX session > close #2 > hide surfaces > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed1.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed1.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.751 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.139 Ignored bad PDB record found on line 4 REMARK INTER: -18.872 Ignored bad PDB record found on line 5 REMARK INTRA: -3.267 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.267 955 messages similar to the above omitted Opened docked_MHET4_seed1.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed2.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed2.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.274 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.142 Ignored bad PDB record found on line 4 REMARK INTER: -16.013 Ignored bad PDB record found on line 5 REMARK INTRA: -6.129 Ignored bad PDB record found on line 6 REMARK UNBOUND: -6.129 955 messages similar to the above omitted Opened docked_MHET4_seed2.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed3.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed3.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.668 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -22.211 Ignored bad PDB record found on line 4 REMARK INTER: -18.711 Ignored bad PDB record found on line 5 REMARK INTRA: -3.500 Ignored bad PDB record found on line 6 REMARK UNBOUND: -3.500 955 messages similar to the above omitted Opened docked_MHET4_seed3.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > close #2 > open > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed4.pdbqt Summary of feedback from opening /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/MHET4_rigid/docked_MHET4_seed4.pdbqt --- warnings \| Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.690 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -21.611 Ignored bad PDB record found on line 4 REMARK INTER: -18.754 Ignored bad PDB record found on line 5 REMARK INTRA: -2.857 Ignored bad PDB record found on line 6 REMARK UNBOUND: -2.857 955 messages similar to the above omitted Opened docked_MHET4_seed4.pdbqt containing 20 structures (1180 atoms, 1240 bonds) > show #2.13#!1 surfaces > save > /Users/jeffreynacasabog/Desktop/Thesis/Results/Jeffrey_Nacasabog/WGS/ANALYSES/enzyme/docking/vina/BxEst1/best_docked.cxs ——— End of log from Wed May 20 01:32:16 2026 ——— > view name session-start opened ChimeraX session Traceback (most recent call last): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 655, in <lambda> QTimer.singleShot(10, lambda s=self, i=scroll_to: s.scrollTo(i)) ^^^^^^^^^^^^^ RuntimeError: wrapped C/C++ object of type ItemTable has been deleted RuntimeError: wrapped C/C++ object of type ItemTable has been deleted File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 655, in QTimer.singleShot(10, lambda s=self, i=scroll_to: s.scrollTo(i)) ^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 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 Air Model Identifier: Mac14,15 Model Number: MQKP3PP/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 22 days, 4 hours, 33 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 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1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 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ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 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#20355	can't reproduce	Crash during startup	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-15.4-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. {"app_name":"ChimeraX","timestamp":"2026-05-19 23:37:07.00 +0800","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.4 (24E248)","roots_installed":0,"name":"ChimeraX","incident_id":"BAFD52E3-942B-4424-94A0-805450342C10"} { "uptime" : 510000, "procRole" : "Unspecified", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "Mac16,12", "coalitionID" : 65797, "osVersion" : { "train" : "macOS 15.4", "build" : "24E248", "releaseType" : "User" }, "captureTime" : "2026-05-19 23:37:01.2361 +0800", "codeSigningMonitor" : 2, "incident" : "BAFD52E3-942B-4424-94A0-805450342C10", "pid" : 40306, "translated" : false, "cpuType" : "ARM-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2026-05-19 23:37:00.3680 +0800", "procStartAbsTime" : 12436057295785, "procExitAbsTime" : 12436074980067, "procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"9F372CAE-16CF-5340-A407-E743D7E95CC3","thirdParty":true}, "parentProc" : "codex", "parentPid" : 66574, "coalitionName" : "com.openai.codex", "crashReporterKey" : "AF6E33C0-1D7A-1F1B-4271-36DD00B576D0", "appleIntelligenceStatus" : {"reasons":["countryLocationIneligible","accessNotGranted","notOptedIn","regionIneligible","countryBillingIneligible"],"state":"unavailable"}, "responsiblePid" : 66508, "responsibleProc" : "Codex", "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "codeSigningAuxiliaryInfo" : 0, "instructionByteStream" 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All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac16,12 Model Number: Z1H90001UCH/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 32 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4 (24E248) Kernel Version: Darwin 24.4.0 Time since boot: 6天12小时6分钟 Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Mi Monitor: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 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1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0
#20352	duplicate	Drag/drop receiving QKeyEvent	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: Linux-6.8.0-111-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.12rc202605082142 (2026-05-08 21:42:16 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- warning \| GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium. UCSF ChimeraX version: 1.12rc202605082142 (2026-05-08) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/raju/Excercise_SMIFFER/PDBs/2F4T.pdb Chain information for 2F4T.pdb #1 --- Chain \| Description A \| No description available B \| No description available Computing secondary structure > open /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.apbs.mrc Opened 2F4T.apbs.mrc as #2, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 0.00173, step 1, values float32 > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.apbs_groove_trimmed_ioncontact.mrc Opened 2F4T.apbs_groove_trimmed_ioncontact.mrc as #3, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 0.00167, step 1, values float32 > volume #2 capFaces false > volume #3 capFaces false > volume #2 level -26.09 > volume #2 style mesh > transparency 50 > volume #3 level -16.4 > hide #!2 models > transparency #3.1 0 > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.groove_ioncontact_marker.mrc Opened 2F4T.groove_ioncontact_marker.mrc as #4, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 5e-05, step 1, values float32 > close #4 > volume #3 level -19.66 > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.groove_ioncontact_marker.mrc Opened 2F4T.groove_ioncontact_marker.mrc as #4, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 5e-05, step 1, values float32 > close #2-4 > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.apbs_groove_trimmed_ioncontact.mrc Opened 2F4T.apbs_groove_trimmed_ioncontact.mrc as #2, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 0.00167, step 1, values float32 > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.apbs_groove_trimmed.mrc Opened 2F4T.apbs_groove_trimmed.mrc as #3, grid size 220,222,263, pixel 0.251,0.251,0.251, shown at level 0.00167, step 1, values float32 > volume #3 capFaces false > volume #2 capFaces false > volume #2 level -16.4 > volume #3 level -19.16 > close #3 > volume #2 level -15.44 > volume #2 level -19 Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 54, in event if self.handle_drag_and_drop(event): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop mw.dragEnterEvent(event) File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 824, in dragEnterEvent md = event.mimeData() ^^^^^^^^^^^^^^ AttributeError: 'QKeyEvent' object has no attribute 'mimeData' AttributeError: 'QKeyEvent' object has no attribute 'mimeData' File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 824, in dragEnterEvent md = event.mimeData() ^^^^^^^^^^^^^^ See log for complete Python traceback. > open > /home/raju/Excercise_SMIFFER/Analysis_all_RNAs/2F4T/2F4T.hbacceptors.mrc Opened 2F4T.hbacceptors.mrc as #3, grid size 220,222,263, pixel 0.25, shown at level 0.543, step 1, values float32 > close #3 Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 54, in event if self.handle_drag_and_drop(event): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop mw.dragEnterEvent(event) File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 824, in dragEnterEvent md = event.mimeData() ^^^^^^^^^^^^^^ AttributeError: 'QKeyEvent' object has no attribute 'mimeData' AttributeError: 'QKeyEvent' object has no attribute 'mimeData' File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 824, in dragEnterEvent md = event.mimeData() ^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 595.58.03 OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.13 Locale: en_GB.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: Precision 7960 Tower OS: Ubuntu 22.04 Architecture: 64bit ELF Virtual Machine: none CPU: 24 Intel(R) Xeon(R) w5-3425 Cache Size: 30720 KB Memory: total used free shared buff/cache available Mem: 62Gi 25Gi 1.9Gi 592Mi 34Gi 37Gi Swap: 2.0Gi 2.0Gi 0.0Ki Graphics: 0000:16:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2783] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:8970] Kernel driver in use: nvidia 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: 1.12rc202605082142 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-LinuxSupport: 1.0.1 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 distro: 1.9.0 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: 0.2.2 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 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: 0.5.2 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.17.1 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: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine: 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 threadpoolctl: 3.6.0 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: 2.7.0 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

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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

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