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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 13869)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20363	duplicate	Crash in QAccessible::uniqueId in Qt 6.10.1	Tom Goddard	chimerax-bug-report@…
#20362	duplicate	Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event	Tom Goddard	chimerax-bug-report@…
#20361	duplicate	Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type	Zach Pearson	matthias.vorlaender@…

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 13869)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20363	duplicate	Crash in QAccessible::uniqueId in Qt 6.10.1	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC) Description Last time you used ChimeraX it crashed. 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Thunderbolt Bus: MacBook Air, Apple Inc. Display: Color LCD, 2560 x 1664 Retina, Main, MirrorOff, Online Display: DELL P2417H, 1920 x 1080 (1080p FHD - Full High Definition), MirrorOff, Online Model: Mac16,12, BootROM 13822.81.10, proc 10:4:6:0 processors, 24 GB, SMC Graphics: Apple M4, Apple M4, Built-In AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4388), wl0: Dec 6 2025 00:30:14 version 23.41.8.0.41.51.201 FWID 01-990604ea IO80211_driverkit-1540.16 "IO80211_driverkit-1540.16" Jan 27 2026 21:02:00 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Log: UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/anz/Downloads/fold_msg51_v2f2/fold_msg51_v2f2_model_0.cif Chain information for fold_msg51_v2f2_model_0.cif #1 --- Chain \| Description A B C \| . F \| . 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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: 3.4.4 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: 0.47.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0
#20362	duplicate	Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.3-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. Fatal Python error: Bus error Current thread 0x00000001f1947080 (most recent call first): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 146 in render File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 115 in _redraw File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55) {"app_name":"ChimeraX","timestamp":"2026-05-20 09:49:20.00 +0200","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":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3 (25D125)","roots_installed":0,"name":"ChimeraX","incident_id":"241F52E7-02C6-431A-8501-4FA7ADA9B59F"} { "uptime" : 440000, "procRole" : "Background", "version" : 2, "userID" : 502, "deployVersion" : 210, "modelCode" : "Mac15,14", "coalitionID" : 45733, "osVersion" : { "train" : "macOS 26.3", "build" : "25D125", "releaseType" : 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"CrBrowserMain", "queue" : "com.apple.main-thread" } }, "logWritingSignature" : "03bc7c701731ece4031efe9a2b22921efa87a636", "bug_type" : "309", "roots_installed" : 0, "trmStatus" : 8192, "trialInfo" : { "rollouts" : [ { "rolloutId" : "67181b10c68c361a728c7cfa", "factorPackIds" : [ ], "deploymentId" : 240000005 }, { "rolloutId" : "61675b89201f677a9a4cbd65", "factorPackIds" : [ "65a855f5f087695cfac03d1f" ], "deploymentId" : 240000272 } ], "experiments" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/osperand/Downloads/Q9E005_1_2153_8qgu.1.B.cif > /Users/osperand/Downloads/AF-0000000365765852-model_v1.cif Summary of feedback from opening /Users/osperand/Downloads/AF-0000000365765852-model_v1.cif --- warning \| Atom H is not in the residue template for ILE /A:1 Q9E005_1_2153_8qgu.1.B.cif title: Model for UniProtKB entries Q9E005 [more info...] Chain information for Q9E005_1_2153_8qgu.1.B.cif #1 --- Chain \| Description A B \| . Color Q9E005_1_2153_8qgu.1.B.cif by residue attribute QMEANDisCo_score Alignment identifier is 1 Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Showing conservation header ("seq_conservation" residue attribute) for alignment 1 Alignment identifier is 2 Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Showing conservation header ("seq_conservation" residue attribute) for alignment 2 Chain information for AF-0000000365765852-model_v1.cif #2 --- Chain \| Description \| UniProt A \| RNA-directed RNA polymerase L \| L_ANDV Color AF-0000000365765852-model_v1.cif by residue attribute pLDDT_score Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Computing secondary structure > matchmaker #1 to #2 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker AF-0000000365765852-model_v1.cif, chain A (#2) with Q9E005_1_2153_8qgu.1.B.cif, chain B (#1), sequence alignment score = 3493.1 RMSD between 335 pruned atom pairs is 1.216 angstroms; (across all 724 pairs: 4.159) > lighting soft > help indeep > indeep predict #1 device cpu clusterPockets true pocketMap ligandability > pocketThreshold 0.95 openPocketMaps true > save /Users/osperand/.local/share/ChimeraX/indeep- > runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb > format pdb models #1 selectedOnly true Running InDeep externally: /Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/scripts/predict_maps.py --exp /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/results/experiments/HPO.exp --pdb /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb --out- prefix /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif --device cpu --cluster-pockets --pocket-map ligandability --pocket-threshold 0.95 --pocket-min-voxels 20 --pocket-contact-radius 4.0 Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep- runtime/.venv/bin/python Run /Users/osperand/.local/share/ChimeraX/indeep- runtime/setup_linux_chimerax_env.sh first. InDeep prediction failed. Check the ChimeraX log for stderr from the external process. > indeep predict #2 device cpu clusterPockets true pocketMap ligandability > pocketThreshold 0.95 openPocketMaps true > save /Users/osperand/.local/share/ChimeraX/indeep- > runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb > format pdb models #2 selectedOnly true Running InDeep externally: /Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/scripts/predict_maps.py --exp /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/results/experiments/HPO.exp --pdb /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb --out-prefix /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif --device cpu --cluster-pockets --pocket-map ligandability --pocket-threshold 0.95 --pocket-min-voxels 20 --pocket-contact-radius 4.0 Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep- runtime/.venv/bin/python Run /Users/osperand/.local/share/ChimeraX/indeep- runtime/setup_linux_chimerax_env.sh first. InDeep prediction failed. Check the ChimeraX log for stderr from the external process. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif Summary of feedback from opening /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif --- warning \| No mmCIF models found. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif Summary of feedback from opening /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif --- warning \| No mmCIF models found. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s_model_0.cif bd43-517-s_model_0.cif title: . [more info...] Chain information for bd43-517-s_model_0.cif #3 --- Chain \| Description B \| . Q \| . Color bd43-517-s_model_0.cif by residue attribute pLDDT_score > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s2_model_0.cif bd43-517-s2_model_0.cif title: . [more info...] Chain information for bd43-517-s2_model_0.cif #4 --- Chain \| Description B \| . Q \| . Color bd43-517-s2_model_0.cif by residue attribute pLDDT_score Computing secondary structure > close #1-2 > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif bd517-43_model_0.cif title: . [more info...] Chain information for bd517-43_model_0.cif #1 --- Chain \| Description B \| . Q \| . Color bd517-43_model_0.cif by residue attribute pLDDT_score Computing secondary structure > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif bd43-517_model_0.cif title: . [more info...] Chain information for bd43-517_model_0.cif #2 --- Chain \| Description B \| . Q \| . Color bd43-517_model_0.cif by residue attribute pLDDT_score Computing secondary structure > matchmaker #1 to #2 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd43-517_model_0.cif, chain Q (#2) with bd517-43_model_0.cif, chain Q (#1), sequence alignment score = 1443.1 RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs: 8.213) > matchmaker #2 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517_model_0.cif, chain Q (#2), sequence alignment score = 1443.1 RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs: 8.213) > matchmaker #3 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517-s_model_0.cif, chain Q (#3), sequence alignment score = 1432.3 RMSD between 205 pruned atom pairs is 0.713 angstroms; (across all 276 pairs: 6.793) > matchmaker #4 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with bd43-517-s2_model_0.cif, chain Q (#4), sequence alignment score = 1417.9 RMSD between 206 pruned atom pairs is 0.624 angstroms; (across all 276 pairs: 5.255) > show atoms > hide #2 models > hide #1 models > hide #3 models > show #2 models > select #2/B:6@CA 1 atom, 1 residue, 1 model selected > view sel > ui tool show "Side View" > select clear > hide #4 models > show #1 models > show #3 models > hide #2 models > show #2 models > show #4 models > hide #3 models > hide #1 models > show #3 models > hide #4 models > hide #2-3 cartoons > show #2-3 cartoons > hide #2-3 cartoons > show #2-3 cartoons > hide #2-3 cartoons > hide #2 models > color #3 bychain > color #3 byhetero > show #3 cartoons > style #3 ball Changed 2346 atom styles > show #2 models > show #2-3 cartoons > hide #3 models > show #1 models > show #3 models > show #4 models > hide cartoons > style ball Changed 9434 atom styles > hide #3 models > hide #4 models > style #1-2 stick Changed 4742 atom styles > show #3 models > hide #3 models > hide #2 models > show #3 models > style #1,3 stick Changed 4716 atom styles > hide #3 models > show #4 models > style #1,4 stick Changed 4716 atom styles > show #3 models > hide #4 models > show #4 models > hide #3 models > show #2 models > hide #1 models > show #3 models > hide #3 models > hide #4 models > show #3 models > show #4 models > show #1 models > hide #1 models > hide #4 models > show #4 models > hide #3 models > hide #4 models > show #3 models > show #1 models > hide #2 models > hide #1 models > show #4 models > show #2 models > hide #2 models > hide #4 models > ui tool show "Show Sequence Viewer" > sequence chain #3/Q #4/Q #1/Q #2/Q Alignment identifier is 1 > select #3/Q:146 #4/Q:146 #1/Q:146 #2/Q:146 24 atoms, 20 bonds, 4 residues, 4 models selected > select #3/Q:146-158 #4/Q:146-158 #1/Q:146-158 #2/Q:146-158 400 atoms, 408 bonds, 52 residues, 4 models selected . [ID: 1] region 4 chains [146-158] RMSD: 0.554 > select #3/Q:196-197 #4/Q:196-197 #1/Q:196-197 #2/Q:196-197 88 atoms, 84 bonds, 8 residues, 4 models selected > select #3/Q:149-196 #4/Q:149-196 #1/Q:149-196 #2/Q:149-196 1500 atoms, 1520 bonds, 192 residues, 4 models selected . [ID: 1] region 4 chains [149-196] RMSD: 0.442 > select #3/Q:115 #4/Q:115 #1/Q:115 #2/Q:115 56 atoms, 60 bonds, 4 residues, 4 models selected > select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129 524 atoms, 544 bonds, 60 residues, 4 models selected . [ID: 1] region 4 chains [115-129] RMSD: 0.766 > select #3/B:6@CA 1 atom, 1 residue, 1 model selected > select #3/B:4@CB 1 atom, 1 residue, 1 model selected > select clear > select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129 524 atoms, 544 bonds, 60 residues, 4 models selected > select > #3/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #4/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #1/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #2/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 2204 atoms, 2208 bonds, 272 residues, 4 models selected > select clear > show #4 models > hide #4 models > show #1 models > hide #3 models > show #4 models > hide #1 models > hide #4 models > show #3 models > show #4 models > hide #4 models > rock > select #3/B:7@O 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 83 atoms, 84 bonds, 10 residues, 1 model selected > select up 136 atoms, 139 bonds, 16 residues, 1 model selected > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > stop > open > /Users/osperand/Downloads/fold_2025_12_02_11_29/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #5 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #5 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#5), sequence alignment score = 1422.7 RMSD between 186 pruned atom pairs is 0.478 angstroms; (across all 276 pairs: 9.241) > hide #5 models > show #5 models > select add #5 2342 atoms, 2387 bonds, 292 residues, 1 model selected > show sel atoms > hide sel cartoons > select clear > hide #!3 models > show #!3 models > hide #!3 models > select add #5 2342 atoms, 2387 bonds, 292 residues, 1 model selected > color sel bychain > color sel byhetero > select clear > show #!3 models > hide #5 models > show #5 models > hide #5 models > open > /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #6 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #6 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#6), sequence alignment score = 1401.1 RMSD between 195 pruned atom pairs is 0.656 angstroms; (across all 276 pairs: 10.056) > show #6#!3 atoms > hide #6#!3 cartoons > hide #6 models > show #6 models > hide #6 models > show #6 models > open > /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_1.cif Chain information for fold_2025_12_02_11_29_model_1.cif #7 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #7 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_1.cif, chain A (#7), sequence alignment score = 1411.9 RMSD between 192 pruned atom pairs is 0.675 angstroms; (across all 276 pairs: 10.634) > show #6-7#!3 atoms > hide #6-7#!3 cartoons > close #7 > hide #!3 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #7 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #7 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score = 1420.9 RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs: 13.990) > color #6-7 bychain > hide #6-7 cartoons > hide #6 models > hide #7 models > show #7 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_1.cif Chain information for fold_2025_12_02_11_29_model_1.cif #8 --- Chain \| Description A \| . B \| . Computing secondary structure > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #9 --- Chain \| Description A \| . B \| . Computing secondary structure > hide #9 models > hide #8 models > close #8-9 > show #7 target m > view #7 clip false No displayed objects specified. > hide #7 models > show #7 models > close #7 > show #4 models > hide #4 models > show #!3 models > show #5 models > hide #5 models > show #6 models > select add #6 2343 atoms, 2387 bonds, 292 residues, 1 model selected > color sel byhetero > select clear > hide #6 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #7 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #7 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score = 1420.9 RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs: 13.990) > show #7#!3 atoms > color #7#!3 bychain > color #7#!3 byhetero > hide #7#!3 cartoons > hide #!3 models > show #!3 models > hide #7 models > show #7 models > hide #!3 models > show #4 models > show #!3 models > hide #7 models > hide #4 models > show #7 models > hide #!3 models > ui tool show H-Bonds > hbonds reveal true 9600 hydrogen bonds found > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7/B:9@CA 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #7/B:10@N 11 atoms, 8 bonds, 3 residues, 1 model selected > select add #7/B:10@C 12 atoms, 8 bonds, 3 residues, 1 model selected > select up 21 atoms, 20 bonds, 3 residues, 1 model selected > show #4 models > hide #8 models > hide #7 models > ui tool show H-Bonds > hbonds reveal true 9600 hydrogen bonds found > show #8 models > show #5 models > hide #4 models > show #4 models > hide #5 models > open > /Users/osperand/Downloads/bd43-517-s-s4/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #9 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #9 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#9), sequence alignment score = 1399.3 RMSD between 175 pruned atom pairs is 0.605 angstroms; (across all 276 pairs: 9.666) > show #4,9 atoms > color #4,9 bychain > color #4,9 byhetero > hide #4,9 cartoons > hide #8 models > hide #4 models > show #!3 models > hide #!3 models > hide #9 models > show #!3 models > show #9 models > hide #!3 models > open "/Users/osperand/Downloads/fold_2025_12_02_11_29 > (4)/fold_2025_12_02_11_29_model_0.cif" Chain information for fold_2025_12_02_11_29_model_0.cif #10 --- Chain \| Description A \| . B \| . Computing secondary structure > matchmaker #10 to #1 Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#10), sequence alignment score = 1422.7 RMSD between 179 pruned atom pairs is 0.632 angstroms; (across all 276 pairs: 10.382) > show #9-10 atoms > hide #9 models > hide #10 cartoons ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/bd43-517-s-s7/bd43-517-s-s7_model_0.cif Chain information for bd43-517-s-s7_model_0.cif #1 --- Chain \| Description A \| . B \| . Computing secondary structure OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Ultra OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac15,14 Model Number: Z1CE000FKFN/A Chip: Apple M3 Ultra Total Number of Cores: 28 (20 Performance and 8 Efficiency) Memory: 96 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3 (25D125) Kernel Version: Darwin 25.3.0 Time since boot: 35 jours, 1 heure et 53 minutes Graphics/Displays: Apple M3 Ultra: Chipset Model: Apple M3 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Studio Display XDR: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 120.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Studio Display XDR: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 120.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-InDeep: 0.1.1 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-SDFFrames: 0.1.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0
#20361	duplicate	Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type	Zach Pearson	matthias.vorlaender@…
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 Blast not working Blast reports an error: Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type Log: Could not find tool "CliX" > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > alias analyse_af_screen_hit runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/analyse_af2_screen_hit.cxc $1 $2 > alias analyse_af3 runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/analyse_af3_prediction.cxc $1 $2 > alias des_ex runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/select_by_exact_match.cxc $1 > alias des runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/select_by_description_match.cxc $1 > alias des_m runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/select_model_by_description_match.cxc $1 $2 > alias analyse_af3_model runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/analyse_af3_prediction_1_model.cxc $1 $2 $3 > alias pol_pdbs cd /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/nascent_PolII_onedrive/pol_II_pdbs > alias analyse_auto-AF runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/analyse_auto-alphafold_prediction.cxc $1 $2 > alias af_hit runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/analyse_af2_screen_hit_rank1.cxc $1 $2 > alias map_missense runscript > /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/scripts/af_missense_coloring.cxc $1 $2 > alias missense mutationscores define avg fromScore amiss setAttribute true > combine mean > runscript /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/chimerax-trimmings/chimerax_trimmings.py > runscript /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- > VBC/ChimeraX/chimerax-trimmings/map_salami.py > camera ortho > cofr centerOfView > mousemode alt rightMode "contour level" > mousemode rightMode clip > mousemode alt leftMode "translate selected models" > mousemode shift leftMode "rotate selected models" > alias cootmode_white set bgColor white; surface cap false; surface style > solid; nucleotides #* atoms; lighting flat; graphics silhouettes false; > style stick; ~rib; color ##num_residues orange; color byhet ; disp > ##num_residues & ##display; ~disp @H; style ions sphere; style solvent > ball; size ballscale 0.2; size stickradius 0.07; transparency 85; cofr > centerofview; clip near -10 far 10 position cofr; color ~##num_residues > medium blue > alias usage cootmode_white synopsis "Apply the white-background Coot-style > display preset" > alias cootmode set bgColor black; surface cap false; surface style solid; > nucleotides # atoms; lighting flat; graphics silhouettes false; style > stick; ~rib; color ##num_residues gold; color byhet ; disp ##num_residues & > ##display; ~disp @H; style ions sphere; style solvent ball; size ballscale > 0.2; size stickradius 0.07; transparency 70; cofr centerofview; clip near > -10 far 10 position cofr; color ~##num_residues cornflower blue > alias usage cootmode synopsis "Apply the dark-background Coot-style display > preset" > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > nucleotides # atoms; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp ##num_residues & ##display; ~disp > @H*; style solvent ball; style ions sphere; size ballscale 0.2; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ~##num_residues #3d60ffff; transparency 50 > alias usage cootmode_mesh synopsis "Apply the mesh Coot-style display > preset" > alias centersel cofr sel; clip near 10 position cofr; clip far -10 position > cofr; cofr centerOfView showpivot true; view sel > alias usage centersel synopsis "Center the view on the selection and apply > local clipping" > functionkey F1 prevmodel > functionkey F2 nextmodel > functionkey F3 centersel > functionkey F4 view all > functionkey F5 togglemaps > functionkey F6 togglemodels > functionkey F7 cyclelighting > functionkey F8 cyclemodeldisplay > functionkey F9 prevmap > functionkey F10 nextmap > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'" > buttonpanel Shortcuts add Model_Panel command "tool show Models" > buttonpanel Shortcuts add Log command "tool show Log" > buttonpanel Shortcuts add togglemaps command togglemaps > buttonpanel Shortcuts add togglemodels command togglemodels > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > buttonpanel Shortcuts add view command view > buttonpanel Shortcuts add selbetween command "ks ri" > buttonpanel Shortcuts add rainbow_last command "rainbow last-opened chain > palette BuPu" > buttonpanel Shortcuts add rainbow command "rainbow chain palette Bupu" > buttonpanel Shortcuts add hide_unsel command "hide ~sel & ##selected c,a,s; > show sel c" UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Populating font family aliases took 98 ms. Replace uses of missing font family "Arial, Helvetica, Sans-serif" with one that exists to avoid this cost. Chain information for fold_2025_01_30_14_44_eif4a3_aly_model_0.cif #1 --- Chain \| Description A \| . B \| . Computing secondary structure > hide #1 atoms > hide #1 surfaces > show #1 cartoons Found 17 residue or atom pairs within distance 3 with pae <= 30 > name frozen af_contact_residues_model_0 > /A:12,14,16,20,172-173,200,205-206,208,230-231,234-235/B:85-87,89-90,121,124,128,164,168,172,244,246,250 > interfaces select #1&/A contacting #1&/B bothSides true 71 contacting residues > rainbow #1 chains palette bupu > color byhetero > name frozen interface_residues_model_0 > /A:12-14,16-18,20,33,76,165,168-169,172-174,179,196,198-200,202-203,205-211,231-232,234-235,286-287/B:6,81,83-93,121,124-125,128,160,163-164,166-172,175,237,243-244,246-247,250-251,254 > select interface_residues_model_0 616 atoms, 601 bonds, 16 pseudobonds, 71 residues, 2 models selected > show interface_residues_model_0 atoms > show interface_residues_model_0 bonds > style interface_residues_model_0 stick Changed 616 atom styles > show af_contact_residues_model_0&sidechain atoms > show af_contact_residues_model_0&sidechain bonds > style af_contact_residues_model_0&sidechain stick Changed 172 atom styles Opened 1 AF3 top hit pair(s). Run metadata was written to: /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- VBC/scripts/python/Mendel_ChimeraX/Example_data/fold_2025_01_30_14_44_eif4a3_aly/analysis/fold_2025_01_30_14_44_eif4a3_aly/af3-top Contacts/interfaces were prepared for display. Files are written only when you use 'Save Contacts and Interfaces' for the active model. Drag select of 126 atoms, 45 residues, 5 pseudobonds, 109 bonds > select clear Drag select of 112 atoms, 39 residues, 4 pseudobonds, 97 bonds Window position QRect(0,994 600x324) outside any known screen, using primary screen Drag select of 147 atoms, 67 residues, 7 pseudobonds, 129 bonds Drag select of 205 atoms, 80 residues, 10 pseudobonds, 181 bonds > select /B:257 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /B:240 12 atoms, 10 bonds, 2 residues, 1 model selected > ks ri > select #2.1/B:240-257 140 atoms, 140 bonds, 18 residues, 1 model selected Drag select of 251 atoms, 205 residues, 12 pseudobonds, 223 bonds Drag select of 15 atoms, 158 residues, 12 bonds > select /A:84-233 /B:236-257 > select /A:84-233 /B:236-257 1343 atoms, 1359 bonds, 3 pseudobonds, 172 residues, 2 models selected Applied PAE hide-unselected to 1 model(s) in this run. > select /A:82-235 /B:231-257 > hide ~sel & ##selected cartoons,atoms,surfaces > show sel cartoons > select /B:99-191 /A:13-18 > select clear > select /B:99-191 /A:13-18 759 atoms, 768 bonds, 3 pseudobonds, 99 residues, 2 models selected > select clear > select /B:257 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /B:240 12 atoms, 10 bonds, 2 residues, 1 model selected > ks ri > select #2.1/B:240-257 140 atoms, 140 bonds, 18 residues, 1 model selected > select /A:30-242 /B:234-257 Chain information for fold_2026_05_13_13_22_alyref_uap56_thoc2_model_0.cif #1 --- Chain \| Description A \| . B \| . C \| . > hide #1 atoms > hide #1 surfaces > show #1 cartoons Found 12 residue or atom pairs within distance 3 with pae <= 30 Found 0 residue or atom pairs within distance 3 with pae <= 30 > name frozen af_contact_residues_model_0 > #1/A:4,6-7,10,235-236,243-244,248,250-251,254/B:208-210,212,218,241,244,275-276,299,309 > interfaces select #1&/A contacting #1&/B bothSides true 48 contacting residues > interfaces select #1&/A contacting #1&/C bothSides true 0 contacting residues > rainbow #1 chains palette bupu > color byhetero > name frozen interface_residues_model_0 > #1/A:1,4-6,8-10,12-13,16-17,235,237-238,240,243-244,246-248,250-251,253-254/B:205-206,208-210,212,215-216,220-221,241,244,271-272,275-276,279,298-299,302,306,309-310,362 > select interface_residues_model_0 424 atoms, 402 bonds, 9 pseudobonds, 48 residues, 2 models selected > show interface_residues_model_0 atoms > show interface_residues_model_0 bonds > style interface_residues_model_0 stick Changed 424 atom styles > show af_contact_residues_model_0&sidechain atoms > show af_contact_residues_model_0&sidechain bonds > style af_contact_residues_model_0&sidechain stick Changed 137 atom styles Opened 1 AF3 top hit pair(s). Run metadata was written to: /Users/matthias.vorlaender/Library/CloudStorage/OneDrive- VBC/scripts/python/Mendel_ChimeraX/Example_data/fold_2026_05_13_13_22_alyref_uap56_thoc2/analysis/fold_2026_05_13_13_22_alyref_uap56_thoc2/af3-top Contacts/interfaces were prepared for display. Files are written only when you use 'Save Contacts and Interfaces' for the active model. Computing secondary structure > select #3.1/B:267 #3.1/A:29 > view Applied PAE hide-unselected to 1 model(s) in this run. > view > hide af_contact_residues_model_0&sidechain atoms > hide af_contact_residues_model_0&sidechain bonds Found 0 residue or atom pairs within distance 3 with pae <= 16 Applied PAE show-only and refreshed AlphaFold contacts at threshold 16 for 1 model(s) in this run. Contact display was refreshed for 1 model(s). Found 0 residue or atom pairs within distance 3 with pae <= 16 No AlphaFold contacts with PAE <= 16 were found for model_0 on chain pair A-C. Found 0 residue or atom pairs within distance 3 with pae <= 16 No AlphaFold contacts with PAE <= 16 were found for model_0 on chain pair A-C. Found 0 residue or atom pairs within distance 3 with pae <= 16 No AlphaFold contacts with PAE <= 16 were found for model_0 on chain pair A-C. > help circosplot No help found for 'circosplot' > circosplot Unknown command: circosplot > circplot Unknown command: circplot > toolshed show Window position QRect(1903,199 657x1177) outside any known screen, using primary screen > circoscontacts circoscontacts: writing intermediate files to /var/folders/l8/nt94jvjd7bg27cksyp_hvxnh0000gp/T/circoscontacts_0g_syu17 227 contacts 375 contacts circoscontacts: wrote /var/folders/l8/nt94jvjd7bg27cksyp_hvxnh0000gp/T/circoscontacts_0g_syu17/contacts_circos.html circoscontacts: use the Save HTML button in the page to copy output elsewhere. circoscontacts: opened HTML in default browser (/var/folders/l8/nt94jvjd7bg27cksyp_hvxnh0000gp/T/circoscontacts_0g_syu17/contacts_circos.html) circoscontacts: temporary directory retained for this run to keep artifacts accessible. > hide #3.1 atoms > hide #3.1 pseudobonds > hide #3.1 surfaces > show #3.1 cartoons > select clear Reset display for AF3 top hit fold_2026_05_13_13_22_alyref_uap56_thoc2. Applied PAE hide-unselected to 1 model(s) in this run. > blastprotein #3 Cannot start BLAST job: please choose exactly one chain (3 were specified) > blastprotein #3/C Webservices job id: DKPPLNOA9FNN357X Webservices job finished: DKPPLNOA9FNN357X Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 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: Mac15,6 Model Number: Z1AU002HPD/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 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: 15 days, 6 hours, 53 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP Z32: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 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-AFPredictionToolbars: 1.3.22 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-CircosContacts: 0.4.21 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-LowpassMap: 0.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0

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Query Language

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

The available operators are:

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

All of these operators can also be negated:

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

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

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

See also: TracTickets, TracReports, TracGuide, TicketQuery

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

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Query Language

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