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 13306)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19533	fixed	Boltz install command in nogui mode only installs torch on linux	Tom Goddard	Tom Goddard
#19531	duplicate	Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event	Tom Goddard	chimerax-bug-report@…
#19530	fixed	'BoltzHistoryPanel' object has no attribute '_results_table'	Tom Goddard	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 13306)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19533	fixed	Boltz install command in nogui mode only installs torch on linux	Tom Goddard	Tom Goddard
Description	Some faulty logic in the boltz install command caused it in nogui mode to not go beyond installing torch on linux and windows and not give any error. I only tried nogui install when I was setting up a boltz server so hadn't noticed before.
#19531	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-26.1-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000030704f000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x0000000306043000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x0000000305037000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000030402b000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000030301f000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x0000000302013000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x0000000301007000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000017f473000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000017e467000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000017d45b000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000017c44f000 (most recent call first): File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Current thread 0x00000001f98f2080 (most recent call first): File "/Applications/ChimeraX-1.11.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.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.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.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.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.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.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, PIL._imaging, 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, PIL._imagingmath, chimerax.graphics._graphics (total: 44) {"app_name":"ChimeraX","timestamp":"2025-12-20 15:09:51.00 +0900","app_version":"1.11.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.1 (25B78)","roots_installed":0,"name":"ChimeraX","incident_id":"14AEEB68-D769-42B5-97F2-54C7B923BDC7"} { "uptime" : 140000, "procRole" : "Background", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "Mac15,3", "coalitionID" : 14781, "osVersion" : { "train" : "macOS 26.1", "build" : "25B78", "releaseType" : "User" }, "captureTime" : "2025-12-20 15:09:36.7098 +0900", "codeSigningMonitor" : 2, "incident" : "14AEEB68-D769-42B5-97F2-54C7B923BDC7", "pid" : 61707, "translated" : false, "cpuType" : "ARM-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2025-12-18 11:59:42.9811 +0900", "procStartAbsTime" : 2574784547422, "procExitAbsTime" : 3558776511526, "procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"2AEF0A82-09C5-56B6-A9DC-8E70CF672D5C","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : 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"CFBundleIdentifier" : "com.apple.HIToolbox", "size" : 3155968, "uuid" : "9ab64c08-0685-3a0d-9a7e-83e7a1e9ebb4", "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox", "name" : "HIToolbox" }, { "source" : "P", "arch" : "arm64e", "base" : 6655660032, "size" : 651108, "uuid" : "b50f5a1a-be81-3068-92e1-3554f2be478a", "path" : "\/usr\/lib\/dyld", "name" : "dyld" }, { "size" : 0, "source" : "A", "base" : 0, "uuid" : "00000000-0000-0000-0000-000000000000" } ], "sharedCache" : { "base" : 6654574592, "size" : 5609635840, "uuid" : "b69ff43c-dbfd-3fb1-b4fe-a8fe32ea1062" }, "vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=1.2G written=79.7M(6%) resident=1442K(0%) swapped_out=78.3M(6%) unallocated=1.2G(94%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 1584K 23 ColorSync 128K 8 CoreAnimation 4608K 135 CoreGraphics 16K 1 CoreImage 64K 2 CoreServices 128K 1 CoreUI image data 5584K 43 Foundation 48K 2 Kernel Alloc Once 96K 2 MALLOC 445.2M 130 MALLOC guard page 3728K 4 Mach message 64K 2 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 880K 55 Stack 432.2M 56 Stack Guard 56.0M 1 VM_ALLOCATE 259.3M 129 VM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated) __AUTH 5878K 653 __AUTH_CONST 89.8M 1042 __CTF 824 1 __DATA 37.7M 1124 __DATA_CONST 59.1M 1172 __DATA_DIRTY 8820K 902 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __INFO_FILTER 8 1 __LINKEDIT 621.3M 126 __OBJC_RO 78.3M 1 __OBJC_RW 2567K 1 __TEXT 1.4G 1193 __TEXT (graphics) 160K 1 __TPRO_CONST 128K 2 dyld private memory 432K 5 mapped file 359.7M 86 page table in kernel 1442K 1 shared memory 3152K 22 =========== ======= ======= TOTAL 4.0G 6937 TOTAL, minus reserved VM space 3.9G 6937 ", "legacyInfo" : { "threadTriggered" : { "name" : "CrBrowserMain", "queue" : "com.apple.main-thread" } }, "logWritingSignature" : "669274142409163f6beb5d894982bc49aecaff50", "trialInfo" : { "rollouts" : [ { "rolloutId" : "644114de41e7236e6177f9bd", "factorPackIds" : [ ], "deploymentId" : 240000013 }, { "rolloutId" : "67648e5334a82511f4acf879", "factorPackIds" : [ ], "deploymentId" : 240000008 } ], "experiments" : [ ] } } ===== Log before crash start ===== Startup Messages --- note \| available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/ryotarotoda/Desktop/emd_8750.map Opened emd_8750.map as #1, grid size 240,240,240, pixel 1.23, shown at level 0.0402, step 1, values float32 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ryotarotoda/Desktop/movie1.mp4 Movie saved to /Users/ryotarotoda/Desktop/movie1.mp4 > set bgColor black > set bgColor white > set bgColor black > volume #1 level 0.04242 > ui tool show "Color Zone" No atoms chosen for color zoning > ui tool show "Surface Color" > color radial #1.1 palette #ed3a5f:#ffffff:#0000ff > color single #1.1 Surface Color: could not parse center "" as 3 numbers > color radial #1.1 palette 118.6,#e12629:256.7,#ffffff:394.8,#0000ff > color radial #1.1 palette 120,#e12629:120,#ff4044:120,#0000ff center > 153.13,147.6,139.68 > set bgColor black > color single #1.1 > color radial #1.1 palette 120,#e12629:120,#ff4044 center 153.13,147.6,139.68 > color single #1.1 > color radial #1.1 palette 120,#0000ff:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#ff9300cd:120,#ff0000 center > 153.13,147.6,139.68 > color radial #1.1 palette 120,#ff8080:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#e58080:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#e576bd:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#929000:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#9437ff:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#d783ff:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#7a81ff:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#ff85ff:120,#ff0000 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#73fdff:120,#ff0000 center 153.13,147.6,139.68 > volume #1 level 0.04242 > color radial #1.1 palette 120,#73fdff:120,#73fa79 center 153.13,147.6,139.68 > color radial #1.1 palette 120,#7a81ff:120,#73fa79 center 153.13,147.6,139.68 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ryotarotoda/Desktop/movie1.mp4 Movie saved to /Users/ryotarotoda/Desktop/movie1.mp4 > open /Users/ryotarotoda/Desktop/emd_8750.map Opened emd_8750.map as #2, grid size 240,240,240, pixel 1.23, shown at level 0.0402, step 1, values float32 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 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: Mac15,3 Model Number: Z1C800069J/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.41.1 OS Loader Version: 13822.41.1 Software: System Software Overview: System Version: macOS 26.1 (25B78) Kernel Version: Darwin 25.1.0 Time since boot: 9日 1時間 19分 Graphics/Displays: Apple M3: Chipset Model: Apple M3 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 XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 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 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 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: 7.13.0 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: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 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: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 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 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0
#19530	fixed	'BoltzHistoryPanel' object has no attribute '_results_table'	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.12.dev202512180555 (2025-12-18 05:55:44 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18) © 2016-2025 Regents of the University of California. All rights reserved. > open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3.cxs" Log from Fri Dec 19 14:52:44 2025UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18) © 2016-2025 Regents of the University of California. All rights reserved. > open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/GH30_Cellobiose_boltz.cxs" Log from Fri Dec 19 09:13:14 2025UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18) © 2016-2025 Regents of the University of California. All rights reserved. > open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH30_boltz.cxs" Log from Thu Dec 18 13:29:25 2025 Startup Messages --- note \| available bundle cache has not been initialized yet UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Boltz > boltz install C:\Users\kieuc/boltz22 Successfully created Boltz Python virtual environment C:\Users\kieuc/boltz22. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... C:\Users\kieuc/boltz22\Scripts\python.exe -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Downloading https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip \- 2.3 MB 6.1 MB/s 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting torch==2.7.1 (from boltz==2.2.0) Downloading torch-2.7.1-cp311-cp311-win_amd64.whl.metadata (28 kB) Requirement already satisfied: numpy<2.0,>=1.26 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from boltz==2.2.0) (1.26.4) Collecting hydra-core==1.3.2 (from boltz==2.2.0) Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB) Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0) Downloading pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB) Collecting rdkit>=2024.3.2 (from boltz==2.2.0) Downloading rdkit-2025.9.3-cp311-cp311-win_amd64.whl.metadata (4.3 kB) Collecting dm-tree==0.1.8 (from boltz==2.2.0) Downloading dm_tree-0.1.8-cp311-cp311-win_amd64.whl.metadata (2.0 kB) Collecting requests==2.32.3 (from boltz==2.2.0) Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) Collecting pandas>=2.2.2 (from boltz==2.2.0) Downloading pandas-2.3.3-cp311-cp311-win_amd64.whl.metadata (19 kB) Collecting types-requests (from boltz==2.2.0) Downloading types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB) Collecting einops==0.8.0 (from boltz==2.2.0) Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB) Collecting einx==0.3.0 (from boltz==2.2.0) Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB) Collecting fairscale==0.4.13 (from boltz==2.2.0) Downloading fairscale-0.4.13.tar.gz (266 kB) \-------------------------------------- 266.3/266.3 kB 2.8 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting mashumaro==3.14 (from boltz==2.2.0) Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB) \-------------------------------------- 114.4/114.4 kB 6.5 MB/s eta 0:00:00 Collecting modelcif==1.2 (from boltz==2.2.0) Downloading modelcif-1.2.tar.gz (66 kB) \---------------------------------------- 66.8/66.8 kB ? eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting wandb==0.18.7 (from boltz==2.2.0) Downloading wandb-0.18.7-py3-none-win_amd64.whl.metadata (9.7 kB) Collecting click==8.1.7 (from boltz==2.2.0) Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting pyyaml==6.0.2 (from boltz==2.2.0) Downloading PyYAML-6.0.2-cp311-cp311-win_amd64.whl.metadata (2.1 kB) Collecting biopython==1.84 (from boltz==2.2.0) Downloading biopython-1.84-cp311-cp311-win_amd64.whl.metadata (13 kB) Collecting scipy==1.13.1 (from boltz==2.2.0) Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl.metadata (60 kB) \---------------------------------------- 60.6/60.6 kB 3.4 MB/s eta 0:00:00 Collecting numba==0.61.0 (from boltz==2.2.0) Downloading numba-0.61.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB) Collecting gemmi==0.6.5 (from boltz==2.2.0) Downloading gemmi-0.6.5-cp311-cp311-win_amd64.whl.metadata (2.3 kB) Collecting scikit-learn==1.6.1 (from boltz==2.2.0) Downloading scikit_learn-1.6.1-cp311-cp311-win_amd64.whl.metadata (15 kB) Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0) Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB) Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0) Downloading cuequivariance_torch-0.8.0-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: setuptools>=46.4.0 in c:\users\kieuc\boltz22\lib\site-packages (from chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0) Requirement already satisfied: colorama in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from click==8.1.7->boltz==2.2.0) (0.4.6) Collecting sympy (from einx==0.3.0->boltz==2.2.0) Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB) Collecting frozendict (from einx==0.3.0->boltz==2.2.0) Downloading frozendict-2.4.7-py3-none-any.whl.metadata (23 kB) Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0) Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB) Collecting antlr4-python3-runtime==4.9.* (from hydra- core==1.3.2->boltz==2.2.0) Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB) \-------------------------------------- 117.0/117.0 kB 6.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: packaging in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from hydra- core==1.3.2->boltz==2.2.0) (25.0) Requirement already satisfied: typing-extensions>=4.1.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from mashumaro==3.14->boltz==2.2.0) (4.15.0) Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from modelcif==1.2->boltz==2.2.0) (2.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.2.0) Downloading llvmlite-0.44.0-cp311-cp311-win_amd64.whl.metadata (5.0 kB) Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0) Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) \---------------------------------------- 57.7/57.7 kB ? eta 0:00:00 Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) Downloading fsspec-2025.12.0-py3-none-any.whl.metadata (10 kB) Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0) Downloading torchmetrics-1.8.2-py3-none-any.whl.metadata (22 kB) Collecting lightning-utilities>=0.10.0 (from pytorch- lightning==2.5.0->boltz==2.2.0) Downloading lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB) Requirement already satisfied: charset-normalizer<4,>=2 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (2.6.2) Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (2025.11.12) Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0) Downloading joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB) Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0) Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB) Requirement already satisfied: filelock in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0) (3.19.1) Requirement already satisfied: networkx in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0) (3.3) Requirement already satisfied: jinja2 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0) (3.1.6) Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0) Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.2.0) Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB) Requirement already satisfied: platformdirs in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from wandb==0.18.7->boltz==2.2.0) (4.5.1) Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.2.0) Downloading protobuf-5.29.5-cp310-abi3-win_amd64.whl.metadata (592 bytes) Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from wandb==0.18.7->boltz==2.2.0) (7.0.0) Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.2.0) Downloading sentry_sdk-2.48.0-py2.py3-none-any.whl.metadata (10 kB) Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0) Downloading setproctitle-1.3.7-cp311-cp311-win_amd64.whl.metadata (11 kB) Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0) Downloading cuequivariance-0.8.0-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: python-dateutil>=2.8.2 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2) Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.3) Requirement already satisfied: Pillow in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from rdkit>=2024.3.2->boltz==2.2.0) (11.3.0) Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from docker- pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0) Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (3.13.1) Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0) Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB) Requirement already satisfied: msgpack in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.1) Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0) Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) Collecting opt-einsum (from cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0) Downloading opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3) Requirement already satisfied: aiohappyeyeballs>=2.5.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (2.6.1) Requirement already satisfied: aiosignal>=1.4.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (1.4.0) Requirement already satisfied: attrs>=17.3.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (25.4.0) Requirement already satisfied: frozenlist>=1.1.1 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (1.8.0) Requirement already satisfied: multidict<7.0,>=4.5 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (6.7.0) Requirement already satisfied: propcache>=0.2.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (0.4.1) Requirement already satisfied: yarl<2.0,>=1.17.0 in c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.2.0) (1.22.0) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0) Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB) Downloading biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB) \---------------------------------------- 2.8/2.8 MB 4.6 MB/s eta 0:00:00 Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB) Downloading click-8.1.7-py3-none-any.whl (97 kB) 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pytorch_lightning-2.5.0-py3-none-any.whl (819 kB) \---------------------------------------- 819.4/819.4 kB 5.2 MB/s eta 0:00:00 Downloading PyYAML-6.0.2-cp311-cp311-win_amd64.whl (161 kB) \--------------------------------------- 162.0/162.0 kB 10.1 MB/s eta 0:00:00 Downloading requests-2.32.3-py3-none-any.whl (64 kB) \---------------------------------------- 64.9/64.9 kB ? eta 0:00:00 Downloading scikit_learn-1.6.1-cp311-cp311-win_amd64.whl (11.1 MB) \---------------------------------------- 11.1/11.1 MB 5.4 MB/s eta 0:00:00 Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB) \---------------------------------------- 46.2/46.2 MB 4.5 MB/s eta 0:00:00 Downloading torch-2.7.1-cp311-cp311-win_amd64.whl (216.1 MB) \---------------------------------------- 216.1/216.1 MB 1.7 MB/s eta 0:00:00 Downloading wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB) \---------------------------------------- 15.5/15.5 MB 2.3 MB/s eta 0:00:00 Downloading cuequivariance_torch-0.8.0-py3-none-any.whl 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llvmlite-0.44.0-cp311-cp311-win_amd64.whl (30.3 MB) \---------------------------------------- 30.3/30.3 MB 2.8 MB/s eta 0:00:00 Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB) \---------------------------------------- 79.5/79.5 kB 4.6 MB/s eta 0:00:00 Downloading protobuf-5.29.5-cp310-abi3-win_amd64.whl (434 kB) \---------------------------------------- 434.8/434.8 kB 3.4 MB/s eta 0:00:00 Downloading sentry_sdk-2.48.0-py2.py3-none-any.whl (414 kB) \---------------------------------------- 414.6/414.6 kB 3.7 MB/s eta 0:00:00 Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB) \---------------------------------------- 6.3/6.3 MB 2.5 MB/s eta 0:00:00 Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Downloading torchmetrics-1.8.2-py3-none-any.whl (983 kB) \---------------------------------------- 983.2/983.2 kB 2.7 MB/s eta 0:00:00 Downloading tqdm-4.67.1-py3-none-any.whl (78 kB) \---------------------------------------- 78.5/78.5 kB 1.5 MB/s eta 0:00:00 Downloading cuequivariance-0.8.0-py3-none-any.whl (266 kB) \---------------------------------------- 266.7/266.7 kB 2.4 MB/s eta 0:00:00 Downloading frozendict-2.4.7-py3-none-any.whl (16 kB) Downloading setproctitle-1.3.7-cp311-cp311-win_amd64.whl (13 kB) Downloading gitdb-4.0.12-py3-none-any.whl (62 kB) \---------------------------------------- 62.8/62.8 kB 1.7 MB/s eta 0:00:00 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB) \---------------------------------------- 536.2/536.2 kB 2.2 MB/s eta 0:00:00 Downloading opt_einsum-3.4.0-py3-none-any.whl (71 kB) \---------------------------------------- 71.9/71.9 kB 4.1 MB/s eta 0:00:00 Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: boltz, fairscale, modelcif, antlr4-python3-runtime Building wheel for boltz (pyproject.toml): started Building wheel for boltz (pyproject.toml): finished with status 'done' Created wheel for boltz: filename=boltz-2.2.0-py3-none-any.whl size=269018 sha256=82e3bcf092870d91ab024996009e2eafbd93fa008661d139448f56053ceaea14 Stored in directory: C:\Users\kieuc\AppData\Local\Temp\pip-ephem-wheel-cache- _i27jzdy\wheels\26\ba\5c\a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4 Building wheel for fairscale (pyproject.toml): started Building wheel for fairscale (pyproject.toml): finished with status 'done' Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl size=332216 sha256=32195bf6b96423a04f827ab5233dff6357b218ed3513e75a439b148210b1bcd4 Stored in directory: c:\users\kieuc\appdata\local\pip\cache\wheels\95\ef\96\5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273 Building wheel for modelcif (setup.py): started Building wheel for modelcif (setup.py): finished with status 'done' Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41204 sha256=141842c3010067f4eafee6bf80ef5380ceafd0220fef1fb8f09963ae31e7c772 Stored in directory: c:\users\kieuc\appdata\local\pip\cache\wheels\d2\3a\8c\e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df Building wheel for antlr4-python3-runtime (setup.py): started Building wheel for antlr4-python3-runtime (setup.py): finished with status 'done' Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144577 sha256=4b9f7a619903267c03f2bd01c519a479710c43f56c1efb800b835e78a7255cee Stored in directory: c:\users\kieuc\appdata\local\pip\cache\wheels\1a\97\32\461f837398029ad76911109f07047fde1d7b661a147c7c56d1 Successfully built boltz fairscale modelcif antlr4-python3-runtime Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types- requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy, requests, rdkit, pyyaml, protobuf, opt-einsum, mashumaro, llvmlite, lightning- utilities, joblib, gemmi, fsspec, frozendict, einops, docker-pycreds, click, biopython, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx, cuequivariance, chembl_structure_pipeline, torchmetrics, hydra-core, gitpython, fairscale, cuequivariance_torch, wandb, pytorch-lightning, boltz Attempting uninstall: scipy Found existing installation: scipy 1.14.0 Not uninstalling scipy at c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages, outside environment C:\Users\kieuc\boltz22 Can't uninstall 'scipy'. No files were found to uninstall. Attempting uninstall: requests Found existing installation: requests 2.32.5 Not uninstalling requests at c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages, outside environment C:\Users\kieuc\boltz22 Can't uninstall 'requests'. No files were found to uninstall. Attempting uninstall: click Found existing installation: click 8.3.1 Not uninstalling click at c:\program files\chimerax 1.12.dev202512180555\bin\lib\site-packages, outside environment C:\Users\kieuc\boltz22 Can't uninstall 'click'. No files were found to uninstall. Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-2.2.0 chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.8.0 cuequivariance_torch-0.8.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.7 fsspec-2025.12.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.3 lightning- utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.3 protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.9.3 requests-2.32.3 scikit- learn-1.6.1 scipy-1.13.1 sentry-sdk-2.48.0 setproctitle-1.3.7 smmap-5.0.2 sympy-1.14.0 threadpoolctl-3.6.0 torch-2.7.1 torchmetrics-1.8.2 tqdm-4.67.1 types-requests-2.32.4.20250913 wandb-0.18.7 [notice] A new release of pip is available: 24.0 -> 25.3 [notice] To update, run: C:\Users\kieuc\boltz22\Scripts\python.exe -m pip install --upgrade pip Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz C:\Users\kieuc/boltz22\Scripts\python.exe C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\download_weights_and_ccd.py Downloading the CCD data to C:\Users\kieuc\\.boltz\mols.tar. This may take a bit of time. You may change the cache directory with the --cache flag. Extracting the CCD data to C:\Users\kieuc\\.boltz\mols. This may take a bit of time. You may change the cache directory with the --cache flag. Downloading the Boltz-2 weights to C:\Users\kieuc\\.boltz\boltz2_conf.ckpt. You may change the cache directory with the --cache flag. Downloading the Boltz-2 affinity weights to C:\Users\kieuc\\.boltz\boltz2_aff.ckpt. You may change the cache directory with the --cache flag. Making CCD atom counts table for 45227 in C:\Users\kieuc/.boltz/mols Boltz model parameters and CCD database are installed in ~/.boltz Successfully installed Boltz program and neural net weights. > boltz predict protein > SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP > ligandCcd 122 affinity 122 Running Boltz prediction of protein with 415 residues, 1 ligands 122 on cpu Using multiple sequence alignment server https://api.colabfold.com Prediction terminated by user > boltz predict protein > SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP Running Boltz prediction of protein with 415 residues on cpu Using cached multiple sequence alignment C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1 Confidence score 0.96, pTM 0.96, ipTM 0.00, pLDDT 0.96 Boltz prediction completed in 2793 seconds (start boltz 6 sec, sequence search 0 sec, load weights 41 sec, structure inference 2746 sec) Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. > open > C:\Users\kieuc/Desktop/boltz_2\boltz_results_boltz_2\predictions\boltz_2\boltz_2_model_0.cif > logInfo false > boltz predict protein > SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP > ligandCcd CEL affinity CEL Running Boltz prediction of protein with 415 residues, 1 ligands CEL on cpu Using cached multiple sequence alignment C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1 > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH30_boltz.cxs" ——— End of log from Thu Dec 18 13:29:25 2025 ——— > view name session-start opened ChimeraX session > ui tool show "Boltz History" > open > C:\Users\kieuc/Desktop\boltz_3\boltz_results_boltz_3\predictions\boltz_3\boltz_3_model_0.cif > hide #1 models > close #1 > open 4PTV 4ptv title: Halothermothrix orenii beta-glucosidase A, thiocellobiose complex [more info...] Chain information for 4ptv #1 --- Chain \| Description \| UniProt A B \| Glycoside hydrolase family 1 \| B8CYA8_HALOH 1-451 Non-standard residues in 4ptv #1 --- BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose) CS — cesium ion PE4 — 2-{2-[2-(2-{2-[2-(2-ethoxy- ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol (polyethylene glycol PEG4000) SGC — 4-thio-beta-D-glucopyranose (4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE; 4-thio-beta-D-glucose; 4-thio-D-glucose; 4-thio-glucose) 4ptv mmCIF Assemblies --- 1\| author_and_software_defined_assembly 2\| author_and_software_defined_assembly 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 7292 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #1 models > hide #2 models > show #1 models > select :BGC 22 atoms, 22 bonds, 2 residues, 1 model selected > select :SGC 24 atoms, 24 bonds, 2 residues, 1 model selected > hide #1 models > show #2 models > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/GH30_Cel_Boltz.pdb" > open 2O9R Summary of feedback from opening 2O9R fetched from pdb --- note \| Fetching compressed mmCIF 2o9r from http://files.rcsb.org/download/2o9r.cif 2o9r title: beta-glucosidase B complexed with thiocellobiose [more info...] Chain information for 2o9r #3 --- Chain \| Description \| UniProt A \| Beta-glucosidase B \| BGLB_PAEPO 4-448 Non-standard residues in 2o9r #3 --- BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose) SGC — 4-thio-beta-D-glucopyranose (4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE; 4-thio-beta-D-glucose; 4-thio-D-glucose; 4-thio-glucose) > ui tool show Boltz > boltz predict protein #2/A ligandCcd BGC,SGC name boltz_3_model_0.cif Running Boltz prediction of protein with 415 residues, 2 ligands BGC, SGC on cpu Using cached multiple sequence alignment C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1 > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/GH30_Thio_andotherPDBwiththiocellobiose.pdb" Confidence score 0.92, pTM 0.97, ipTM 0.81, pLDDT 0.95 Boltz prediction completed in 3241 seconds (start boltz 6 sec, sequence search 0 sec, load weights 34 sec, structure inference 3200 sec) > open > C:\Users\kieuc/Desktop/boltz_boltz_3_model_0.cif\boltz_results_boltz_3_model_0.cif\predictions\boltz_3_model_0.cif\boltz_3_model_0.cif_model_0.cif > logInfo false Matchmaker boltz_3_model_0.cif, chain A (#2) with boltz_3_model_0.cif_model_0.cif, chain A (#4), sequence alignment score = 2157.8 RMSD between 413 pruned atom pairs is 0.395 angstroms; (across all 415 pairs: 0.429) > hide #3 models > hide #2 models > show #2 models > hide #4 models QWindowsWindow::setGeometry: Unable to set geometry 1920x1127+0+35 (frame: 1942x1183-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1". Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45, 11, 11 minimum size: 557x751 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858, y=1183))) QWindowsWindow::setGeometry: Unable to set geometry 1920x1232+0+35 (frame: 1942x1288-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1". Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45, 11, 11 minimum size: 557x821 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858, y=1288))) > boltz predict protein #2/A forEachSmilesLigand > "ligand1,C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O" > name boltz_3_model_0.cif affinity each Running Boltz prediction of protein with 415 residues, 1 ligands C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O on cpu Using cached multiple sequence alignment C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1 > close #2 > show #4 models QWindowsWindow::setGeometry: Unable to set geometry 1920x1418+0+35 (frame: 1942x1474-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1". Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45, 11, 11 minimum size: 557x945 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858, y=1474))) Ligand C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O predicted binding affinity 5.4 uM, predicted binding probability 0.47 Boltz prediction completed in 5295 seconds (start boltz 6 sec, sequence search 0 sec, load weights 52 sec, structure inference 3156 sec, load affinity weights 56 sec, affinity inference 2025 sec) > open > C:\Users\kieuc/Desktop/boltz_boltz_3_model_0.cif_1\boltz_results_ligand1\predictions\ligand1\ligand1_model_0.cif > logInfo false > hide #2 models > hide #4 models > show #2 models > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3-cellobiose- > Boltz.pdb" > close #4 > rename #2 GH30-Cellulobio.cif > rename #2 GH30-Cellulobiose.cif > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/GH30_Cellobiose_boltz.cxs" ——— End of log from Fri Dec 19 09:13:14 2025 ——— > view name session-start opened ChimeraX session > hide #2 models > show #1 models > select ~sel & ##selected 7785 atoms, 7580 bonds, 1313 residues, 1 model selected > select clear > show #3 models > hide #1 models > ui tool show "Boltz History" > open Missing or invalid "fileNames" argument: Expected a file name Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2585, in <lambda> self.ui_area.contextMenuEvent = lambda e, , self=self: self.show_context_menu(e) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2759, in show_context_menu _show_context_menu(event, self.tool_window.tool_instance, self.tool_window, File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2809, in _show_context_menu fill_cb(menu, pos.x(), pos.y()) File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2585, in <lambda> self.ui_area.contextMenuEvent = lambda e, , self=self: self.show_context_menu(e) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2759, in show_context_menu _show_context_menu(event, self.tool_window.tool_instance, self.tool_window, File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2809, in _show_context_menu fill_cb(menu, pos.x(), pos.y()) File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > ui tool show Boltz > open > C:\Users\kieuc/Desktop\boltz_Gh3_cellobiose\boltz_results_Gh3_cellobiose\predictions\Gh3_cellobiose\Gh3_cellobiose_model_0.cif > ui tool show Matchmaker > matchmaker #2 to #4 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 Gh3_cellobiose_model_0.cif, chain A (#4) with GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95 RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs: 28.468) > matchmaker #2 to #4 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 Gh3_cellobiose_model_0.cif, chain A (#4) with GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95 RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs: 28.468) > ui tool show Matchmaker > matchmaker #2 to #4 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 Gh3_cellobiose_model_0.cif, chain A (#4) with GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95 RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs: 28.468) > matchmaker #2 to #4 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 Gh3_cellobiose_model_0.cif, chain A (#4) with GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95 RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs: 28.468) > ui tool show Matchmaker > 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 4ptv, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4), sequence alignment score = 121.4 RMSD between 21 pruned atom pairs is 1.094 angstroms; (across all 379 pairs: 30.950) > 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 4ptv, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4), sequence alignment score = 121.4 RMSD between 21 pruned atom pairs is 1.094 angstroms; (across all 379 pairs: 30.950) > show #1 models > hide #3 models > select #3/A 3755 atoms, 3737 bonds, 575 residues, 1 model selected > hide #1 models > hide #4 models > show #4 models > show #1 models > select #1/B 3853 atoms, 3778 bonds, 627 residues, 1 model selected > delete #1/B > delete #1/D > hide #1 models > select add #4 4307 atoms, 4378 bonds, 567 residues, 1 model selected > close #1 > close #2 > close #3 QWindowsWindow::setGeometry: Unable to set geometry 1920x1115+0+35 (frame: 1942x1171-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1". Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45, 11, 11 minimum size: 557x743 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858, y=1171))) > boltz predict protein /A ligandSmiles > C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)OC2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)OC3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O)O > name Gh3_laminarin.cif Running Boltz prediction of protein with 566 residues, 1 ligands C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)OC2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)OC3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O)O on cpu Using cached multiple sequence alignment C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_4 > open 6SZ6 Summary of feedback from opening 6SZ6 fetched from pdb --- notes \| Fetching compressed mmCIF 6sz6 from http://files.rcsb.org/download/6sz6.cif Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif Fetching CCD MAN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif 6sz6 title: Chaetomium thermophilum beta-glucosidase [more info...] Chain information for 6sz6 #1 --- Chain \| Description \| UniProt A \| Beta-glucosidase \| A6YRT4_9PEZI 32-867 Non-standard residues in 6sz6 #1 --- BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose) BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 6820 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Matchmaker > 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 6sz6, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4), sequence alignment score = 632.3 RMSD between 241 pruned atom pairs is 0.997 angstroms; (across all 492 pairs: 9.752) > 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 6sz6, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4), sequence alignment score = 632.3 RMSD between 241 pruned atom pairs is 0.997 angstroms; (across all 492 pairs: 9.752) > select clear > hide #1 models > show #1 models > hide #4 models > open 3zyz Summary of feedback from opening 3zyz fetched from pdb --- notes \| Fetching compressed mmCIF 3zyz from http://files.rcsb.org/download/3zyz.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif Fetching CCD PEG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif 3zyz title: Crystal structure of a glycoside hydrolase family 3 beta-glucosidase, Bgl1 from Hypocrea jecorina at 2.1A resolution. [more info...] Chain information for 3zyz #2 --- Chain \| Description \| UniProt A \| BETA-D-GLUCOSIDE GLUCOHYDROLASE \| Q12715_TRIRE 1-713 Non-standard residues in 3zyz #2 --- BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose) GOL — glycerol (glycerin; propane-1,2,3-triol) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PEG — di(hydroxyethyl)ether 56 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #1 models > open 2X40 Summary of feedback from opening 2X40 fetched from pdb --- notes \| Fetching compressed mmCIF 2x40 from http://files.rcsb.org/download/2x40.cif Fetching CCD BR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BR/BR.cif 2x40 title: Structure of beta-glucosidase 3B from Thermotoga neapolitana in complex with glycerol [more info...] Chain information for 2x40 #3 --- Chain \| Description \| UniProt A \| BETA-GLUCOSIDASE \| Q0GC07_THENN 1-721 Non-standard residues in 2x40 #3 --- BR — bromide ion GOL — glycerol (glycerin; propane-1,2,3-triol) 2x40 mmCIF Assemblies --- 1\| author_and_software_defined_assembly 5660 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #2 models > open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/GH3_fold_2025_09_27_06_25/fold_2025_09_27_06_25_model_0.cif" Chain information for fold_2025_09_27_06_25_model_0.cif #5 --- Chain \| Description A \| . Computing secondary structure > hide #5 models Confidence score 0.97, pTM 0.97, ipTM 0.97, pLDDT 0.97 Boltz prediction completed in 6389 seconds (start boltz 7 sec, sequence search 0 sec, load weights 36 sec, structure inference 6347 sec) > open > C:\Users\kieuc/Desktop/boltz_Gh3_laminarin\boltz_results_Gh3_laminarin\predictions\Gh3_laminarin\Gh3_laminarin_model_0.cif > logInfo false > open 8VA3 Summary of feedback from opening 8VA3 fetched from pdb --- notes \| Fetching compressed mmCIF 8va3 from http://files.rcsb.org/download/8va3.cif Fetching CCD EPE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif Fetching CCD NA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif Fetching CCD PGE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif Fetching CCD PO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif 8va3 title: Crystal structure of CapGH3b enzyme retrieved from capybara gut metagenome [more info...] Chain information for 8va3 #7 --- Chain \| Description A B \| Glycoside hydrolase family 3 Non-standard residues in 8va3 #7 --- EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion NA — sodium ion PEG — di(hydroxyethyl)ether PGE — triethylene glycol PO4 — phosphate ion 43 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 11824 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > close #3 > hide #!7 models > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường > Dương/Gh3_laminarin1_boltz.pdb" > close #1 > close #2 > show #!7 models > hide #6 models > select #7/B 6635 atoms, 6096 bonds, 7 pseudobonds, 1425 residues, 3 models selected > delete #7/B > show #5 models > ui tool show Matchmaker > matchmaker #5 to #7 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 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A (#5), sequence alignment score = 1149.7 RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs: 4.765) > matchmaker #5 to #7 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 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A (#5), sequence alignment score = 1149.7 RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs: 4.765) > mmaker #4,5,6 to #7 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 8va3, chain A (#7) with Gh3_cellobiose_model_0.cif, chain A (#4), sequence alignment score = 1142.8 RMSD between 443 pruned atom pairs is 0.951 angstroms; (across all 551 pairs: 5.421) Matchmaker 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A (#5), sequence alignment score = 1149.7 RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs: 4.765) Matchmaker 8va3, chain A (#7) with Gh3_laminarin_model_0.cif, chain A (#6), sequence alignment score = 1139.2 RMSD between 426 pruned atom pairs is 0.951 angstroms; (across all 550 pairs: 4.769) > hide #5 models > show #6 models > hide #6 models > show #4 models > hide #4 models > save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3.cxs" ——— End of log from Fri Dec 19 14:52:44 2025 ——— > view name session-start opened ChimeraX session > hide #!7 models > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > close session > ui tool show "Boltz History" Confidence score 0.93, pTM 0.96, ipTM 0.85, pLDDT 0.95 Boltz prediction completed in 4766 seconds (start boltz 60 sec, sequence search 0 sec, load weights 151 sec, structure inference 4555 sec) Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. > open > C:\Users\kieuc/Desktop/boltz_GH30-xylan_1\boltz_results_GH30-xylan\predictions\GH30-xylan\GH30-xylan_model_0.cif > logInfo false Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2585, in <lambda> self.ui_area.contextMenuEvent = lambda e, *, self=self: self.show_context_menu(e) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2759, in show_context_menu _show_context_menu(event, self.tool_window.tool_instance, self.tool_window, File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\ui\gui.py", line 2809, in _show_context_menu fill_cb(menu, pos.x(), pos.y()) File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table' File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site- packages\chimerax\boltz\history.py", line 190, in fill_context_menu if self._results_table: ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 32.0.101.7077 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.11.9 Locale: en_US.cp1252 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: Dell Inc. Model: XPS 13 9310 OS: Microsoft Windows 11 Pro (Build 26100) Memory: 34,052,284,416 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i7-1195G7 @ 2.90GHz OSLanguage: en-US Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 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: 2025.11.12 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: 1.61.5 ChimeraX-AtomicLibrary: 14.2.2 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: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202512180555 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8 ChimeraX-Label: 1.3 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: 1.7 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: 1.50 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 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.13.0 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: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pywin32: 311 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 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 WMI: 1.5.1 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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