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Version 2 (modified by trac, 9 years ago) ( diff )
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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 13752)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20234	duplicate	Crash in QDockWidget::event() in Qt 6.9.2	Tom Goddard	chimerax-bug-report@…
#20230	can't reproduce	Minimize: Residue template with the same override level already exists	Eric Pettersen	chimerax-bug-report@…
#20229	limitation	vop maximum: ArrayMemoryError	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 13752)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#20234	duplicate	Crash in QDockWidget::event() in Qt 6.9.2	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.4.1-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: Segmentation fault Thread 0x0000000310c37000 (most recent call first): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000030e833000 (most recent call first): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x000000030c2f3000 (most recent call first): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Thread 0x00000003035df000 (most recent call first): File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap Current thread 0x00000001f64d18c0 (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/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.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 58) {"app_name":"ChimeraX","timestamp":"2026-04-28 14:25:51.00 +0100","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.4.1 (25E253)","roots_installed":0,"name":"ChimeraX","incident_id":"60E283BC-DCB0-419A-BF8B-99F348CF7B15"} { "uptime" : 57000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "Mac17,9", "coalitionID" : 1627, "osVersion" : { "train" : "macOS 26.4.1", "build" : "25E253", "releaseType" : "User" }, "captureTime" : "2026-04-28 14:25:50.0891 +0100", "codeSigningMonitor" : 2, "incident" : "60E283BC-DCB0-419A-BF8B-99F348CF7B15", "pid" : 27941, "translated" : false, "cpuType" : "ARM-64", "procLaunch" : "2026-04-28 14:16:06.2759 +0100", "procStartAbsTime" : 1361139053368, "procExitAbsTime" : 1375150505420, "procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"548AABE6-C7C3-5E39-9E15-AF7A3E2E864B","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "F757CBBA-C716-7781-2B0E-A61AE18E0FF4", "appleIntelligenceStatus" : {"state":"available"}, "developerMode" : 1, "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "codeSigningAuxiliaryInfo" : 0, "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="}, "bootSessionUUID" : "D461F6F8-2CD9-479D-9065-606F506F833A", "wakeTime" : 24058, "sleepWakeUUID" : "60A71D30-1A34-49F0-9981-63A684132CB9", "sip" : "enabled", "vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4378198008 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 104f60000-104f64000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX", "exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":27941}, "vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4378198008 REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 104f60000-104f64000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX", "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 0, "threads" : [{ "threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":54077995672},{"value":104},{"value":111},{"value":0},{"value":0},{"value":12969719820539662363},{"value":12969719813328931035},{"value":14757395258967641293},{"value":4294967286},{"value":54077995602},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8450514720},{"value":0},{"value":11},{"value":259},{"value":8427215264 ,"symbolLocation":224,"symbol": 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"a05a390aa82a7db582d69a66b4cff51870e02139", "roots_installed" : 0, "bug_type" : "309", "trmStatus" : 1, "trialInfo" : { "rollouts" : [ { "rolloutId" : "64c025b28b7f0e739e4fbe58", "factorPackIds" : [ ], "deploymentId" : 240000041 }, { "rolloutId" : "63f9578e238e7b23a1f3030a", "factorPackIds" : [ ], "deploymentId" : 240000005 } ], "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/Ania/Desktop/HPI/DALI12_Viridis.cxs format session > view name session-start opened ChimeraX session > matchmaker #2-25 to #1 showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#2), sequence alignment score = 174.9 Alignment identifier is 16 Showing conservation header ("seq_conservation" residue attribute) for alignment 16 Hiding conservation header for alignment 16 Chains used in RMSD evaluation for alignment 16: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #2/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 16 RMSD between 43 pruned atom pairs is 0.933 angstroms; (across all 111 pairs: 6.059) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 17 Showing conservation header ("seq_conservation" residue attribute) for alignment 17 Hiding conservation header for alignment 17 Chains used in RMSD evaluation for alignment 17: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 17 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#4), sequence alignment score = 516.2 Alignment identifier is 18 Showing conservation header ("seq_conservation" residue attribute) for alignment 18 Hiding conservation header for alignment 18 Chains used in RMSD evaluation for alignment 18: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #4/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 18 RMSD between 108 pruned atom pairs is 0.524 angstroms; (across all 117 pairs: 1.674) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb, chain A (#5), sequence alignment score = 390.3 Alignment identifier is 19 Showing conservation header ("seq_conservation" residue attribute) for alignment 19 Hiding conservation header for alignment 19 Chains used in RMSD evaluation for alignment 19: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb #5/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 19 RMSD between 95 pruned atom pairs is 0.708 angstroms; (across all 116 pairs: 2.958) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#6), sequence alignment score = 469.7 Alignment identifier is 20 Showing conservation header ("seq_conservation" residue attribute) for alignment 20 Hiding conservation header for alignment 20 Chains used in RMSD evaluation for alignment 20: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #6/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 20 RMSD between 95 pruned atom pairs is 0.789 angstroms; (across all 116 pairs: 2.259) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#7), sequence alignment score = 158.4 Alignment identifier is 21 Showing conservation header ("seq_conservation" residue attribute) for alignment 21 Hiding conservation header for alignment 21 Chains used in RMSD evaluation for alignment 21: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #7/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 21 RMSD between 74 pruned atom pairs is 1.067 angstroms; (across all 114 pairs: 6.727) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#8), sequence alignment score = 152.8 Alignment identifier is 22 Showing conservation header ("seq_conservation" residue attribute) for alignment 22 Hiding conservation header for alignment 22 Chains used in RMSD evaluation for alignment 22: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #8/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 22 RMSD between 51 pruned atom pairs is 0.947 angstroms; (across all 110 pairs: 6.406) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#9), sequence alignment score = 162.9 Alignment identifier is 23 Showing conservation header ("seq_conservation" residue attribute) for alignment 23 Hiding conservation header for alignment 23 Chains used in RMSD evaluation for alignment 23: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #9/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 23 RMSD between 70 pruned atom pairs is 1.087 angstroms; (across all 114 pairs: 5.182) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#10), sequence alignment score = 145 Alignment identifier is 24 Showing conservation header ("seq_conservation" residue attribute) for alignment 24 Hiding conservation header for alignment 24 Chains used in RMSD evaluation for alignment 24: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #10/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 24 RMSD between 30 pruned atom pairs is 0.794 angstroms; (across all 111 pairs: 7.058) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#11), sequence alignment score = 130.9 Alignment identifier is 25 Showing conservation header ("seq_conservation" residue attribute) for alignment 25 Hiding conservation header for alignment 25 Chains used in RMSD evaluation for alignment 25: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #11/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 25 RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 112 pairs: 7.396) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#12), sequence alignment score = 135.5 Alignment identifier is 26 Showing conservation header ("seq_conservation" residue attribute) for alignment 26 Hiding conservation header for alignment 26 Chains used in RMSD evaluation for alignment 26: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #12/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 26 RMSD between 48 pruned atom pairs is 0.986 angstroms; (across all 110 pairs: 8.206) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#13), sequence alignment score = 190.7 Alignment identifier is 27 Showing conservation header ("seq_conservation" residue attribute) for alignment 27 Hiding conservation header for alignment 27 Chains used in RMSD evaluation for alignment 27: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #13/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 27 RMSD between 64 pruned atom pairs is 1.020 angstroms; (across all 113 pairs: 7.144) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#14), sequence alignment score = 153.1 Alignment identifier is 28 Showing conservation header ("seq_conservation" residue attribute) for alignment 28 Hiding conservation header for alignment 28 Chains used in RMSD evaluation for alignment 28: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #14/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 28 RMSD between 51 pruned atom pairs is 0.975 angstroms; (across all 111 pairs: 6.729) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#15), sequence alignment score = 136.5 Alignment identifier is 29 Showing conservation header ("seq_conservation" residue attribute) for alignment 29 Hiding conservation header for alignment 29 Chains used in RMSD evaluation for alignment 29: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #15/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 29 RMSD between 52 pruned atom pairs is 0.944 angstroms; (across all 110 pairs: 8.095) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#16), sequence alignment score = 377.2 Alignment identifier is 30 Showing conservation header ("seq_conservation" residue attribute) for alignment 30 Hiding conservation header for alignment 30 Chains used in RMSD evaluation for alignment 30: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #16/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 30 RMSD between 98 pruned atom pairs is 0.757 angstroms; (across all 115 pairs: 1.981) > show #3 models > hide #3 models > show #3 models > matchmaker #2-25 to #1 showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#2), sequence alignment score = 174.9 RMSD between 43 pruned atom pairs is 0.933 angstroms; (across all 111 pairs: 6.059) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#4), sequence alignment score = 516.2 RMSD between 108 pruned atom pairs is 0.524 angstroms; (across all 117 pairs: 1.674) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb, chain A (#5), sequence alignment score = 390.3 RMSD between 95 pruned atom pairs is 0.708 angstroms; (across all 116 pairs: 2.958) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#6), sequence alignment score = 469.7 RMSD between 95 pruned atom pairs is 0.789 angstroms; (across all 116 pairs: 2.259) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#7), sequence alignment score = 158.4 RMSD between 74 pruned atom pairs is 1.067 angstroms; (across all 114 pairs: 6.727) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#8), sequence alignment score = 152.8 RMSD between 51 pruned atom pairs is 0.947 angstroms; (across all 110 pairs: 6.406) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#9), sequence alignment score = 162.9 RMSD between 70 pruned atom pairs is 1.087 angstroms; (across all 114 pairs: 5.182) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#10), sequence alignment score = 145 RMSD between 30 pruned atom pairs is 0.794 angstroms; (across all 111 pairs: 7.058) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#11), sequence alignment score = 130.9 RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 112 pairs: 7.396) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#12), sequence alignment score = 135.5 RMSD between 48 pruned atom pairs is 0.986 angstroms; (across all 110 pairs: 8.206) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#13), sequence alignment score = 190.7 RMSD between 64 pruned atom pairs is 1.020 angstroms; (across all 113 pairs: 7.144) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#14), sequence alignment score = 153.1 RMSD between 51 pruned atom pairs is 0.975 angstroms; (across all 111 pairs: 6.729) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#15), sequence alignment score = 136.5 RMSD between 52 pruned atom pairs is 0.944 angstroms; (across all 110 pairs: 8.095) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#16), sequence alignment score = 377.2 RMSD between 98 pruned atom pairs is 0.757 angstroms; (across all 115 pairs: 1.981) > matchmaker #3 to #1 showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 1 Showing conservation header ("seq_conservation" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > hide #2 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > hide #13 models > hide #14 models > hide #15 models > hide #16 models > 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > ui tool show Matchmaker > matchmaker #3 to #1 showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 2 Showing conservation header ("seq_conservation" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > matchmaker #3 to #1 showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 Iteration cutoff \| 2 Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 3 Showing conservation header ("seq_conservation" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > matchmaker #3 to #1 cutoffDistance none showAlignment true Parameters --- Chain pairing \| bb Alignment algorithm \| Needleman-Wunsch Similarity matrix \| BLOSUM-62 SS fraction \| 0.3 Gap open (HH/SS/other) \| 18/18/6 Gap extend \| 1 SS matrix \| \| \| H \| S \| O ---\|---\|---\|--- H \| 6 \| -9 \| -6 S \| \| 6 \| -6 O \| \| \| 4 No iteration Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 4 Showing conservation header ("seq_conservation" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4 RMSD between 99 atom pairs is 15.829 angstroms > open "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain1.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain6.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain7.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain8.pdb" > "/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain9.pdb" Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain1.pdb #18 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #19 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #20 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb #22 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain6.pdb #23 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain7.pdb #24 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain8.pdb #25 --- Chain \| Description A \| No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain9.pdb #26 --- Chain \| Description A \| No description available Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 17: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 1: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 2: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 3: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 4: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Computing secondary structure > select #3/A:351 #21/A:351 34 atoms, 32 bonds, 2 residues, 2 models selected > hide #1 models > hide #3 models > show #3 models > hide #3 models ===== 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 OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M5 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: Mac17,9 Model Number: Z1ML0017VB/A Chip: Apple M5 Pro Total Number of Cores: 18 (6 Super and 12 Performance) Memory: 64 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 1 day, 3 hours, 27 minutes Graphics/Displays: Apple M5 Pro: Chipset Model: Apple M5 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 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: 4.12.1 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-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-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
#20230	can't reproduce	Minimize: Residue template with the same override level already exists	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: Windows-10-10.0.26200 ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "C:/Users/Малын Керлынский/Desktop/Никзав/Молекула 9/6PV7ligand.pdb" Summary of feedback from opening C:/Users/Малын Керлынский/Desktop/Никзав/Молекула 9/6PV7ligand.pdb --- warnings \| Start residue of secondary structure not found: HELIX 1 1 SER A 1 PHE A 12 1 12 Start residue of secondary structure not found: HELIX 2 2 ILE A 218 PHE A 226 1 9 Start residue of secondary structure not found: HELIX 3 3 LEU A 227 THR A 228 1 2 Start residue of secondary structure not found: HELIX 4 4 VAL A 229 LEU A 234 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 240 ILE A 263 1 24 100 messages similar to the above omitted 6PV7ligand.pdb title: Human Α3Β4 nicotinic acetylcholine receptor In complex with nicotine [more info...] Chain information for 6PV7ligand.pdb --- Chain \| Description \| UniProt 1.1/A 1.1/D \| fusion protein of neuronal acetylcholine receptor subunit α-3 and soluble cytochrome B562 \| ACHA3_HUMAN 1-327 331-474 1.1/B 1.1/C 1.1/E \| fusion protein of neuronal acetylcholine receptor subunit β-4 and soluble cytochrome B562 \| ACHB4_HUMAN 1-328 332-477 > select add #1 15774 atoms, 16189 bonds, 5 pseudobonds, 1936 residues, 4 models selected > select subtract #1 Nothing selected > select add #1 15774 atoms, 16189 bonds, 5 pseudobonds, 1936 residues, 4 models selected > select subtract #1 Nothing selected > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > rename #1 id 2 > rename #2 group > hide #!2 models > show #!2 models > ui favorite true "Model Panel" > combine #2.1,2.2 close true No structures specified > rename #2 id 3 > rename #3 group > ui tool show "Command Line Interface" > ui tool show "Model Panel" > ui tool show "Modeller Comparative" > combine #2.1,2.2 modelId #3 No structures specified > rename #3 id 2 > rename #2 group > combine #2.1,2.2 modelId #3 No structures specified > combine #2.1-2.2 name complex No structures specified > combine #2.1-2.2 name complex No structures specified > combine #2 name complex Remapping chain ID ' ' in 6PV7ligand.pdb #2.2 to 'F' Computing secondary structure > hide #2.2 models > show #2.2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #2.2 models > hide #!2.1 models > hide #!1 models > show #!1 models > ui tool show "Minimize Structure" > minimize #1 Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to complex #1 --- notes \| Termini for complex (#1) chain A determined from SEQRES records Termini for complex (#1) chain B determined from SEQRES records Termini for complex (#1) chain C determined from SEQRES records Termini for complex (#1) chain D determined from SEQRES records Termini for complex (#1) chain E determined from SEQRES records Chain-initial residues that are actual N termini: complex #1/A SER 1, complex #1/B ARG 1, complex #1/D SER 1, complex #1/E ARG 1 Chain-initial residues that are not actual N termini: complex #1/A ILE 410, complex #1/B ARG 400, complex #1/C ASN 4, complex #1/C ARG 400, complex #1/D ILE 410, complex #1/E ARG 400 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: complex #1/A ARG 327, complex #1/A MET 469, complex #1/B ARG 328, complex #1/B PRO 459, complex #1/C ARG 328, complex #1/C PRO 459, complex #1/D ARG 327, complex #1/D MET 469, complex #1/E ARG 328, complex #1/E PRO 459 1335 hydrogen bonds Adding 'H' to complex #1/A ILE 410 Adding 'H' to complex #1/B ARG 400 Adding 'H' to complex #1/C ASN 4 Adding 'H' to complex #1/C ARG 400 Adding 'H' to complex #1/D ILE 410 1 messages similar to the above omitted complex #1/A MET 469 is not terminus, removing H atom from 'C' complex #1/B PRO 459 is not terminus, removing H atom from 'C' complex #1/C PRO 459 is not terminus, removing H atom from 'C' complex #1/D MET 469 is not terminus, removing H atom from 'C' complex #1/E PRO 459 is not terminus, removing H atom from 'C' 16039 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\8DD3~1\AppData\Local\Temp\tmpg0pfbsk1\ante.in.mol2 -fi mol2 -o C:\Users\8DD3~1\AppData\Local\Temp\tmpg0pfbsk1\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (UNL) `` (UNL) `Welcome to antechamber 20.0: molecular input file processor.` (UNL) `` (UNL) `Info: Finished reading file (C:\Users\8DD3~1\AppData\Local\Temp\tmpg0pfbsk1\ante.in.mol2); atoms read (26), bonds read (27).` (UNL) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNL) `Running: "C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `Info: Total number of electrons: 118; net charge: 0` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX 1.11.1/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX 1.11.1/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` Charges for residue UNL determined Dock prep finished Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\tool.py", line 101, in minimize run(self.session, cmd) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize dock_prep_caller(session, [structure], memorize_name="minimization", nogui=True, File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller run_steps(session, state, structures) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\prep.py", line 107, in prep callback(session, state, structures) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep callback(session, state, structures) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep callback(session, state, structures) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 156, in run_steps callback() File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\prep.py", line 106, in <lambda> state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb()) ^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\cmd.py", line 43, in <lambda> steps=max_steps: _minimize(ses, struct, updates, log, steps), kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\cmd.py", line 172, in _minimize forcefield.registerResidueTemplate(template) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\openmm\app\forcefield.py", line 481, in registerResidueTemplate raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel)) ValueError: Residue template F-UNL-1 with the same override level 0 already exists. ValueError: Residue template F-UNL-1 with the same override level 0 already exists. File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\openmm\app\forcefield.py", line 481, in registerResidueTemplate raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 581.29 OpenGL renderer: NVIDIA GeForce RTX 2050/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.9 Locale: ru_RU.cp1251 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: Micro-Star International Co., Ltd. Model: Thin 15 B12UCX OS: Майкрософт Windows 11 Pro (Build 26200) Memory: 16,868,990,976 MaxProcessMemory: 137,438,953,344 CPU: 16 12th Gen Intel(R) Core(TM) i7-12650H OSLanguage: ru-RU 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 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: 2026.1.4 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-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-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 comtypes: 1.4.11 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 narwhals: 2.16.0 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: 2.4.2 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 plotly: 6.5.2 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 pyKVFinder: 0.9.0 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 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: 2.8.3 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 tomlkit: 0.14.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 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 WMI: 1.5.1 yarl: 1.22.0
#20229	limitation	vop maximum: ArrayMemoryError	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: Windows-10-10.0.26200 ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- note \| available bundle cache has not been initialized yet 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 "D:/FUS/map/1 postprocess_masked.mrc" "D:/FUS/map/2 > postprocess_masked.mrc" Opened 1 postprocess_masked.mrc as #1.1, grid size 360,360,360, pixel 0.83, shown at level 0.00268, step 2, values float32 Opened 2 postprocess_masked.mrc as #1.2, grid size 360,360,360, pixel 0.83, shown at level 0.00232, step 2, values float32 > select add #1.1 2 models selected > select add #1 5 models selected > select add #1.2 5 models selected > select subtract #1.1 3 models selected > select subtract #1.2 1 model selected > select add #1.2 3 models selected > select subtract #1 Nothing selected > select subtract #1.2 Nothing selected > select add #1 5 models selected > show target m > select subtract #1 Nothing selected > close #1.1-2 > close > open "D:/FUS/map/1 postprocess_masked.mrc" Opened 1 postprocess_masked.mrc as #1, grid size 360,360,360, pixel 0.83, shown at level 0.00268, step 2, values float32 > open "D:/FUS/map/1 postprocess_masked.mrc" Opened 1 postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83, shown at level 0.00268, step 2, values float32 > set bgColor white > volume #1 step 1 > volume #2 step 1 > surface dust #1 size 8.3 > surface dust #2 size 8.3 > select add #1 2 models selected > select add #2 4 models selected > select subtract #2 2 models selected > ui mousemode right "translate selected models" > view matrix models #1,1,0,0,-0.50591,0,1,0,1.5243,0,0,1,-27.125 > ui mousemode right "rotate selected models" > view matrix models > #1,0.99814,-0.06098,-0.0027381,10.003,0.060983,0.99814,0.00083898,-7.0922,0.0026818,-0.0010044,1,-27.349 > fitmap #1 inMap #2 Fit map 1 postprocess_masked.mrc in map 1 postprocess_masked.mrc using 466122 points correlation = 0.4606, correlation about mean = 0.2832, overlap = 27.96 steps = 80, shift = 2.53, angle = 1.28 degrees Position of 1 postprocess_masked.mrc (#1) relative to 1 postprocess_masked.mrc (#2) coordinates: Matrix rotation and translation 0.99924853 -0.03875574 -0.00060823 5.99664513 0.03875602 0.99924859 0.00046486 -5.75976826 0.00058976 -0.00048808 0.99999971 -28.94412208 Axis -0.01229166 -0.01545252 0.99980505 Axis point 162.90892987 142.39723081 0.00000000 Rotation angle (degrees) 2.22153801 Shift along axis -28.92318514 > vop add #1 #2 Opened volume sum as #3, grid size 376,376,397, pixel 0.83, shown at step 1, values float32 > select subtract #1 Nothing selected > show #!1 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > close #1-3 > open D:/FUS/map/1fl-postprocess_masked.mrc Opened 1fl-postprocess_masked.mrc as #1, grid size 360,360,360, pixel 0.83, shown at level 0.0195, step 2, values float32 > volume #1 step 1 > select add #1 2 models selected > select subtract #1 Nothing selected > open D:/FUS/map/1fl-postprocess_masked.mrc Opened 1fl-postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83, shown at level 0.0195, step 2, values float32 > select add #2 2 models selected > ui mousemode right "translate selected models" > view matrix models #2,1,0,0,2.01,0,1,0,1.0956,0,0,1,-70.623 > ui mousemode right "rotate selected models" > view matrix models > #2,0.97241,-0.23322,0.0049349,42.859,0.23314,0.97235,0.013201,-29.317,-0.0078773,-0.011687,0.9999,-67.607 > ui mousemode right "translate selected models" > view matrix models > #2,0.97241,-0.23322,0.0049349,43.895,0.23314,0.97235,0.013201,-28.624,-0.0078773,-0.011687,0.9999,-105.73 > ui mousemode right "rotate selected models" > view matrix models > #2,0.97404,-0.22423,-0.031107,47.564,0.22469,0.97435,0.012301,-27.62,0.027551,-0.018972,0.99944,-109.48 > view matrix models > #2,0.97415,-0.22545,-0.014357,45.258,0.2251,0.97408,-0.022383,-22.483,0.019031,0.018572,0.99965,-114.38 > ui mousemode right "translate selected models" > view matrix models > #2,0.97415,-0.22545,-0.014357,50.791,0.2251,0.97408,-0.022383,-21.85,0.019031,0.018572,0.99965,-161.79 > ui mousemode right "rotate selected models" > view matrix models > #2,0.87385,-0.48427,-0.043208,111.06,0.48415,0.87487,-0.013902,-43.657,0.044534,-0.0087712,0.99897,-160.87 > ui mousemode right "translate selected models" > view matrix models > #2,0.87385,-0.48427,-0.043208,119.32,0.48415,0.87487,-0.013902,-41.43,0.044534,-0.0087712,0.99897,-236.5 > view matrix models > #2,0.87385,-0.48427,-0.043208,106.75,0.48415,0.87487,-0.013902,-45.324,0.044534,-0.0087712,0.99897,-241.17 > view matrix models > #2,0.87385,-0.48427,-0.043208,104.22,0.48415,0.87487,-0.013902,-46.441,0.044534,-0.0087712,0.99897,-241.14 > ui mousemode right "rotate selected models" > view matrix models > #2,0.87856,-0.47758,0.0068468,95.036,0.47758,0.87859,0.0018762,-48.457,-0.0069115,0.0016215,0.99997,-235.71 > view matrix models > #2,0.878,-0.47866,0.0018663,96.031,0.47855,0.8777,-0.025248,-44.422,0.010447,0.023061,0.99968,-241.58 > view matrix models > #2,0.87813,-0.47774,0.025449,92.361,0.47812,0.87823,-0.010958,-46.568,-0.017115,0.02179,0.99962,-237.47 > view matrix models > #2,0.97079,-0.23951,0.013984,42.484,0.23964,0.97082,-0.0086093,-28.208,-0.011514,0.011709,0.99987,-236.67 > ui mousemode right "translate selected models" > view matrix models > #2,0.97079,-0.23951,0.013984,38.817,0.23964,0.97082,-0.0086093,-31.105,-0.011514,0.011709,0.99987,-236.47 > ui tool show "Fit in Map" > fitmap #2 inMap #1 Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using 58317 points correlation = 0.2941, correlation about mean = -0.1467, overlap = 3.618 steps = 456, shift = 1.6, angle = 4.5 degrees Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl- postprocess_masked.mrc (#1) coordinates: Matrix rotation and translation 0.94999639 -0.31223914 -0.00368588 55.05316242 0.31225092 0.94999421 0.00322065 -40.01774346 0.00249595 -0.00421052 0.99998802 -237.19241841 Axis -0.01189815 -0.00989782 0.99988023 Axis point 158.40981953 141.90150669 0.00000000 Rotation angle (degrees) 18.19683430 Shift along axis -237.42295150 > vop add #1 #2 Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1, values float32 > select subtract #2 Nothing selected > hide #!3 models > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!2 models > show #!1 models > fitmap #2 inMap #1 Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using 58317 points correlation = 0.2941, correlation about mean = -0.1466, overlap = 3.618 steps = 2000, shift = 0.107, angle = 0.0586 degrees Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl- postprocess_masked.mrc (#1) coordinates: Matrix rotation and translation 0.94998360 -0.31228042 -0.00347856 54.99020667 0.31229348 0.94997630 0.00422089 -40.26974608 0.00198644 -0.00509611 0.99998504 -236.98426583 Axis -0.01491515 -0.00874866 0.99985049 Axis point 157.93787073 139.45676358 0.00000000 Rotation angle (degrees) 18.19992350 Shift along axis -237.41671475 > vop add #1 #2 Opened volume sum as #4, grid size 457,458,649, pixel 0.83, shown at step 1, values float32 > close #3 > surface dust #4 size 8.3 > volume #2 step 1 > hide #!4 models > show #!1 models > fitmap #2 inMap #1 Fit map 1fl-postprocess_masked.mrc in map 1fl-postprocess_masked.mrc using 466035 points correlation = 0.2942, correlation about mean = -0.1424, overlap = 28.83 steps = 276, shift = 0.0649, angle = 0.0383 degrees Position of 1fl-postprocess_masked.mrc (#2) relative to 1fl- postprocess_masked.mrc (#1) coordinates: Matrix rotation and translation 0.95000571 -0.31221144 -0.00362945 55.03151100 0.31222383 0.95000185 0.00357324 -40.11234919 0.00233238 -0.00452780 0.99998703 -237.13444407 Axis -0.01297170 -0.00954632 0.99987029 Axis point 158.31933814 141.04709587 0.00000000 Rotation angle (degrees) 18.19536912 Shift along axis -237.43461297 > vop add #1 #2 Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1, values float32 > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > close #3-4 > vop add #1 #2 Opened volume sum as #3, grid size 458,457,649, pixel 0.83, shown at step 1, values float32 > volume #3 level 0.0139 > close #3 > vop maximum #1 #2 Opened volume maximum as #3, grid size 458,457,649, pixel 0.83, shown at step 1, values float32 > hide #!3 models > show #!3 models > vop maximum #1 #2 Opened volume maximum as #4, grid size 458,457,649, pixel 0.83, shown at step 1, values float32 > select add #4 2 models selected > view matrix models #4,1,0,0,-4.8803,0,1,0,3.292,0,0,1,-113.56 > ui mousemode right "rotate selected models" > view matrix models > #4,0.96976,-0.24123,0.037135,36.402,0.24327,0.96766,-0.066779,-23.396,-0.019825,0.073794,0.99708,-122.4 > ui mousemode right "translate selected models" > view matrix models > #4,0.96976,-0.24123,0.037135,30.115,0.24327,0.96766,-0.066779,-17.417,-0.019825,0.073794,0.99708,-299.44 > view matrix models > #4,0.96976,-0.24123,0.037135,24.115,0.24327,0.96766,-0.066779,-7.0937,-0.019825,0.073794,0.99708,-461.14 > view matrix models > #4,0.96976,-0.24123,0.037135,27.584,0.24327,0.96766,-0.066779,-12.869,-0.019825,0.073794,0.99708,-462.3 > ui mousemode right "move picked models" > ui mousemode right "rotate selected models" > view matrix models > #4,0.85931,-0.49721,0.11984,80.981,0.50315,0.86388,-0.023637,-33.839,-0.091774,0.080608,0.99251,-453.25 > view matrix models > #4,0.86041,-0.50193,0.088073,82.527,0.50152,0.86468,0.028397,-35.295,-0.090408,0.019737,0.99571,-443.89 > ui mousemode right "translate selected models" > view matrix models > #4,0.86041,-0.50193,0.088073,85.163,0.50152,0.86468,0.028397,-59.977,-0.090408,0.019737,0.99571,-441.61 > ui mousemode right "rotate selected models" > view matrix models > #4,0.86244,-0.50197,0.064943,85.577,0.4994,0.86479,0.052323,-60.414,-0.082427,-0.012693,0.99652,-437.61 > view matrix models > #4,0.85966,-0.51082,0.0074625,89.082,0.51078,0.85969,0.0062147,-59.81,-0.00959,-0.0015308,0.99995,-449.6 > ui mousemode right "translate selected models" > view matrix models > #4,0.85966,-0.51082,0.0074625,92.979,0.51078,0.85969,0.0062147,-62.11,-0.00959,-0.0015308,0.99995,-449.33 > fitmap #4 inMap #3 Fit map volume maximum in map volume maximum using 832367 points correlation = 0.3042, correlation about mean = -0.06039, overlap = 48.57 steps = 2000, shift = 7.34, angle = 3.87 degrees Position of volume maximum (#4) relative to volume maximum (#3) coordinates: Matrix rotation and translation 0.82388197 -0.56674472 -0.00434924 113.07062923 0.56675694 0.82388169 0.00235099 -59.62493542 0.00225085 -0.00440190 0.99998778 -450.22360112 Axis -0.00595735 -0.00582254 0.99996530 Axis point 155.35546833 146.49583432 0.00000000 Rotation angle (degrees) 34.52532809 Shift along axis -450.53441223 > fitmap #4 inMap #3 Fit map volume maximum in map volume maximum using 832367 points correlation = 0.3044, correlation about mean = -0.06281, overlap = 48.18 steps = 2000, shift = 1.11, angle = 0.246 degrees Position of volume maximum (#4) relative to volume maximum (#3) coordinates: Matrix rotation and translation 0.82383182 -0.56677890 -0.00792566 113.82374451 0.56682124 0.82382723 0.00472929 -60.60296097 0.00384891 -0.00838857 0.99995741 -450.11955906 Axis -0.01157046 -0.01038563 0.99987912 Axis point 159.34107616 142.09685863 0.00000000 Rotation angle (degrees) 34.53215045 Shift along axis -450.75274381 > select subtract #4 Nothing selected > select add #4 2 models selected > select subtract #4 Nothing selected > vop maximum #3 #4 Opened volume maximum as #5, grid size 643,641,1197, pixel 0.83, shown at step 1, values float32 > save D:/FUS/halfpitch_HC/donor1.cxs > vop maximum #3 #4 Opened volume maximum as #6, grid size 643,641,1197, pixel 0.83, shown at step 1, values float32 > select add #6 2 models selected > view matrix models #6,1,0,0,-2.9146,0,1,0,-18.212,0,0,1,-422.7 > view matrix models #6,1,0,0,-4.8565,0,1,0,-29.155,0,0,1,-677.77 > ui mousemode right "rotate selected models" > view matrix models > #6,0.80391,-0.59465,0.01102,116.31,0.59459,0.80398,0.0086864,-80.079,-0.014025,-0.00043079,0.9999,-675.77 > ui mousemode right "translate selected models" > view matrix models > #6,0.80391,-0.59465,0.01102,116.8,0.59459,0.80398,0.0086864,-102.32,-0.014025,-0.00043079,0.9999,-843.37 > view matrix models > #6,0.80391,-0.59465,0.01102,112.02,0.59459,0.80398,0.0086864,-108.66,-0.014025,-0.00043079,0.9999,-896.89 > view matrix models > #6,0.80391,-0.59465,0.01102,115.21,0.59459,0.80398,0.0086864,-77.871,-0.014025,-0.00043079,0.9999,-897.46 > ui mousemode right "rotate selected models" > view matrix models > #6,0.80516,-0.59177,0.038981,120.05,0.59263,0.80532,-0.01544,-82.519,-0.022256,0.035533,0.99912,-902.02 > view matrix models > #6,0.8035,-0.59529,0.0044595,114.08,0.59526,0.80332,-0.018748,-83.221,0.0075783,0.017719,0.99981,-903.29 > view matrix models > #6,0.59535,-0.80339,0.01154,176.55,0.8006,0.59437,0.075959,-61.109,-0.067883,-0.035983,0.99704,-885.04 > view matrix models > #6,0.58974,-0.80727,0.02295,180.16,0.80735,0.59002,0.007616,-74.733,-0.019689,0.014037,0.99971,-898.94 > view matrix models > #6,0.50954,-0.86044,-0.0040741,194.26,0.86014,0.50922,0.02934,-65.383,-0.023171,-0.018454,0.99956,-893.48 > view matrix models > #6,0.50996,-0.85997,0.019719,198.78,0.86013,0.51007,0.00096818,-71.057,-0.010891,0.016467,0.99981,-900.53 > ui mousemode right "translate selected models" > view matrix models > #6,0.50996,-0.85997,0.019719,200.64,0.86013,0.51007,0.00096818,-63.838,-0.010891,0.016467,0.99981,-900.43 > fitmap #6 inMap #5 Fit map volume maximum in map volume maximum using 1500382 points correlation = 0.2441, correlation about mean = -0.02013, overlap = 48.85 steps = 2000, shift = 20.2, angle = 9.67 degrees Position of volume maximum (#6) relative to volume maximum (#5) coordinates: Matrix rotation and translation 0.36347783 -0.93132250 -0.02285316 245.12223471 0.93160180 0.36340491 0.00741385 -49.33659096 0.00140027 -0.02398481 0.99971134 -893.26862208 Axis -0.01685068 -0.01301605 0.99977329 Axis point 159.67794754 137.84283237 0.00000000 Rotation angle (degrees) 68.69718276 Shift along axis -896.55441969 > select subtract #6 Nothing selected > select add #6 2 models selected > select add #5 4 models selected > vop maximum #5 #6 Opened volume maximum as #7, grid size 860,842,2288, pixel 0.83, shown at step 1, values float32 > volume #7 level 0.02349 > volume #7 level 0.01862 > volume #7 level 0.01695 > save D:/FUS/halfpitch_HC/donor1.cxs ChimeraX session files cannot include maps over 4 Gbytes in size. You tried to save map "volume maximum", size 860,842,2288, type float32. Instead save the map in a map file (e.g. .mrc, .cmap) then save the session file and it will reference the map file instead of including the map data in the session file. [Repeated 1 time(s)] > close #1-4 > save D:/FUS/halfpitch_HC/donor1.cxs Ran out of memory trying to save a session including 3 maps (9.8 Gbytes). To save the session you will either have to save the maps to separate files (then only the path to the file is included in the session) or close some of the maps. #5 "volume maximum" (1882 MB) #6 "volume maximum" (1882 MB) #7 "volume maximum" (6320 MB) [Repeated 1 time(s)] > vop maximum #5 #6 Opened volume maximum as #1, grid size 860,842,2288, pixel 0.83, shown at step 1, values float32 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\cmd_line\tool.py", line 322, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3258, in run result = ci.function( ^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3855, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp> cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 465, in combine_operation rv.combine_interpolated_values(v, op, subregion = subregion, step = step, File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1538, in combine_interpolated_values values, const_values = v.interpolate_on_grid(self, subregion, step) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1598, in interpolate_on_grid values = empty(shape, floatc) ^^^^^^^^^^^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an array with shape (2288, 842, 860) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an array with shape (2288, 842, 860) and data type float32 File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1598, in interpolate_on_grid values = empty(shape, floatc) ^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > hide #!1 models > show #!1 models > select subtract #5 2 models selected > select subtract #6 Nothing selected > hide #!7 models > show #!7 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > hide #!7 models > show #!5 models > show #!6 models > hide #!1 models > vop maximum #5 #6 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\cmd_line\tool.py", line 322, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3258, in run result = ci.function( ^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3855, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3237, in run result = ci.function(session, kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp> cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 445, in combine_operation rg = gv.region_grid(r, value_type = value_type, new_spacing = spacing, clamp = False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1084, in region_grid m = zeros(shape, value_type) ^^^^^^^^^^^^^^^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an array with shape (2288, 842, 860) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 6.17 GiB for an array with shape (2288, 842, 860) and data type float32 File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1084, in region_grid m = zeros(shape, value_type) ^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > open D:/FUS/map/1fl-postprocess_masked.mrc Opened 1fl-postprocess_masked.mrc as #2, grid size 360,360,360, pixel 0.83, shown at level 0.0195, step 2, values float32 > hide #!2 models > show #!2 models > hide #!5 models > hide #!6 models > volume #2 step 1 > volume #2 level 0.017 > show #!7 models > select add #7 2 models selected > select subtract #7 Nothing selected > select add #2 2 models selected > view matrix models #2,1,0,0,0.13582,0,1,0,-4.1492,0,0,1,187.39 > view matrix models #2,1,0,0,-1.6283,0,1,0,-3.9812,0,0,1,240.08 > ui mousemode right "rotate selected models" > view matrix models > #2,0.95969,0.281,-0.0061322,-40.517,-0.28102,0.9597,-0.002514,42.602,0.0051787,0.0041359,0.99998,238.69 > ui mousemode right "translate selected models" > view matrix models > #2,0.95969,0.281,-0.0061322,-38.374,-0.28102,0.9597,-0.002514,44.09,0.0051787,0.0041359,0.99998,238.73 > view matrix models > #2,0.95969,0.281,-0.0061322,-37.546,-0.28102,0.9597,-0.002514,47.395,0.0051787,0.0041359,0.99998,238.51 > fitmap #2 inMap #7 Fit map 1fl-postprocess_masked.mrc in map volume maximum using 579630 points correlation = 0.3083, correlation about mean = -0.1259, overlap = 35.4 steps = 1816, shift = 4.05, angle = 1.94 degrees Position of 1fl-postprocess_masked.mrc (#2) relative to volume maximum (#7) coordinates: Matrix rotation and translation 0.94997360 0.31232123 0.00236816 -39.20468276 -0.31230905 0.94997020 -0.00443594 54.23474088 -0.00363512 0.00347443 0.99998736 237.48431186 Axis 0.01266249 0.00960972 -0.99987365 Axis point 158.33376227 141.26193920 0.00000000 Rotation angle (degrees) 18.20118733 Shift along axis -237.42955340 > select subtract #2 Nothing selected > vop maximum #2 #7 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\cmd_line\tool.py", line 322, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3258, in run result = ci.function( ^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3855, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 350, in volume_maximum rv = combine_op(volumes, 'maximum', on_grid, bounding_grid, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in combine_op cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 406, in <listcomp> cv = [combine_operation(volumes, operation, subregion, step, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map_filter\vopcommand.py", line 445, in combine_operation rg = gv.region_grid(r, value_type = value_type, new_spacing = spacing, clamp = False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1084, in region_grid m = zeros(shape, value_type) ^^^^^^^^^^^^^^^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.3 GiB for an array with shape (2576, 1079, 1091) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 11.3 GiB for an array with shape (2576, 1079, 1091) and data type float32 File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\map\volume.py", line 1084, in region_grid m = zeros(shape, value_type) ^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 591.55 OpenGL renderer: NVIDIA GeForce RTX 4060 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.9 Locale: zh_CN.cp936 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: HP Model: Victus by HP 15L Gaming Desktop TG02-2xxx OS: Microsoft Windows 11 家庭中文版 (Build 26200) Memory: 16,920,178,688 MaxProcessMemory: 137,438,953,344 CPU: 28 Intel(R) Core(TM) i7-14700F OSLanguage: zh-CN 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 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: 2026.1.4 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-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-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 comtypes: 1.4.11 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 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: 3.3.2 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 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: 2.8.3 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 tzdata: 2025.3 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 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

Note: See TracWiki for help on using the wiki.

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Query Language

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