Context Navigation

Trac Ticket Queries

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

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

Filters

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

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

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

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

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

Some shortcuts can be used to manipulate checkbox filters.

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

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

Navigating Tickets

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

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

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

Saving Queries

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

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

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

Using TracLinks

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

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

Which is displayed as:

Active tickets against 1.0

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

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

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

Which is displayed as:

Assigned tickets by owner

Customizing the table format

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

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

This is displayed as:

Results (1 - 3 of 13433)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19799	can't reproduce	Minimize: could not map OpenMM atom to ChimeraX atom	Eric Pettersen	chimerax-bug-report@…
#19798	can't reproduce	glClear: invalid framebuffer operation on statusbar expose	Tom Goddard	jflecken@…
#19797	can't reproduce	Minimize: Could not find typename for atom	Eric Pettersen	chimerax-bug-report@…

1 2 3 4 5 6 7 8 9 10 11 →

Full rows

In table format you can also have full rows by using rows=<field>:

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

This is displayed as:

Results (1 - 3 of 13433)

1 2 3 4 5 6 7 8 9 10 11 →


Ticket	Resolution	Summary	Owner	Reporter
#19799	can't reproduce	Minimize: could not map OpenMM atom to ChimeraX atom	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/Mannoaz Pandiian > m/OneDrive/Documents/acadicell/docking/protein/emodin/bcl2/bcl 2 > 9O14.pdb.gz" bcl 2 9O14.pdb.gz title: Crystal structure of BCL-2 In complex with A stapled bad BH3 peptide bad sahb 4.2 [more info...] Chain information for bcl 2 9O14.pdb.gz #1 --- Chain \| Description \| UniProt A \| apoptosis regulator BCL-2,BCL-2-like protein 1 \| BCL2_HUMAN 1-75 92-207, B2CL1_HUMAN 76-91 B \| stapled bad BH3 peptide bad sahb 4.2 \| Non-standard residues in bcl 2 9O14.pdb.gz #1 --- ACE — acetyl group MK8 — 2-methyl-L-norleucine NI — nickel (II) ion NLE — norleucine NTA — nitrilotriacetic acid 1346 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > select ::name="NTA" 19 atoms, 18 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select ::name="NLE" 8 atoms, 7 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select ::name="NI" 2 atoms, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > select ::name="MK8" 18 atoms, 17 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > select ::name="HOH" 104 atoms, 104 residues, 1 model selected > delete atoms sel > delete bonds sel > select ::name="ACE" 6 atoms, 5 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > ui tool show "Add Charges" > addh #!1 Summary of feedback from adding hydrogens to bcl 2 9O14.pdb.gz #1 --- notes \| Termini for bcl 2 9O14.pdb.gz (#1) chain A determined from SEQRES records Termini for bcl 2 9O14.pdb.gz (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A TYR 9, /A VAL 92, /B TRP 303, /B ALA 305, /B GLY 309, /B SER 316 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ALA 32, /A MET 206, /B TRP 303, /B ARG 307, /B ARG 314, /B PHE 323 172 hydrogen bonds Adding 'H' to /A TYR 9 Adding 'H' to /A VAL 92 Adding 'H' to /B TRP 303 Adding 'H' to /B ALA 305 Adding 'H' to /B GLY 309 1 messages similar to the above omitted /A MET 206 is not terminus, removing H atom from 'C' /B PHE 323 is not terminus, removing H atom from 'C' 1245 hydrogens added Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS Using Amber 20 recommended default charges and atom types for standard residues > 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 bcl 2 9O14.pdb.gz #1 --- notes \| Termini for bcl 2 9O14.pdb.gz (#1) chain A determined from SEQRES records Termini for bcl 2 9O14.pdb.gz (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A TYR 9, /A VAL 92, /B TRP 303, /B ALA 305, /B GLY 309, /B SER 316 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ALA 32, /A MET 206, /B TRP 303, /B ARG 307, /B ARG 314, /B PHE 323 164 hydrogen bonds /A MET 206 is not terminus, removing H atom from 'C' /B PHE 323 is not terminus, removing H atom from 'C' 0 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues 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 157, in _minimize if cx_atom.num_bonds == 0: ^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'num_bonds' AttributeError: 'NoneType' object has no attribute 'num_bonds' File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\cmd.py", line 157, in _minimize if cx_atom.num_bonds == 0: ^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 32.0.101.7026 OpenGL renderer: Intel(R) Arc(TM) 140V GPU (16GB) OpenGL vendor: Intel Python: 3.11.9 Locale: en_IN.cp1252 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: LENOVO Model: 83JQ OS: Microsoft Windows 11 Home Single Language (Build 26200) Memory: 33,840,226,304 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) Ultra 7 258V OSLanguage: en-US Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 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
#19798	can't reproduce	glClear: invalid framebuffer operation on statusbar expose	Tom Goddard	jflecken@…
Description	The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/jamesfleckenstein/Downloads/all-models.cxs format session Log from Wed Jan 7 13:23:09 2026UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_1.cxs Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #1.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #1.3.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #1.3.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #1.3.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #1.3.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #1.3.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #1.3.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #1.3.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #1.3.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #1.3.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #1.3.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #1.3.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #1.4, grid size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #2.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #2.3.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #2.3.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #2.3.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #2.3.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #2.3.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #2.3.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #2.3.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #2.3.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #2.3.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #2.3.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #2.3.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #2.4, grid size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as #2.5, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #3.2.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #3.2.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #3.2.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #3.2.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #3.2.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #3.2.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #3.2.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #3.2.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #3.2.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #3.4, grid size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as #3.5, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #4.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #4.4.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #4.4.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #4.4.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #4.4.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #4.4.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #4.4.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #4.4.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #4.4.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #4.4.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #4.4.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #4.4.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #4.5, grid size 356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #4.6, grid size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #4.7, grid size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 0 as #4.8.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 1 as #4.8.2, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 2 as #4.8.3, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 3 as #4.8.4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 4 as #4.8.5, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 5 as #4.8.6, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 6 as #4.8.7, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 7 as #4.8.8, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 8 as #4.8.9, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 9 as #4.8.10, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #4.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #4.10.1, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #4.10.2, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #4.10.3, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #4.10.4, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #4.10.5, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #4.10.6, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #4.10.7, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #4.10.8, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #4.10.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #4.10.10, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4.11, grid size 356,356,356, pixel 0.86, shown at level 17.6, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked as #4.12, grid size 84,78,83, pixel 0.86, shown at level 12.5, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #4.13, grid size 84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #4.14, grid size 84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #5.3.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #5.3.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #5.3.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #5.3.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #5.3.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #5.3.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #5.3.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #5.3.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #5.3.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #5.3.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #5.3.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6.1, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #6.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #6.4.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #6.4.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #6.4.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #6.4.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #6.4.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #6.4.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #6.4.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #6.4.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #6.4.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #6.4.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Log from Wed Jan 7 13:06:56 2026UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4-edit2.cxs Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size 356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356, pixel 0.86, shown at level 17.6, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83, pixel 0.86, shown at level 12.5, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size 84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size 84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as #37, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as #38, grid size 65,50,86, pixel 0.928, shown at level 0.578, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as #39, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values float32 Log from Wed Dec 10 17:24:00 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final- > sessions\\\all-maps-aligned_Fig4-edit2.cxs Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size 356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356, pixel 0.86, shown at level 17.6, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83, pixel 0.86, shown at level 12.5, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size 84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size 84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as #37, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as #38, grid size 65,50,86, pixel 0.928, shown at level 0.578, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as #39, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values float32 Log from Wed Nov 26 13:25:16 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final- > sessions\\\all-maps-aligned_Fig4-edit2.cxs Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size 356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Log from Mon Nov 17 16:44:16 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final- > sessions\\\all-maps-aligned_Fig4-edit.cxs Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size 356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32 Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32 Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32 Log from Sun Nov 16 18:26:26 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final- > sessions\\\all-maps-aligned_Fig4-edit.cxs restore_snapshot for "Volume" returned None restore_snapshot for "VolumeSurface" returned None Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size 320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size 356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as #21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values float32 restore_snapshot for "ZoneColor" returned None Log from Sun Nov 2 23:30:54 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4.cxs [deleted to fit within ticket limits] > ui tool show Matchmaker QWindowsWindow::setGeometry: Unable to set geometry 640x574+880+428 (frame: 658x621+871+390) on QWidgetWindow/"QDockWidgetClassWindow" on "\\\\.\DISPLAY1". Resulting geometry: 638x566+881+435 (frame: 656x613+872+397) margins: 9, 38, 9, 9 minimum size: 486x321 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=626, y=448))) > matchmaker #!22 to #11 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 SepA-Fab40_RSR_real_space_refined_208.pdb, chain A (#11) with EatA- FabG12_RSR_real_space_refined_013.pdb, chain A (#22), sequence alignment score = 2568.8 RMSD between 531 pruned atom pairs is 1.321 angstroms; (across all 745 pairs: 2.371) > select clear > fitmap #22 inMap #4 Fit molecule EatA-FabG12_RSR_real_space_refined_013.pdb (#22) to map composite_map_J1626+J1599+J1295.ccp4 (#4) using 8934 atoms average map value = 16.96, steps = 64 shifted from previous position = 0.164 rotated from previous position = 0.494 degrees atoms outside contour = 2766, contour level = 11 Position of EatA-FabG12_RSR_real_space_refined_013.pdb (#22) relative to composite_map_J1626+J1599+J1295.ccp4 (#4) coordinates: Matrix rotation and translation 0.99999997 0.00016736 -0.00019720 0.00453544 -0.00016737 0.99999998 -0.00005185 0.02561694 0.00019719 0.00005188 0.99999998 -0.03116835 Axis 0.19660280 -0.74754244 -0.63445065 Axis point 153.18392184 0.00000000 21.46109238 Rotation angle (degrees) 0.01511415 Shift along axis 0.00151670 > select clear > hide #!22 models > show #!22 models > ui tool show "Color Zone" > color zone #4 near #22 distance 4.84 > volume splitbyzone #4 Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size 356,356,356, pixel 0.86, shown at level 11, step 1, values float32 > color #27.10 #6ea098b4 models > color #27.9 #2c514cb4 models > color #27.8 #ff69b4b4 models > color #27.7 #ff0000b4 models > color #27.6 #7dcdd2b4 models > color #27.5 #ffd700b4 models > hide #!27.4 models > show #!27.4 models > color #27.4 #ffffffb4 models > color #27.3 #ff00ffb4 models > color #27.2 #6495edb4 models > color #27.1 #b2b2b208 models > color #27.1 #b2b2b2b4 models > hide #!27.1 models > show #!27.1 models > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1 > licorice > select clear > hide #!27 models > show #!27 models > hide #!27.9 models > hide #!27.10 models > hide #!27 models > show #!27 models > hide #!27.1 models > show #!27.1 models > hide #!27.1 models > show #!27.1 models > show #!27.9 models > show #!27.10 models > graphics silhouettes width 4 > save C:\Users\David/Desktop/new-snaps/test4.png supersample 4 width 3000 > height 2600 > show #!4 models > hide #!4 models > volume gaussin #4 sd 1 Expected a density maps specifier or a keyword > volume gaussian #4 sDev 1 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size 356,356,356, pixel 0.86, shown at step 1, values float32 > hide #!27 models > volume #28 level 5.995 > show #!27 models > color #28 #b2b2b2b4 models > volume #28 level 6.455 > hide #!27 models > color zone #28 near #22 distance 5.16 > color zone #28 near #22 distance 6.01 > volume splitbyzone #28 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size 356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32 > color #29.10 #6ea098b4 models > color #29.9 #2c514cb4 models > color #29.8 #ff69b4b4 models > color #29.7 #ff0000b4 models > color #29.6 #7dcdd2b4 models > color #29.5 #ffd700b4 models > color #29.4 #ffffffb4 models > color #29.3 #ff00ffb4 models > color #29.2 #6495edb4 models > color #29.1 #b2b2b2b4 models > hide #!29.9 models > hide #!29.10 models > show #!29.9 models > show #!29.10 models > save C:\Users\David/Desktop/new-snaps/test4.png supersample 4 width 3000 > height 2600 > hide #!29 models > hide #!22 models > show #!17 models > show #!8 models > save C:\Users\David/Desktop/new-snaps/test5.png supersample 4 width 3000 > height 2600 > hide #!8 models > hide #!17 models > show #!4 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > hide #!4 models > show #!23 models > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4-edit2.cxs ——— End of log from Mon Nov 17 16:44:16 2025 ——— opened ChimeraX session > show #!1 models > hide #!1 models > show #!7 models > hide #!7 models > show #16 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!28 models > hide #!28 models > show #!22 models > show #!17 models > hide #!17 models > show #!8 models > show #!9 models > select #8/A 6266 atoms, 6372 bonds, 8 pseudobonds, 829 residues, 2 models selected > select #8/A #9/A #22/A 17860 atoms, 18152 bonds, 37 pseudobonds, 2360 residues, 6 models selected > hide sel cartoons > hide #!23 models > show #!23 models > hide #!22 models > show #!22 models > show #!28 models > hide #!28 models > hide #16 models > show #16 models > select #8/B,C #9/B,C #16/A,B #22/B,C 12634 atoms, 12934 bonds, 16 pseudobonds, 1656 residues, 7 models selected > show sel surfaces > transparency (#!8-9,16,22 & sel) 90 > select clear > show #!28 models > hide #!28 models > show #!28 models > show #!15 models > hide #!15 models > hide #!28 models > show #!17 models > hide #!16 models > show #!16 models > hide #!8 models > hide #!9 models > show #!18 models > show #!28 models > show #!15 models > hide #!16 models > hide #!15 models > show #10 models > hide #10 models > show #!1 models > show #!16 models > hide #!16 models > show #!16 models > volume mask #1 surfaces #16 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid size 78,80,66, pixel 0.928, shown at step 1, values float32 > hide #!28 models > hide #!18 models > hide #!17 models > hide #!16 models > volume #30 level 0.5583 > hide #!22 models > show #!22 models > show #!29 models > hide #!30 models > show #!30 models > hide #!22 models > show #!22 models > hide #!30 models > show #!30 models > hide #!29 models > show #!29 models > hide #!22 models > show #!22 models > volume mask #29 surfaces #22 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 masked as #31, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 masked as #32, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 masked as #33, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 masked as #34, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 masked as #35, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 masked as #36, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 masked as #37, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 masked as #38, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 masked as #39, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 masked as #40, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > hide #!22 models > hide #!31 models > hide #!32 models > hide #!33 models > hide #!34 models > hide #!35 models > hide #!36 models > hide #!37 models > hide #!38 models > hide #!39 models > hide #!40 models > show #!40 models > show #!39 models > close #31-40 > show #!28 models > volume mask #28 surfaces #22 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #31, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > volume #31 level 5.226 > color #31 #b2b2b2ff models > select clear > close #31 > show #!27 models > hide #!27 models > show #!4 models > hide #!4 models > volume gaussian #4 sDev 2 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #31, grid size 356,356,356, pixel 0.86, shown at step 1, values float32 > volume #31 level 6.321 > volume #31 level 2.736 > volume mask #31 surfaces #22 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #32, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > volume #32 level -0.265 > close #32 > close #31 > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL- > FINAL-MAP/composite_map_J1626+J1599+J1295.ccp4 Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356, pixel 0.86, shown at level 1.85, step 2, values float32 > volume #31 step 1 > volume #31 level 17.64 > select clear > select #31 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #31,0.99663,-0.081706,0.0071854,10.201,0.081724,0.99665,-0.0023133,-11.764,-0.0069724,0.0028927,0.99997,0.69415 > ui tool show "Fit in Map" > fitmap #31 inMap #5 Fit map composite_map_J1626+J1599+J1295.ccp4 in map SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 38473 points correlation = 0.3863, correlation about mean = 0.09089, overlap = 8.407e+04 steps = 236, shift = 6.51, angle = 5.32 degrees Position of composite_map_J1626+J1599+J1295.ccp4 (#31) relative to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.99748278 -0.02886231 0.06476929 -9.64591594 0.02591303 0.99860886 0.04592236 -15.11779553 -0.06600461 -0.04412839 0.99684305 13.79263787 Axis -0.53613713 0.77859142 0.32611713 Axis point 210.99850006 0.00000000 174.51925630 Rotation angle (degrees) 4.81743578 Shift along axis -2.10103676 > select clear > volume gaussian #31 sDev 2 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #32, grid size 356,356,356, pixel 0.86, shown at step 1, values float32 > volume #32 level 5.17 > show #!22 models > color #32 #ffb2b2b4 models > select #22 8934 atoms, 9092 bonds, 28 pseudobonds, 1172 residues, 2 models selected > hide sel surfaces > volume #32 level 3.948 > volume #32 level 1.505 > volume #32 level 0.1262 > volume #32 level 0.5648 > select #22/B,C 3153 atoms, 3227 bonds, 6 pseudobonds, 410 residues, 2 models selected > show sel surfaces > volume mask #32 surfaces #22 Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #33, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > select clear > hide #!22 models > color #33 #ffb2b2ff models > volume #33 level 0.1293 > close #33 > volume #32 level 2.288 > close #32 > show #!22 models > hide #!22 models > volume mask #31 surfaces #22 Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > hide #!32 models > show #!32 models > volume #32 level 12.48 > volume gaussian #32 sDev 1 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > volume #33 level 4.866 > volume #33 level 6.086 > volume gaussian #32 sDev 2 Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size 84,78,83, pixel 0.86, shown at step 1, values float32 > hide #!33 models > volume #34 level 2.789 > show #!17 models > show #!18 models > show #!7 models > show #!8 models > hide #!17 models > hide #!18 models > hide #!8 models > hide #!7 models > show #!8 models > show #!9 models > show #!17 models > show #!18 models > hide #!9 models > hide #!8 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > hide #!17 models > hide #!18 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > show #!8 models > show #!9 models > volume mask #2 surfaces #8 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid size 65,50,86, pixel 0.928, shown at step 1, values float32 > volume mask #3 surfaces #9 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid size 65,49,89, pixel 0.928, shown at step 1, values float32 > hide #!8 models > hide #!9 models > select #23 7500 atoms, 7628 bonds, 1006 residues, 1 model selected > transparency (#!23 & sel) 90 > select clear > volume #30 level 0.5205 > volume gaussian #30 sDev 1 Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as #37, grid size 78,80,66, pixel 0.928, shown at step 1, values float32 > volume #37 level 0.2599 > volume #37 level 0.3494 > volume #37 level 0.5661 > volume gaussian #35 sDev 1 Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as #38, grid size 65,50,86, pixel 0.928, shown at step 1, values float32 > volume gaussian #36sd 1 Missing or invalid "volumes" argument: only initial part "#36" of atom specifier valid > volume gaussian #36 sDev 1 Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as #39, grid size 65,49,89, pixel 0.928, shown at step 1, values float32 > volume #38 level 0.5776 > volume #39 level 0.7292 > volume #37 level 0.5317 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4-edit2.cxs > volume #38 color #36558f > volume #39 color #ecb0e1 > select clear > volume #37 color rebeccapurple > volume #33 color #2c514c > volume #33 level 8.306 > ui tool show "Color Zone" > color zone #33 near #22 distance 5.16 > show #!7 models > hide #!7 models > hide #!23 models > show #!16 models > show #!23 models > select #16/B 1616 atoms, 1650 bonds, 211 residues, 1 model selected > color (#!16 & sel) #7b5d99ff > select clear > hide #!16 models > color zone #37 near #16 distance 5.57 > color #33 #6ea098ff models > select clear > color #37 #7b5d99ff models > select clear > volume #33 level 10.09 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4-edit2.cxs ——— End of log from Wed Nov 26 13:25:16 2025 ——— opened ChimeraX session > hide #!37 models > hide #!38 models > hide #!39 models > hide #!33 models > show #!7 models > hide #!7 models > show #!8 models > show #!9 models > show #10 models > hide #10 models > show #!11 models > hide #!11 models > show #!16 models > transparency #8-9,16,23#!29 0 > select #8 #9 #16 21560 atoms, 21994 bonds, 25 pseudobonds, 2844 residues, 5 models selected > hide sel surfaces > hide #!23 models > show #!23 models > select clear > open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL- > FINAL-MAP/EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb Chain information for EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb #40 --- Chain \| Description A \| No description available B \| No description available C \| No description available > ui tool show Matchmaker > matchmaker #!40 to #10 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 EatA-FabG12_RSR_real_space_refined_010.pdb, chain A (#10) with EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb, chain A (#40), sequence alignment score = 3231.2 RMSD between 747 pruned atom pairs is 0.372 angstroms; (across all 762 pairs: 0.770) > licorice > select #40/A 5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected > hide sel cartoons > hide sel atoms > select clear > select #40/B 1690 atoms, 1735 bonds, 1 pseudobond, 221 residues, 2 models selected > color (#!40 & sel) #2c514cff > select clear > select #40/C 1572 atoms, 1613 bonds, 209 residues, 1 model selected > color sel #6ea098ff > select clear > save C:\Users\David/Desktop/high_res_image-COMPLEX.png supersample 4 width > 3000 height 2200 [Repeated 1 time(s)] > hide #!40 models > show #!40 models > hide #!40 models > show #!40 models > save C:\Users\David/Desktop/high_res_image-COMPLEX.png supersample 4 width > 3000 height 2200 [Repeated 1 time(s)] > hide #!40 models > hide #!16 models > hide #!9 models > hide #!8 models > save C:\Users\David/Desktop/high_res_image-5J44.png supersample 4 width 3000 > height 2200 > show #!40 models > show #!28 models > hide #!28 models > show #!29.1 models > show #!29.2 models > show #!29.3 models > show #!29.4 models > show #!29.5 models > show #!29.6 models > show #!29.7 models > show #!29.8 models > show #!29.9 models > show #!29.10 models > hide #!23 models > select #40/A 5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected > show sel cartoons > select #40/A 5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected > color (#!40 & sel) #ffffffff > select #40/A:1-256 1600 atoms, 1633 bonds, 6 pseudobonds, 210 residues, 2 models selected > color (#!40 & sel) cornflower blue > select clear > select #40/A:78,106,211 24 atoms, 22 bonds, 3 residues, 1 model selected > color sel magenta > select clear > select #40/A:481-560 151 atoms, 149 bonds, 1 pseudobond, 19 residues, 2 models selected > ui tool show "Color Actions" > color sel gold [Repeated 1 time(s)] > select clear > select #40/A:611-629 117 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected > ui tool show "Color Actions" > color (#!40 & sel) #7dcdd2ff > select #40/A:669-699 185 atoms, 182 bonds, 3 pseudobonds, 27 residues, 2 models selected > color (#!40 & sel) #ff0000ff > select clear > hide #!29.10 models > hide #!29.9 models > ui tool show "Side View" > save C:\Users\David/Desktop/high_res_image-COMPLEX-ZOOM.png supersample 4 > width 3000 height 2200 [Repeated 1 time(s)] > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_Fig4-edit2.cxs ——— End of log from Wed Dec 10 17:24:00 2025 ——— opened ChimeraX session > view > hide #!29 models > show #!29 models > hide #!29 models > hide #!40 models > show #!7 models > show #!8 models > show #!9 models > show #10 models > show #!11 models > show #!12 models > show #!39 models > hide #!39 models > hide #10 models > show #10 models > show #!40 models > show #!1 models > hide #!1 models > close #10 > show #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!13 models > hide #!13 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!17 models > hide #!17 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!25 models > hide #!25 models > show #!26 models > hide #!26 models > show #!27 models > hide #!27 models > rename #1 id #50 > rename #2 #8 #17 #35 id #1 > hide #!1.2 models > show #!1.2 models > hide #!7 models > hide #!9 models > hide #!11 models > hide #!12 models > hide #!1.2 models > show #!1.2 models > hide #!1 models > show #!1 models > show #!1.1 models > hide #!1.1 models > rename #3 #9 #18 #36 #39 id #2 > show #!2.4 models > hide #!2.4 models > show #!2.5 models > hide #!2.5 models > show #!2.5 models > hide #!2.5 models > show #!2.4 models > hide #!2.4 models > show #!2.3 models > hide #!2.3 models > show #!2.3 models > hide #!2.3 models > show #!2.2 models > hide #!2.2 models > show #!2.1 models > hide #!2.1 models > rename #7 #15 #16 #30 #37 #50 id #3 > show #!3.1 models > show #!3.2 models > hide #!3.2 models > show #!3.3 models > hide #!3.3 models > show #!3.4 models > hide #!3.4 models > show #!3.3 models > hide #!3.3 models > show #!3.5 models > hide #!3.5 models > rename #4 id #50 > show #!50 models > close #22 > rename #27-34 id #51 > rename #51.1 id #52 > rename #51.2 id #53 > rename #51.3 id #54 > rename #51.4 id #55 > rename #51.5 id #56 > rename #51.6 id #57 > rename #51.7 id #58 > close #51 > rename #50 #40 #13 #19 #24 #25 #26 #52-58 id #4 > hide #!4.1 models > hide #!4.2 models > show #!4.2 models > show #!4.3 models > hide #!4.3 models > show #!4.4 models > hide #!4.4 models > show #!4.5 models > hide #!4.5 models > show #!4.6 models > hide #!4.6 models > show #!4.7 models > hide #!4.7 models > show #!4.8 models > hide #!4.8 models > show #!4.9 models > hide #!4.9 models > show #!4.10 models > hide #!4.10 models > show #!4.11 models > hide #!4.11 models > show #!4.12 models > hide #!4.12 models > show #!4.13 models > hide #!4.13 models > show #!4.14 models > hide #!4.14 models > show #!2.2 models > rename #5 id #50 > rename #50 #11 #20 id #5 > show #!5.2 models > show #!38 models > hide #!38 models > close #38 > rename #6 id #50 > rename #50 #12 #14 #21 id #6 > show #!6.1 models > hide #!6.1 models > show #!6.2 models > show #!23 models > hide #!23 models > rename #1 EatA-15 > rename #2 EatA-40 > rename #3 EatA-25 > rename #4 EatA-G12 > rename #5 SepA-40 > rename #6 Pic-40 > rename #23 id #7 > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps- > aligned_1.cxs includeMaps true ——— End of log from Wed Jan 7 13:06:56 2026 ——— opened ChimeraX session > close #1.1 > close #1.3-4 > close #2.1 > close #2.3-5 > close #3.2-6 > close #4.1 > close #4.3-14 > close #5.1 > close #5.3 > close #6.1 > close #6.3-4 > show #!7 models > hide #!7 models > select #2/A 5813 atoms, 5915 bonds, 7 pseudobonds, 769 residues, 2 models selected > hide #!2 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!1 models > show sel atoms > hide sel atoms > show sel cartoons > select clear > hide #!2.2 models > show #!2.2 models > hide #!2 models > hide #!5.2 models > show #!5.2 models > show #!2 models > select #5/A 6163 atoms, 6259 bonds, 6 pseudobonds, 830 residues, 2 models selected > show sel cartoons > select clear > hide #!5.2 models > hide #!2 models > select #6/A 5739 atoms, 5840 bonds, 14 pseudobonds, 828 residues, 2 models selected > show sel cartoons > select clear > show #!5.2 models > show #!2 models > select clear > select #2/A 5813 atoms, 5915 bonds, 7 pseudobonds, 769 residues, 2 models selected > ui tool show Matchmaker > select #2/A #5/A #6/A 17715 atoms, 18014 bonds, 27 pseudobonds, 2427 residues, 6 models selected > matchmaker #!5.2#!6.2 & sel to #2.2 & sel 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 EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#2.2) with SepA-Fab40_RSR_real_space_refined_208.pdb, chain A (#5.2), sequence alignment score = 3055 RMSD between 762 pruned atom pairs is 0.490 angstroms; (across all 768 pairs: 1.177) Matchmaker EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#2.2) with Pic- Fab40_RSR_real_space_refined_199.pdb, chain A (#6.2), sequence alignment score = 1978.2 RMSD between 643 pruned atom pairs is 0.933 angstroms; (across all 689 pairs: 1.962) > select clear > save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all- > models.cxs includeMaps true ——— End of log from Wed Jan 7 13:23:09 2026 ——— > view name session-start opened ChimeraX session Desktop color scheme is dark Traceback (most recent call last): File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 98, in _expose_event self.status(self._last_message, self._last_color) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 164, in status r.draw_background() File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 1238, in draw_background GL.glClear(flags) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 98, in _expose_event self.status(self._last_message, self._last_color) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 164, in status r.draw_background() File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 1238, in draw_background GL.glClear(flags) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 98, in _expose_event self.status(self._last_message, self._last_color) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py", line 164, in status r.draw_background() File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 1238, in draw_background GL.glClear(flags) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File "src/errorchecker.pyx", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17H000CGLL/A Chip: Apple M2 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 7 days, 9 hours, 55 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: V5K6P7RJ2X Display Firmware Version: Version 17.0 (Build 21A329) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: NNQ2Q230MJ Display Firmware Version: Version 17.0 (Build 21A329) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14
#19797	can't reproduce	Minimize: Could not find typename for atom	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: Windows-10-10.0.22631 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/kzhang/OneDrive - City of Hope National Medical > Center/Documents/USP22_clean.pdb" Chain information for USP22_clean.pdb #1 --- Chain \| Description A \| No description available Computing secondary structure > ui tool show "Minimize Structure" > minimize #1 Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A LYS 519: phi -61.5, psi none trans Applying LYS rotamer (chi angles: 179.6 -178.0 -75.8 70.6) to /A LYS 519 Summary of feedback from adding hydrogens to USP22_clean.pdb #1 --- notes \| No usable SEQRES records for USP22_clean.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 21 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A LYS 519 409 hydrogen bonds /A LYS 519 is not terminus, removing H atom from 'C' 3921 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Dock prep finished Traceback (most recent call last): File "C:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\tool.py", line 101, in minimize run(self.session, cmd) File "C:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\prep.py", line 107, in prep callback(session, state, structures) File "C:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\dock_prep\cmd.py", line 156, in run_steps callback() File "C:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\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:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\chimerax\minimize\cmd.py", line 173, in _minimize system = forcefield.createSystem(top, nonbondedCutoff=1nanometer, constraints=HBonds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\openmm\app\forcefield.py", line 1280, in createSystem raise Exception(msg) Exception: Could not find typename 'N' for atom '<Atom 7902 (N) of chain 0 residue 498 (A-LYS-519)>' in list of known atom types. Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard- Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+', 'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-', 'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+', 'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+', 'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+', 'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+', 'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+', 'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+', 'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+', 'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+', 'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+', 'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+', 'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+', 'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+', 'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+', 'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+', 'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+', 'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+', 'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein- CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT', 'protein-CV', 'protein-CW', 'protein-C', 'protein-CX', 'protein-H', 'protein- HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO', 'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB', 'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH', 'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C', 'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA- CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5', 'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N', 'DNA-O', 'DNA-O2', 'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C', 'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT', 'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5', 'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N', 'RNA-O', 'RNA-O2', 'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL', 'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs', 'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx', 'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc', 'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2', 'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx', 'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm', 'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3', 'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6', 'sh', 'ss', 'sx', 'sy', 'sp', 'sq']) Exception: Could not find typename 'N' for atom '' in list of known atom types. Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard- Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+', 'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-', 'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+', 'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+', 'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+', 'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+', 'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+', 'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+', 'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+', 'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+', 'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+', 'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+', 'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+', 'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+', 'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+', 'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+', 'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+', 'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+', 'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein- CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT', 'protein-CV', 'protein-CW', 'protein-C', 'protein-CX', 'protein-H', 'protein- HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO', 'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB', 'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH', 'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C', 'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA- CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5', 'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N', 'DNA-O', 'DNA-O2', 'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C', 'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT', 'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5', 'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2', 'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL', 'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs', 'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx', 'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc', 'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2', 'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx', 'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm', 'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3', 'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6', 'sh', 'ss', 'sx', 'sy', 'sp', 'sq']) File "C:\Users\kzhang\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site- packages\openmm\app\forcefield.py", line 1280, in createSystem raise Exception(msg) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 30.0.100.9955 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.11.9 Locale: zh_CN.cp1252 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: Dell Inc. Model: Latitude 7420 OS: Microsoft Windows 11 Enterprise (Build 22631) Memory: 16,892,956,672 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz OSLanguage: en-US Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 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

1 2 3 4 5 6 7 8 9 10 11 →

Query Language

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

The available operators are:

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

All of these operators can also be negated:

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

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

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

See also: TracTickets, TracReports, TracGuide, TicketQuery

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

Note: See TracWiki for help on using the wiki.

Download in other formats:

Plain Text

Context Navigation

Trac Ticket Queries

Table of Contents

Filters

Navigating Tickets

Saving Queries

Using TracLinks

Customizing the table format

Results (1 - 3 of 13433)

Full rows

Results (1 - 3 of 13433)

Query Language

Download in other formats: