id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19024 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003168ab000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031589f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000314893000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000313887000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031287b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031186f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000310863000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f857000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030e84b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030d83f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030c833000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030b827000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030a81b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000020a2220c0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment (total: 60) {""app_name"":""ChimeraX"",""timestamp"":""2025-09-29 00:48:47.00 -0400"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6 (24G84)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""3DFF73CF-CAB3-464F-96E1-BB5B914A8C18""} { ""uptime"" : 4300000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, 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pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14, shown at level 0.0112, step 1, values float32 Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel 2.14, shown at level 0.00974, step 1, values float32 Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at level 0.157, step 1, values float32 Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level 0.0283, step 1, values float32 Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at level 0.00404, step 1, values float32 Log from Sat Sep 27 12:14:37 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Volumes/Lab Backup/Jun Liu Lab 2025/Project > files/C.jejuni/2nd_paper/For-2nd-manuscript/After- > review/Manuscript/09202025/Composition-with-color.cxs"" Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at level 0.027, step 1, values float32 Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881, step 1, values float32 Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at level 0.0166, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14, shown at level 0.0112, step 1, values float32 Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel 2.14, shown at level 0.00974, step 1, values float32 Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at level 0.157, step 1, values float32 Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level 0.0283, step 1, values float32 Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at level 0.00404, step 1, values float32 Log from Sat Sep 20 19:10:23 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Volumes/Lab Backup/Jun Liu Lab 2025/Project > files/C.jejuni/2nd_paper/For-2nd-manuscript/After- > review/Updated_Figures/09122025/For_Composition- > maps/Building_Whole_Model_09102025_Backup.cxs"" Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at level 0.027, step 1, values float32 Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881, step 1, values float32 Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at level 0.0166, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200, pixel 2.14, shown at level 0.000997, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size 200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32 Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14, shown at level 0.0112, step 1, values float32 Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel 2.14, shown at level 0.00974, step 1, values float32 Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at level 0.157, step 1, values float32 Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level 0.0283, step 1, values float32 Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at level 0.00404, step 1, values float32 Log from Wed Sep 10 10:46:36 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/shoichi/Desktop/For_Composition- > maps/Building_Whole_Model_09102025.cxs Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at level 0.027, step 1, values float32 Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881, step 1, values float32 Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at level 0.0166, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200, pixel 2.14, shown at level 0.000576, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200, pixel 2.14, shown at level 0.000793, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14, shown at level 0.000785, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14, shown at level 0.00107, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14, shown at level 0.000848, step 1, values float32 Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14, [deleted to fit within ticket limits] > hide #!34 models > volume #33 level 0.0282 > color #33 #42424233 models > select clear > open /Users/shoichi/Library/CloudStorage/OneDrive- > YaleUniversity/Jun_Lab_documents/Project-documents/Shigella- > Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1 6rwy.pdb1 title: Export apparatus core and inner rod of the shigella type 3 secretion system [more info...] Chain information for 6rwy.pdb1 #35 --- Chain | Description A G H I J K | No description available B C D E F | No description available L M N O P Q R S T U V | No description available a b c d e | No description available f | No description available g h i j k | No description available > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected > view matrix models #35,1,0,0,-4.6654,0,1,0,-2.1689,0,0,1,2.2084 > view matrix models #35,1,0,0,-91.196,0,1,0,-40.005,0,0,1,205.21 > view matrix models #35,1,0,0,-75.528,0,1,0,-74.953,0,0,1,205.52 > fitmap #35 inMap #33 Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms average map value = 0.03909, steps = 60 shifted from previous position = 10.9 rotated from previous position = 3.76 degrees atoms outside contour = 11081, contour level = 0.0282 Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.99741760 -0.03266759 -0.06396064 -43.37423719 0.03327497 0.99941048 0.00845379 -87.59819848 0.06364677 -0.01056025 0.99791661 -187.77700704 Axis -0.13122930 -0.88070887 0.45511620 Axis point 2905.35176727 0.00000000 -800.81795837 Rotation angle (degrees) 4.15448090 Shift along axis -2.61987781 > fitmap #35 inMap #33 Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms average map value = 0.03909, steps = 24 shifted from previous position = 0.00687 rotated from previous position = 0.126 degrees atoms outside contour = 11085, contour level = 0.0282 Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.99749474 -0.03046883 -0.06384280 -44.16910568 0.03108711 0.99947870 0.00871326 -86.97208983 0.06354403 -0.01067612 0.99792193 -187.70382242 Axis -0.13577780 -0.89205051 0.43105716 Axis point 2945.80706779 0.00000000 -801.76090259 Rotation angle (degrees) 4.09446743 Shift along axis 2.66960472 > hide sel atoms > show sel cartoons > view orient > turn x 90 [Repeated 2 time(s)] > view matrix models > #35,0.99788,0.012764,-0.063768,-59.237,-0.01212,0.99987,0.010477,-74.276,0.063894,-0.0096822,0.99791,195.83 > fitmap #35 inMap #33 Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms average map value = 0.03909, steps = 60 shifted from previous position = 18.5 rotated from previous position = 0.279 degrees atoms outside contour = 11083, contour level = 0.0282 Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.99763100 -0.02561100 -0.06384716 -45.85770181 0.02625088 0.99961302 0.00920332 -85.57822793 0.06358675 -0.01085756 0.99791725 -187.65065701 Axis -0.14428373 -0.91654180 0.37300580 Axis point 3013.35399803 0.00000000 -796.02195102 Rotation angle (degrees) 3.98635331 Shift along axis 15.05776032 > split #35 Split 6rwy.pdb1 (#35) into 33 models Chain information for 6rwy.pdb1 A #35.1 --- Chain | Description A | No description available Chain information for 6rwy.pdb1 B #35.2 --- Chain | Description B | No description available Chain information for 6rwy.pdb1 C #35.3 --- Chain | Description C | No description available Chain information for 6rwy.pdb1 D #35.4 --- Chain | Description D | No description available Chain information for 6rwy.pdb1 E #35.5 --- Chain | Description E | No description available Chain information for 6rwy.pdb1 F #35.6 --- Chain | Description F | No description available Chain information for 6rwy.pdb1 G #35.7 --- Chain | Description G | No description available Chain information for 6rwy.pdb1 H #35.8 --- Chain | Description H | No description available Chain information for 6rwy.pdb1 I #35.9 --- Chain | Description I | No description available Chain information for 6rwy.pdb1 J #35.10 --- Chain | Description J | No description available Chain information for 6rwy.pdb1 K #35.11 --- Chain | Description K | No description available Chain information for 6rwy.pdb1 L #35.12 --- Chain | Description L | No description available Chain information for 6rwy.pdb1 M #35.13 --- Chain | Description M | No description available Chain information for 6rwy.pdb1 N #35.14 --- Chain | Description N | No description available Chain information for 6rwy.pdb1 O #35.15 --- Chain | Description O | No description available Chain information for 6rwy.pdb1 P #35.16 --- Chain | Description P | No description available Chain information for 6rwy.pdb1 Q #35.17 --- Chain | Description Q | No description available Chain information for 6rwy.pdb1 R #35.18 --- Chain | Description R | No description available Chain information for 6rwy.pdb1 S #35.19 --- Chain | Description S | No description available Chain information for 6rwy.pdb1 T #35.20 --- Chain | Description T | No description available Chain information for 6rwy.pdb1 U #35.21 --- Chain | Description U | No description available Chain information for 6rwy.pdb1 V #35.22 --- Chain | Description V | No description available Chain information for 6rwy.pdb1 a #35.23 --- Chain | Description a | No description available Chain information for 6rwy.pdb1 b #35.24 --- Chain | Description b | No description available Chain information for 6rwy.pdb1 c #35.25 --- Chain | Description c | No description available Chain information for 6rwy.pdb1 d #35.26 --- Chain | Description d | No description available Chain information for 6rwy.pdb1 e #35.27 --- Chain | Description e | No description available Chain information for 6rwy.pdb1 f #35.28 --- Chain | Description f | No description available Chain information for 6rwy.pdb1 g #35.29 --- Chain | Description g | No description available Chain information for 6rwy.pdb1 h #35.30 --- Chain | Description h | No description available Chain information for 6rwy.pdb1 i #35.31 --- Chain | Description i | No description available Chain information for 6rwy.pdb1 j #35.32 --- Chain | Description j | No description available Chain information for 6rwy.pdb1 k #35.33 --- Chain | Description k | No description available > hide #!20 models > hide #35.12 models > hide #35.13 models > hide #35.14 models > hide #35.15 models > hide #35.16 models > hide #35.17 models > hide #35.18 models > hide #35.19 models > hide #35.20 models > hide #35.21 models > hide #35.22 models > hide #35.7 models > hide #35.8 models > hide #35.9 models > hide #35.10 models > hide #35.11 models > hide #35.2 models > hide #35.3 models > hide #35.4 models > hide #35.6 models > hide #35.5 models > hide #35.1 models > select add #35.23 1643 atoms, 1678 bonds, 208 residues, 1 model selected > select add #35.24 3286 atoms, 3356 bonds, 416 residues, 2 models selected > select add #35.25 4929 atoms, 5034 bonds, 624 residues, 3 models selected > select add #35.26 6572 atoms, 6712 bonds, 832 residues, 4 models selected > select add #35.28 8453 atoms, 8641 bonds, 1072 residues, 5 models selected > select add #35.27 10096 atoms, 10319 bonds, 1280 residues, 6 models selected > select add #35.30 10759 atoms, 10995 bonds, 1366 residues, 7 models selected > select add #35.29 11422 atoms, 11671 bonds, 1452 residues, 8 models selected > select add #35.31 11996 atoms, 12257 bonds, 1 pseudobond, 1527 residues, 10 models selected > select add #35.32 12524 atoms, 12797 bonds, 2 pseudobonds, 1595 residues, 12 models selected > select add #35.33 12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 14 models selected > save /Users/shoichi/Desktop/Exp_6rwy.pdb selectedOnly true > open /Users/shoichi/Library/CloudStorage/OneDrive- > YaleUniversity/Jun_Lab_documents/Project-documents/Shigella- > Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive- YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-Projects/Project- with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13 Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1 17 Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39 Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1 13 Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1 17 754 messages similar to the above omitted Chain information for Exp_6rwy.pdb --- Chain | Description 36.1/a 36.2/b 36.3/c 36.4/d 36.5/e | No description available 36.6/f | No description available 36.7/g 36.8/h | No description available 36.9/i | No description available 36.10/j | No description available 36.11/k | No description available > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 37 models selected > select subtract #35 Nothing selected > hide #!35 models > select add #36 12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 15 models selected > view orient > turn x 90 [Repeated 2 time(s)] > view matrix models #36,1,0,0,1.8402,0,1,0,-7.3614e-15,0,0,1,22.102 > combine #36 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 316 shifted from previous position = 14.7 rotated from previous position = 20.6 degrees atoms outside contour = 2517, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.97215783 0.23225297 -0.03110797 -36.48471750 -0.21917028 0.94819832 0.22996594 -39.18940239 0.08290680 -0.21674525 0.97270137 -310.80580561 Axis -0.69231910 -0.17670165 -0.69962190 Axis point 156.75641938 -568.23716310 0.00000000 Rotation angle (degrees) 18.82141158 Shift along axis 249.63044579 > select subtract #36 Nothing selected > hide #!36 models > show #!35 models > hide #!35 models > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 44 shifted from previous position = 0.0237 rotated from previous position = 0.537 degrees atoms outside contour = 2518, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.97005550 0.24114627 -0.02899658 -39.23648975 -0.22826290 0.94593773 0.23042975 -36.50652393 0.08299623 -0.21691080 0.97265684 -310.77604186 Axis -0.67981987 -0.17019457 -0.71335738 Axis point 156.72094753 -535.52573200 0.00000000 Rotation angle (degrees) 19.20894193 Shift along axis 254.58134139 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 44 shifted from previous position = 0.0162 rotated from previous position = 0.248 degrees atoms outside contour = 2519, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96904395 0.24527257 -0.02819900 -40.42088046 -0.23247603 0.94495711 0.23024108 -35.07248352 0.08311866 -0.21655813 0.97272497 -310.93483988 Axis -0.67337250 -0.16776719 -0.72001642 Axis point 157.89194862 -520.78803134 0.00000000 Rotation angle (degrees) 19.37577446 Shift along axis 256.98051248 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.0648 rotated from previous position = 0.0971 degrees atoms outside contour = 2509, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96863326 0.24682847 -0.02872841 -40.40134866 -0.23388087 0.94461726 0.23021288 -34.59326791 0.08396044 -0.21627282 0.97271615 -311.22221523 Axis -0.67072132 -0.16928384 -0.72213288 Axis point 160.83362397 -516.13702243 0.00000000 Rotation angle (degrees) 19.44123990 Shift along axis 257.69792107 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 40 shifted from previous position = 0.0997 rotated from previous position = 1.18 degrees atoms outside contour = 2519, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96366431 0.26609641 -0.02331951 -46.71349923 -0.25378087 0.93929856 0.23089713 -28.45567455 0.08334488 -0.21658928 0.97269868 -310.98516898 Axis -0.64462062 -0.15365398 -0.74890234 Axis point 157.55723427 -450.67017193 0.00000000 Rotation angle (degrees) 20.30960300 Shift along axis 267.38233255 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 28 shifted from previous position = 0.0588 rotated from previous position = 0.0884 degrees atoms outside contour = 2507, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96394851 0.26497357 -0.02433681 -45.95977070 -0.25246266 0.93964523 0.23093169 -28.89301795 0.08405877 -0.21646213 0.97266555 -311.18545152 Axis -0.64599219 -0.15651244 -0.74712646 Axis point 159.68219339 -455.04109604 0.00000000 Rotation angle (degrees) 20.26021000 Shift along axis 266.70665549 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 36 shifted from previous position = 0.059 rotated from previous position = 0.834 degrees atoms outside contour = 2517, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96020555 0.27853448 -0.02058754 -50.30086275 -0.26646024 0.93567851 0.23131074 -24.47016918 0.08369134 -0.21662010 0.97266206 -311.05082031 Axis -0.62813123 -0.14622976 -0.76424343 Axis point 157.45642500 -412.32042966 0.00000000 Rotation angle (degrees) 20.88898113 Shift along axis 272.89235505 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 28 shifted from previous position = 0.0572 rotated from previous position = 0.201 degrees atoms outside contour = 2501, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.96102174 0.27557271 -0.02229133 -48.89154354 -0.26321841 0.93663567 0.23114862 -25.45689706 0.08457710 -0.21627137 0.97266305 -311.36854755 Axis -0.63154775 -0.15084823 -0.76052104 Axis point 160.51258554 -422.13786937 -0.00000000 Rotation angle (degrees) 20.74595341 Shift along axis 271.51980439 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 40 shifted from previous position = 0.114 rotated from previous position = 0.934 degrees atoms outside contour = 2516, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.95677138 0.29034963 -0.01690027 -54.24303291 -0.27874957 0.93202561 0.23157490 -20.51184159 0.08298917 -0.21685329 0.97267027 -310.81188942 Axis -0.61311299 -0.13657373 -0.77810030 Axis point 154.50693313 -377.00324123 0.00000000 Rotation angle (degrees) 21.45053528 Shift along axis 277.90131068 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06746, steps = 28 shifted from previous position = 0.0915 rotated from previous position = 0.405 degrees atoms outside contour = 2500, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.95862930 0.28399751 -0.01937193 -51.83607203 -0.27204105 0.93405344 0.23138247 -22.64444243 0.08380646 -0.21654005 0.97266998 -311.10230759 Axis -0.62088266 -0.14301955 -0.77074647 Axis point 157.48594051 -396.19307279 0.00000000 Rotation angle (degrees) 21.14407053 Shift along axis 275.20372299 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0325 rotated from previous position = 0.935 degrees atoms outside contour = 2497, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.95402487 0.29929815 -0.01603642 -56.17567245 -0.28767749 0.92937671 0.23130194 -17.37440552 0.08413212 -0.21605449 0.97274984 -311.34959895 Axis -0.60065328 -0.13449356 -0.78811619 Axis point 157.82962251 -352.91585473 0.00000000 Rotation angle (degrees) 21.86318717 Shift along axis 281.45850608 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0938 rotated from previous position = 0.597 degrees atoms outside contour = 2503, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.95112319 0.30856628 -0.01230992 -59.65431835 -0.29745493 0.92612763 0.23196590 -14.37103207 0.08297741 -0.21696650 0.97264602 -310.76314943 Axis -0.59055654 -0.12534750 -0.79720197 Axis point 153.01157515 -327.45218791 0.00000000 Rotation angle (degrees) 22.33942125 Shift along axis 284.77161490 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.0668 rotated from previous position = 0.454 degrees atoms outside contour = 2498, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.95337543 0.30141874 -0.01490093 -57.11152235 -0.28994531 0.92854514 0.23180951 -16.84120644 0.08370792 -0.21668104 0.97264706 -311.02884295 Axis -0.59901117 -0.13170356 -0.78983530 Axis point 155.58109502 -347.05758758 0.00000000 Rotation angle (degrees) 21.98470642 Shift along axis 282.09004500 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06748, steps = 40 shifted from previous position = 0.0247 rotated from previous position = 1.12 degrees atoms outside contour = 2497, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.94755539 0.31943266 -0.01007796 -62.53011616 -0.30846488 0.92235933 0.23259983 -10.88040410 0.08359549 -0.21729252 0.97252031 -310.77431451 Axis -0.57819656 -0.12038806 -0.80696682 Axis point 152.95845016 -300.88561926 0.00000000 Rotation angle (degrees) 22.89527177 Shift along axis 288.24912922 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06748, steps = 196 shifted from previous position = 0.275 rotated from previous position = 6.03 degrees atoms outside contour = 2516, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.91061366 0.41271950 0.02110411 -91.92267912 -0.40571723 0.88311805 0.23557598 22.71238621 0.07858938 -0.22308101 0.97162677 -307.49389271 Axis -0.48795796 -0.06115768 -0.87072198 Axis point 136.22711377 -115.71161571 0.00000000 Rotation angle (degrees) 28.03273362 Shift along axis 311.20705701 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0948 rotated from previous position = 0.898 degrees atoms outside contour = 2512, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90430007 0.42608641 0.02630122 -96.27299907 -0.41984476 0.87651820 0.23547022 28.07916406 0.07727716 -0.22397816 0.97152562 -306.86169323 Axis -0.47660751 -0.05287975 -0.87752436 Axis point 134.26059045 -94.76874164 0.00000000 Rotation angle (degrees) 28.81602027 Shift along axis 313.67822778 > select add #37 12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 2 models selected > view orient > turn x 90 [Repeated 2 time(s)] > view matrix models > #37,0.88528,0.46366,0.036102,-106.56,-0.45862,0.8575,0.23315,43.037,0.077144,-0.22296,0.97177,79.067 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 72 shifted from previous position = 20.8 rotated from previous position = 0.481 degrees atoms outside contour = 2511, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90079049 0.43330196 0.02873850 -98.32308247 -0.42743077 0.87300777 0.23486244 31.19999943 0.07667743 -0.22384557 0.97160369 -306.76491610 Axis -0.46974220 -0.04909210 -0.88143759 Axis point 134.11253872 -83.92177367 0.00000000 Rotation angle (degrees) 29.22595638 Shift along axis 315.04895705 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.0881 rotated from previous position = 0.69 degrees atoms outside contour = 2506, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89556547 0.44382392 0.03134996 -100.99634174 -0.43819349 0.86759990 0.23506782 35.26655153 0.07712950 -0.22425597 0.97147326 -306.70958011 Axis -0.46139810 -0.04598628 -0.88600060 Axis point 134.86180551 -69.97063128 0.00000000 Rotation angle (degrees) 29.85139496 Shift along axis 316.72261334 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.113 rotated from previous position = 0.92 degrees atoms outside contour = 2514, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90246639 0.42989237 0.02733078 -97.18986602 -0.42378755 0.87469951 0.23516987 29.70709181 0.07719151 -0.22381535 0.97156995 -306.89335347 Axis -0.47292364 -0.05137489 -0.87960437 Axis point 134.59471718 -89.23458408 0.00000000 Rotation angle (degrees) 29.02974247 Shift along axis 314.38192225 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0358 rotated from previous position = 0.539 degrees atoms outside contour = 2508, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89842276 0.43815904 0.02920975 -99.19110537 -0.43221066 0.87054189 0.23526742 32.88583296 0.07765624 -0.22399437 0.97149165 -306.92433299 Axis -0.46611467 -0.04916939 -0.88335694 Axis point 135.40426879 -78.11433990 0.00000000 Rotation angle (degrees) 29.51483713 Shift along axis 315.74119313 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.105 rotated from previous position = 0.62 degrees atoms outside contour = 2504, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89393780 0.44692368 0.03368125 -102.50135810 -0.44172928 0.86584329 0.23492687 36.69464322 0.07583170 -0.22488801 0.97142933 -306.18633286 Axis -0.45914720 -0.04208924 -0.88736258 Axis point 133.02904390 -64.97443284 0.00000000 Rotation angle (degrees) 30.04811532 Shift along axis 317.21705560 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.115 rotated from previous position = 0.804 degrees atoms outside contour = 2510, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89992272 0.43507607 0.02911888 -98.73409564 -0.42922052 0.87207973 0.23504615 31.83387789 0.07686897 -0.22402179 0.97154794 -306.74154948 Axis -0.46852644 -0.04873392 -0.88210429 Axis point 134.31242573 -81.69650868 0.00000000 Rotation angle (degrees) 29.33441145 Shift along axis 315.28618152 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 36 shifted from previous position = 0.0953 rotated from previous position = 0.448 degrees atoms outside contour = 2504, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89659216 0.44173645 0.03148658 -100.79748505 -0.43619417 0.86858072 0.23516415 34.45417341 0.07653194 -0.22458060 0.97144553 -306.45943993 Axis -0.46343059 -0.04540649 -0.88496912 Axis point 133.73323211 -72.40106826 0.00000000 Rotation angle (degrees) 29.73725103 Shift along axis 316.35533473 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.11 rotated from previous position = 0.771 degrees atoms outside contour = 2513, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90230337 0.43022137 0.02753538 -97.33949968 -0.42415013 0.87451703 0.23519489 29.83327906 0.07710571 -0.22389628 0.97155811 -306.84469626 Axis -0.47271932 -0.05104183 -0.87973358 Axis point 134.42082336 -88.71395964 0.00000000 Rotation angle (degrees) 29.05083100 Shift along axis 314.43310092 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0181 rotated from previous position = 0.511 degrees atoms outside contour = 2507, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89844147 0.43814279 0.02887597 -99.02578382 -0.43210877 0.87055337 0.23541205 32.78427291 0.07800602 -0.22398151 0.97146659 -307.00647837 Axis -0.46625270 -0.04986361 -0.88324517 Axis point 135.80530966 -78.46119855 0.00000000 Rotation angle (degrees) 29.51453840 Shift along axis 315.69828774 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 36 shifted from previous position = 0.101 rotated from previous position = 0.522 degrees atoms outside contour = 2506, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89466699 0.44554139 0.03261660 -101.81955415 -0.44014180 0.86661685 0.23505410 36.02578634 0.07646023 -0.22465108 0.97143488 -306.41395689 Axis -0.46023802 -0.04389445 -0.88670979 Axis point 133.84591683 -67.26281795 0.00000000 Rotation angle (degrees) 29.96170923 Shift along axis 316.98015163 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.101 rotated from previous position = 0.826 degrees atoms outside contour = 2512, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90086803 0.43314603 0.02865865 -98.26801868 -0.42723813 0.87302139 0.23516215 31.02573130 0.07683994 -0.22409412 0.97153355 -306.71089778 Axis -0.47032174 -0.04934219 -0.88111453 Axis point 134.07806725 -84.40785637 0.00000000 Rotation angle (degrees) 29.22472317 Shift along axis 314.93413586 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 36 shifted from previous position = 0.0873 rotated from previous position = 0.516 degrees atoms outside contour = 2507, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89702346 0.44087858 0.03122484 -100.56014533 -0.43530634 0.86903240 0.23514055 34.12334041 0.07653303 -0.22451896 0.97145969 -306.48305045 Axis -0.46408011 -0.04574392 -0.88461130 Axis point 133.74442886 -73.53778176 0.00000000 Rotation angle (degrees) 29.68539583 Shift along axis 316.22539615 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.115 rotated from previous position = 0.831 degrees atoms outside contour = 2513, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.90315769 0.42846252 0.02694538 -96.81966205 -0.42230950 0.87539339 0.23524690 29.11132680 0.07720667 -0.22384433 0.97156206 -306.88791911 Axis -0.47424756 -0.05192061 -0.87885921 Axis point 134.49541167 -91.31340629 0.00000000 Rotation angle (degrees) 28.94832832 Shift along axis 314.11628340 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0364 rotated from previous position = 0.588 degrees atoms outside contour = 2509, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89875096 0.43749997 0.02899116 -99.00445363 -0.43152127 0.87087727 0.23529168 32.61101453 0.07769236 -0.22397892 0.97149233 -306.93891595 Axis -0.46667981 -0.04948688 -0.88304077 Axis point 135.42086570 -79.04471548 0.00000000 Rotation angle (degrees) 29.47618687 Shift along axis 315.62913969 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 40 shifted from previous position = 0.0995 rotated from previous position = 0.601 degrees atoms outside contour = 2507, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89441850 0.44598789 0.03332197 -102.20916020 -0.44078288 0.86646626 0.23440704 36.55563001 0.07567034 -0.22434575 0.97156728 -306.34974761 Axis -0.45907197 -0.04237783 -0.88738776 Axis point 133.36087951 -65.78360653 0.00000000 Rotation angle (degrees) 29.97700279 Shift along axis 317.22322991 > fitmap #37 inMap #33 Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms average map value = 0.06747, steps = 28 shifted from previous position = 0.0922 rotated from previous position = 0.746 degrees atoms outside contour = 2514, contour level = 0.0282 Position of combination (#37) relative to Exp.mrc (#33) coordinates: Matrix rotation and translation 0.89997567 0.43495953 0.02922328 -98.78534713 -0.42911600 0.87208028 0.23523485 31.71397404 0.07683259 -0.22424582 0.97149913 -306.65274386 Axis -0.46895168 -0.04859065 -0.88188620 Axis point 134.01873267 -81.91850950 0.00000000 Rotation angle (degrees) 29.33413674 Shift along axis 315.21737538 > close #35-36 > open /Users/shoichi/Library/CloudStorage/OneDrive- > YaleUniversity/Jun_Lab_documents/Project-documents/Shigella- > Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1 6rwy.pdb1 title: Export apparatus core and inner rod of the shigella type 3 secretion system [more info...] Chain information for 6rwy.pdb1 #35 --- Chain | Description A G H I J K | No description available B C D E F | No description available L M N O P Q R S T U V | No description available a b c d e | No description available f | No description available g h i j k | No description available > matchmaker #37 to #35 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 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence alignment score = 1227.8 RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs: 0.001) > matchmaker #35 to #37 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 combination, chain f (#37) with 6rwy.pdb1, chain f (#35), sequence alignment score = 1227.8 RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs: 0.001) > show #!7 models > hide #!7 models > show #!12 models > hide #!37 models > hide #!35 models > hide #!33 models > show #!35 models > fitmap #35 inMap #12 Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743 atoms average map value = 0.05154, steps = 76 shifted from previous position = 11.5 rotated from previous position = 15 degrees atoms outside contour = 4533, contour level = 0.012281 Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation 0.87803641 0.47858703 -0.00255505 -192.64047971 -0.47852090 0.87798327 0.01277250 119.46473498 0.00835605 -0.00999207 0.99991516 209.09071995 Axis -0.02377648 -0.01139611 -0.99965234 Axis point 130.99637747 446.12669410 0.00000000 Rotation angle (degrees) 28.60186207 Shift along axis -205.79914853 > fitmap #35 inMap #12 Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743 atoms average map value = 0.05154, steps = 24 shifted from previous position = 0.027 rotated from previous position = 0.102 degrees atoms outside contour = 4531, contour level = 0.012281 Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation 0.87884036 0.47710585 -0.00310138 -192.24835410 -0.47703354 0.87879083 0.01287176 118.65116797 0.00886666 -0.00983277 0.99991235 208.88473927 Axis -0.02378722 -0.01253874 -0.99963841 Axis point 129.94428451 446.20277398 0.00000000 Rotation angle (degrees) 28.50544415 Shift along axis -205.72389102 > fitmap #35 inMap #12 Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743 atoms average map value = 0.05154, steps = 24 shifted from previous position = 0.00171 rotated from previous position = 0.102 degrees atoms outside contour = 4529, contour level = 0.012281 Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation 0.87967555 0.47556249 -0.00335195 -191.93472314 -0.47548863 0.87962901 0.01278152 117.88941222 0.00902689 -0.00964978 0.99991269 208.77241920 Axis -0.02357725 -0.01301123 -0.99963734 Axis point 129.27153288 446.50117910 0.00000000 Rotation angle (degrees) 28.40481137 Shift along axis -205.70530071 > matchmaker #37 to #35 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 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence alignment score = 1227.8 RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs: 0.001) > hide #!35 models > show #!35 models > select subtract #37 Nothing selected > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected > hide sel atoms > show sel cartoons Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 35/f Alignment identifier is 5 > select #35/A,G-K:59 30 atoms, 24 bonds, 6 residues, 1 model selected > select #35/A,G-K:25-59 1050 atoms, 1044 bonds, 210 residues, 1 model selected > select #35/f:210-256 387 atoms, 397 bonds, 47 residues, 1 model selected > select #35/f 1881 atoms, 1929 bonds, 240 residues, 1 model selected > select clear > select #35/a-e 8215 atoms, 8390 bonds, 1040 residues, 1 model selected > select clear > select #35/a-e 8215 atoms, 8390 bonds, 1040 residues, 1 model selected > color sel #e34affff > color sel #e34bffff > color sel #e44dffff > color sel #e34effff > color sel #e24effff > color sel #e04fffff > color sel #de56ffff > color sel #df61ffff > color sel #e46fffff > color sel #e572ffff > color sel #e473ffff > color sel #ce73ffff > color sel #cd73ffff > color sel #ca72ffff > color sel #c773ffff > color sel #bd73ffff > color sel #b472ffff > color sel #ab6effff > color sel #9d6affff > color sel #7c5effff > color sel #6c5affff > color sel #6960ffff > color sel #6b65ffff > color sel #7771ffff > color sel #7c77ffff > color sel #8079ffff > color sel #9081ffff > color sel #9686ffff > color sel #ab96ffff > color sel #bb9effff > color sel #c4a6ffff > color sel #cdb0ffff > color sel #ccb0ffff > color sel #c4adffff > color sel #b6a7ffff > color sel #b2a5ffff > color sel #aba0ffff > color sel #a69cffff > color sel #a199ffff > color sel #9d96ffff > color sel #9c95ffff > color sel #9c94ffff > color sel #9994ffff > color sel #9093ffff > color sel #8e93ffff > color sel #8e94ffff > color sel #9097ffff > color sel #979dffff > color sel #999effff > color sel #9ca0ffff > color sel #e5c7ffff > color sel #ffc5e7ff > color sel #ff9da2ff > color sel #ff9596ff > color sel #ff9494ff > color sel #ff9790ff > color sel #ff998dff > color sel #ffa184ff > color sel #ffa27cff > color sel #ff9e75ff > color sel #ff9667ff > color sel #ff8e5cff > color sel #ff8c59ff > color sel #ff7d54ff > color sel #ff7255ff > color sel #ff5e50ff > color sel #ff364cff [Repeated 1 time(s)] > color sel #ff3950ff > color sel #ff3d53ff > color sel #ff475cff > color sel #ff5364ff > color sel #ff5b68ff > color sel #ff616bff > color sel #ff646aff > color sel #ff6469ff > color sel #ff6966ff > color sel #ff7167ff > color sel #ff7767ff > color sel #ff7e66ff > color sel #ff7e65ff > color sel #ff7d64ff > color sel #ff7a61ff > color sel #ff7a60ff > color sel #ff624cff > color sel #ff5c49ff > color sel #ff5747ff > color sel #ff5647ff > select #35/f:256 11 atoms, 10 bonds, 1 residue, 1 model selected > select #35/f 1881 atoms, 1929 bonds, 240 residues, 1 model selected > color sel #ff5647ff > select #35/g-k:86 35 atoms, 30 bonds, 5 residues, 1 model selected > select #35/g-k 2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected > color sel #ff5647ff > select clear > show #!20 models > hide #!20 models > show #!37 models > close #37 > show #!27 models > hide #!27 models > show #!26 models > hide #!26 models > show #21 models > hide #21 models > show #21 models > matchmaker #21 to #35 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 6rwy.pdb1, chain M (#35) with 6zni.pdb, chain A (#21), sequence alignment score = 471.3 RMSD between 68 pruned atom pairs is 0.800 angstroms; (across all 73 pairs: 1.078) > select add #21 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > view matrix models > #21,-0.3511,-0.93587,-0.029745,518.01,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,873.02 > open /Users/shoichi/Library/CloudStorage/OneDrive- > YaleUniversity/Jun_Lab_documents/Project-documents/Shigella- > Projects/Project-with-Bill/MxiG_Linker/Manuscript- > start-2023/Newest_ver/Figures-maps/PDB/6zni.pdb 6zni.pdb title: Structure of the shigella mxih needle filament attached to the basal body [more info...] Chain information for 6zni.pdb #36 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83 > matchmaker #36 to #21 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 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#36), sequence alignment score = 488.1 RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs: 0.000) > select add #36 29624 atoms, 30038 bonds, 3772 residues, 2 models selected > hide sel atoms > show sel cartoons > view matrix models > #21,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.003362,379.08,0.007299,0.029031,-0.99955,909.24,#36,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.0033619,379.08,0.007299,0.029031,-0.99955,909.24 > undo > select subtract #21 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > view matrix models > #36,-0.3511,-0.93587,-0.029745,503.75,-0.93631,0.35116,0.0033619,377.16,0.007299,0.029031,-0.99955,987.31 > select add #21 29624 atoms, 30038 bonds, 3772 residues, 2 models selected > combine #21,36 Remapping chain ID 'A' in 6zni.pdb #36 to 'X' Remapping chain ID 'B' in 6zni.pdb #36 to 'Y' Remapping chain ID 'C' in 6zni.pdb #36 to 'Z' Remapping chain ID 'D' in 6zni.pdb #36 to 'a' Remapping chain ID 'E' in 6zni.pdb #36 to 'b' Remapping chain ID 'F' in 6zni.pdb #36 to 'c' Remapping chain ID 'G' in 6zni.pdb #36 to 'd' Remapping chain ID 'H' in 6zni.pdb #36 to 'e' Remapping chain ID 'I' in 6zni.pdb #36 to 'f' Remapping chain ID 'J' in 6zni.pdb #36 to 'g' Remapping chain ID 'K' in 6zni.pdb #36 to 'h' Remapping chain ID 'L' in 6zni.pdb #36 to 'i' Remapping chain ID 'M' in 6zni.pdb #36 to 'j' Remapping chain ID 'N' in 6zni.pdb #36 to 'k' Remapping chain ID 'O' in 6zni.pdb #36 to 'l' Remapping chain ID 'P' in 6zni.pdb #36 to 'm' Remapping chain ID 'Q' in 6zni.pdb #36 to 'n' Remapping chain ID 'R' in 6zni.pdb #36 to 'o' Remapping chain ID 'S' in 6zni.pdb #36 to 'p' Remapping chain ID 'T' in 6zni.pdb #36 to 'q' Remapping chain ID 'U' in 6zni.pdb #36 to 'r' Remapping chain ID 'V' in 6zni.pdb #36 to 's' Remapping chain ID 'W' in 6zni.pdb #36 to 't' > select subtract #36 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > hide #36 models > hide #21 models > select subtract #21 Nothing selected > color #37 #ffcdc1ff > color #37 #fff0b9ff > color #37 #fffab8ff > color #37 #cdca94ff > select add #37 29624 atoms, 30038 bonds, 3772 residues, 1 model selected > color sel #ff5647ff > color #37 #cdca94ff > select #35/B-F:33-73 1025 atoms, 1020 bonds, 205 residues, 1 model selected > select #35/B-F:11-73 1575 atoms, 1570 bonds, 315 residues, 1 model selected > color sel #cdca94ff > select #35/A,G-K:59 30 atoms, 24 bonds, 6 residues, 1 model selected > select #35/A,G-K:25-59 1050 atoms, 1044 bonds, 210 residues, 1 model selected > color sel #cdca94ff > select #35/L-V:39-83 4004 atoms, 4059 bonds, 495 residues, 1 model selected > select #35/L-V 6281 atoms, 6347 bonds, 803 residues, 1 model selected > color sel #cdca94ff > select clear > select #35/g-k:86 35 atoms, 30 bonds, 5 residues, 1 model selected > select #35/g-k 2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected > select #35/B-F:73 25 atoms, 20 bonds, 5 residues, 1 model selected > select #35/B-F:11-73 1575 atoms, 1570 bonds, 315 residues, 1 model selected > select #35/A,G-K:25-59 1050 atoms, 1044 bonds, 210 residues, 1 model selected > select #35/A,G-K:25-59 1050 atoms, 1044 bonds, 210 residues, 1 model selected > select #35/L-V:83 121 atoms, 110 bonds, 11 residues, 1 model selected > select #35/L-V 6281 atoms, 6347 bonds, 803 residues, 1 model selected > select clear > select #35/a-e 8215 atoms, 8390 bonds, 1040 residues, 1 model selected > select #35/f:214-256 355 atoms, 364 bonds, 43 residues, 1 model selected > select #35/f 1881 atoms, 1929 bonds, 240 residues, 1 model selected > select #35/g-k:86 35 atoms, 30 bonds, 5 residues, 1 model selected > select #35/g-k 2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected > select subtract #35 Nothing selected > hide #!35 models > show #!35 models > fitmap #37 inMap #12 Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624 atoms average map value = 0.06417, steps = 548 shifted from previous position = 70.3 rotated from previous position = 11.1 degrees atoms outside contour = 8428, contour level = 0.012281 Position of combination (#37) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation -0.49153012 -0.85972065 -0.13884720 566.36821533 -0.86955619 0.49323881 0.02423863 329.40732755 0.04764637 0.13264946 -0.99001714 908.59071574 Axis 0.50204458 -0.86364149 -0.04554785 Axis point 350.50708701 0.00000000 464.01580445 Rotation angle (degrees) 173.80173096 Shift along axis -41.53209647 > fitmap #37 inMap #12 Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624 atoms average map value = 0.06423, steps = 48 shifted from previous position = 0.0821 rotated from previous position = 1.4 degrees atoms outside contour = 8424, contour level = 0.012281 Position of combination (#37) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation -0.51261344 -0.84748446 -0.13783161 568.00591214 -0.85732198 0.51402279 0.02792129 321.77742772 0.04718573 0.13247890 -0.99006204 908.81302700 Axis 0.49146888 -0.86966667 -0.04624087 Axis point 347.11623201 0.00000000 463.91377007 Rotation angle (degrees) 173.89374851 Shift along axis -42.70617861 > view orient > turn x 90 [Repeated 2 time(s)] > select add #37 29624 atoms, 30038 bonds, 3772 residues, 1 model selected > view matrix models > #37,-0.51261,-0.84748,-0.13783,569.7,-0.85732,0.51402,0.027921,321.78,0.047186,0.13248,-0.99006,856.35 > close #37 > show #36 models > show #21 models > fitmap #36 inMap #12 Fit molecule 6zni.pdb (#36) to map Needle.mrc gaussian (#12) using 14812 atoms average map value = 0.0782, steps = 132 shifted from previous position = 32.5 rotated from previous position = 1.92 degrees atoms outside contour = 571, contour level = 0.012281 Position of 6zni.pdb (#36) relative to Needle.mrc gaussian (#12) coordinates: Matrix rotation and translation -0.33643885 -0.94170519 -0.00049053 521.74293397 -0.94170368 0.33643919 -0.00169149 382.53410278 0.00175792 -0.00010715 -0.99999845 975.28376338 Axis 0.57600370 -0.81744690 0.00055009 Axis point 395.23518164 0.00000000 487.99286048 Rotation angle (degrees) 179.92120163 Shift along axis -11.63896146 > view orient > turn x 90 [Repeated 2 time(s)] > select add #36 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > view matrix models > #36,-0.33644,-0.94171,-0.00049053,521.99,-0.9417,0.33644,-0.0016915,382.53,0.0017579,-0.00010715,-1,1003.3 > select subtract #36 Nothing selected > select add #21 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > view matrix models > #21,-0.3511,-0.93587,-0.029745,531.02,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,883.73 > turn y 10 [Repeated 47 time(s)] > select add #36 29624 atoms, 30038 bonds, 3772 residues, 2 models selected > view matrix models > #21,-0.3511,-0.93587,-0.029745,530.99,-0.93631,0.35116,0.003362,377.58,0.007299,0.029031,-0.99955,877.32,#36,-0.33644,-0.94171,-0.00049053,521.96,-0.9417,0.33644,-0.0016915,382.48,0.0017579,-0.00010715,-1,996.86 > turn y 10 [Repeated 40 time(s)] > select clear > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected > hide #!35 models > show #!35 models > select #35/A,G-K:58-59 60 atoms, 54 bonds, 12 residues, 1 model selected > select #35/A,G-K:25-59 1050 atoms, 1044 bonds, 210 residues, 1 model selected > hide sel cartoons > select #35/B-F:73 25 atoms, 20 bonds, 5 residues, 1 model selected > select #35/B-F:11-73 1575 atoms, 1570 bonds, 315 residues, 1 model selected > hide sel cartoons > select #35/L-V:40-83 3905 atoms, 3960 bonds, 484 residues, 1 model selected > select #35/L-V 6281 atoms, 6347 bonds, 803 residues, 1 model selected > hide sel cartoons > select clear > select #35/a-e 8215 atoms, 8390 bonds, 1040 residues, 1 model selected > hide sel cartoons > select #35/f:209-256 396 atoms, 406 bonds, 48 residues, 1 model selected > select #35/f 1881 atoms, 1929 bonds, 240 residues, 1 model selected > hide sel cartoons > select #35/g-k:86 35 atoms, 30 bonds, 5 residues, 1 model selected > select #35/g-k 2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected > hide sel cartoons > select clear > hide #21 models > hide #!12 models Drag select of 194 residues > color sel #cdca94ff > select clear > select add #35 22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected > show sel cartoons > select subtract #35 Nothing selected > select add #36 14812 atoms, 15019 bonds, 1886 residues, 1 model selected > show #21 models > show sel surfaces > select add #21 29624 atoms, 30038 bonds, 3772 residues, 25 models selected > show sel surfaces > show sel cartoons > combine #21,36 Remapping chain ID 'A' in 6zni.pdb #36 to 'X' Remapping chain ID 'B' in 6zni.pdb #36 to 'Y' Remapping chain ID 'C' in 6zni.pdb #36 to 'Z' Remapping chain ID 'D' in 6zni.pdb #36 to 'a' Remapping chain ID 'E' in 6zni.pdb #36 to 'b' Remapping chain ID 'F' in 6zni.pdb #36 to 'c' Remapping chain ID 'G' in 6zni.pdb #36 to 'd' Remapping chain ID 'H' in 6zni.pdb #36 to 'e' Remapping chain ID 'I' in 6zni.pdb #36 to 'f' Remapping chain ID 'J' in 6zni.pdb #36 to 'g' Remapping chain ID 'K' in 6zni.pdb #36 to 'h' Remapping chain ID 'L' in 6zni.pdb #36 to 'i' Remapping chain ID 'M' in 6zni.pdb #36 to 'j' Remapping chain ID 'N' in 6zni.pdb #36 to 'k' Remapping chain ID 'O' in 6zni.pdb #36 to 'l' Remapping chain ID 'P' in 6zni.pdb #36 to 'm' Remapping chain ID 'Q' in 6zni.pdb #36 to 'n' Remapping chain ID 'R' in 6zni.pdb #36 to 'o' Remapping chain ID 'S' in 6zni.pdb #36 to 'p' Remapping chain ID 'T' in 6zni.pdb #36 to 'q' Remapping chain ID 'U' in 6zni.pdb #36 to 'r' Remapping chain ID 'V' in 6zni.pdb #36 to 's' Remapping chain ID 'W' in 6zni.pdb #36 to 't' > select subtract #36 14812 atoms, 15019 bonds, 1886 residues, 47 models selected > select subtract #21 23 models selected > hide #!21 models > hide #!36 models > select add #37 29624 atoms, 30038 bonds, 3772 residues, 1 model selected > color sel #cdca94ff > show sel surfaces > select add #35 52367 atoms, 53116 bonds, 3 pseudobonds, 6932 residues, 49 models selected > show sel surfaces > select clear > show #!36 models > hide #!36 models > close #36 > close #34 > show #!33 models > hide #!33 models > show #!33 models > show #!32 models > show #!31 models > hide #!31 models > hide #!32 models > hide #!33 models > hide #!35 models > show #!35 models > show #!26 models > hide #!26 models > close #26 > show #!27 models > save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06252025.cxs includeMaps > true ——— End of log from Wed Jun 25 10:52:06 2025 ——— opened ChimeraX session > hide #!37 models > show #!37 models > show #!33 models > hide #!33 models > show #!33 models > show #!32 models > show #!28 models > hide #!13 models > show #!15 models > hide #!15 models > show #!16 models > show #!15 models > color #16 #42424208 models > color #16 #4242421e models > color #16 #42424240 models > hide #!15 models > color #14 #5e5e5eff models > color #14 #5e5e5e81 models > set bgColor black > color #14 #5e5e5e80 models > color #14 #5e5e5e67 models > color #14 darkgrey models > color #14 #a9a9a95b models > color #14 #a9a9a967 models > color #9 #a9a9a967 models > show #!20 models > show #!23 models > select add #23 124488 atoms, 126648 bonds, 15424 residues, 3 models selected > show sel surfaces > select clear > hide #!27 models > hide #!23 models > show #!23 models > hide #!37 models > hide #!35 models > show #!7 models > hide #!7 models > show #!12 models > view orient > turn x 90 [Repeated 2 time(s)] > view name P1 > save /Users/shoichitachiyama/Desktop/IMring.png supersample 2 > transparentBackground true > color #9 darkgrey models > color #9 #a9a9a980 models > color #10 #a9a9a980 models > color #12 #a9a9a980 models > color #16 #a9a9a980 models > color #28 #a9a9a980 models > color #32 #a9a9a980 models > color #33 #a9a9a980 models > save /Users/shoichitachiyama/Desktop/IMring.png supersample 2 > transparentBackground true > turn x 90 > ui tool show ""Side View"" > hide #!9 models > save /Users/shoichitachiyama/Desktop/IMring-2.png supersample 2 > transparentBackground true > view P1 > show #!9 models > show #!22 models > show #!24 models > show #!21 models > hide #!21 models > color #22 #009193ff > color #22 #005493ff > color #22 #009193ff > color #22 #005759ff > color #22 #005051ff > color #24 #bfa292ff models > color #24 #bf6943ff models > color #24 #bf726cff models > color #24 #bf746eff models > color #24 #bf7570ff models > color #24 #bf713aff models > color #24 #bf5e32ff models > show #!29 models > color #29 #b6bfb4ff models > color #29 #afbfbaff models > color #29 #abaebfff models > color #29 #92a0bfff models > color #29 #99a9bfff models > color #29 #94a0bfff models > show #!30 models > color #30 #bcbfa6ff models > color #30 #bfb590ff models > save /Users/shoichitachiyama/Desktop/Sorting_platform.png supersample 2 > transparentBackground true > save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs > includeMaps true > turn x 90 [Repeated 2 time(s)] > save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2 > transparentBackground true > hide #!9 models > save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2 > transparentBackground true > hide #!14 models > save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2 > transparentBackground true > save /Users/shoichitachiyama/Desktop/Sorting2_platform.png supersample 2 > transparentBackground true > turn x 90 > show #!21 models > hide #!21 models > show #!37 models > show #!35 models > show #!31 models > hide #!31 models > show #!27 models > color #27 #d27473ff > color #27 #d26969ff > color #27 #d26968ff > show #!9 models > show #!14 models > volume #312 region 60,0,0,120,120,200 No volumes specified > volume #9 region 60,0,0,120,120,200 > volume #9 region 0,60,0,120,120,200 > volume #14 region 0,60,0,120,120,200 > volume #14 region 0,0,0,120,120,200 > volume #9 region 0,0,0,120,120,200 > save /Users/shoichitachiyama/Desktop/Overall.png supersample 2 > transparentBackground true > volume #14 region 0,60,0,120,120,200 > volume #9 region 0,60,0,120,120,200 > hide #!24.6 models > show #!24.6 models > hide #!24.5 models > show #!24.5 models > hide #!24 models > show #!24 models > hide #!24.1 models > show #!24.1 models > hide #!24.2 models > hide #!24.3 models > hide #!29.2 models > show #!29.2 models > hide #!29.5 models > hide #!29.6 models > hide #!29.4 models > hide #!29.3 models > hide #!30.2 models > show #!30.2 models > hide #!30 models > show #!30 models > hide #!30.5 models > show #!30.5 models > hide #!30.6 models > hide #!30.1 models > hide #!10 models > hide #!12 models > hide #!16 models > show #!24.3 models > hide #!24.3 models > show #!24.2 models > show #!29.3 models > show #!29.4 models > show #!30.6 models > show #!21 models > hide #!21 models > hide #!28 models > hide #!32 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #!29.6 models > show #!29.5 models > show #!30.1 models > show #!24.3 models > save /Users/shoichitachiyama/Desktop/Overall2.png supersample 2 > transparentBackground true > hide #!24.3 models > hide #!29.5 models > hide #!29.6 models > hide #!30.1 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #23.1.1 models > show #23.1.1 models > hide #23.1.13 models > show #23.1.13 models > hide #23.1.20 models > show #23.1.20 models > hide #23.1.48 models > show #23.1.48 models > hide #23.1.44 models > show #23.1.44 models > hide #23.1.36 models > hide #23.1.35 models > show #23.1.35 models > show #23.1.36 models > hide #23.1.34 models > hide #23.1.33 models > hide #23.1.32 models > hide #23.1.31 models > hide #23.1.30 models > hide #23.1.29 models > hide #23.1.28 models > show #23.1.28 models > select add #23.1.29 2766 atoms, 340 residues, 1 model selected > select add #23.1.30 5532 atoms, 680 residues, 2 models selected > select add #23.1.31 8298 atoms, 1020 residues, 3 models selected > select add #23.1.32 11064 atoms, 1360 residues, 4 models selected > select add #23.1.33 13830 atoms, 1700 residues, 5 models selected > select add #23.1.34 16596 atoms, 2040 residues, 6 models selected > hide sel cartoons > select subtract #23.1.29 13830 atoms, 1700 residues, 7 models selected > select subtract #23.1.30 11064 atoms, 1360 residues, 6 models selected > select subtract #23.1.31 8298 atoms, 1020 residues, 5 models selected > select subtract #23.1.32 5532 atoms, 680 residues, 4 models selected > select subtract #23.1.33 2766 atoms, 340 residues, 3 models selected > select subtract #23.1.34 1 model selected > hide #23.1.7 models > show #23.1.7 models > hide #23.1.4 models > hide #23.1.3 models > hide #23.1.5 models > hide #23.1.2 models > hide #23.1.1 models > hide #!23.1 models > show #!23.1 models > hide #23.1.48 models > show #23.1.48 models > hide #23.1.6 models > hide #23.1.18 models > show #23.1.18 models > hide #23.1.17 models > show #23.1.17 models > hide #23.1.15 models > show #23.1.15 models > hide #23.1.12 models > show #23.1.12 models > hide #23.1.13 models > show #23.1.13 models > hide #23.1.8 models > show #23.1.8 models > hide #23.1.7 models > show #23.1.7 models > hide #23.1.24 models > show #23.1.24 models > hide #23.1.22 models > show #23.1.22 models > hide #23.1.21 models > hide #23.1.22 models > hide #23.1.20 models > hide #23.1.23 models > show #23.1.22 models > hide #23.1.22 models > select add #23.1.23 1403 atoms, 177 residues, 1 model selected > select add #23.1.22 2806 atoms, 354 residues, 2 models selected > select add #23.1.21 4209 atoms, 531 residues, 3 models selected > select add #23.1.20 5612 atoms, 708 residues, 4 models selected > hide sel cartoons > select add #23.1.6 7015 atoms, 885 residues, 5 models selected > select add #23.1.5 8418 atoms, 1062 residues, 6 models selected > select add #23.1.4 9821 atoms, 1239 residues, 7 models selected > select add #23.1.3 11224 atoms, 1416 residues, 8 models selected > select add #23.1.2 12627 atoms, 1593 residues, 9 models selected > select add #23.1.1 14030 atoms, 1770 residues, 10 models selected > hide sel cartoons [Repeated 1 time(s)] > hide #!23 models > show #!23 models > select clear > hide #!33 models > save /Users/shoichitachiyama/Desktop/Overall3.png supersample 2 > transparentBackground true > save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs > includeMaps true ——— End of log from Mon Jul 7 21:04:45 2025 ——— opened ChimeraX session > hide #!37 models > hide #!30 models > hide #!29 models > hide #!35 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!20 models > hide #!14 models > hide #!9 models > select add #27 22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected > hide sel surfaces > show sel cartoons > select clear > open ""/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA- > project/Data_Images/07072025/fold_2025_05_14_18_58mxia1/fold_2025_05_14_18_58mxia1_model_0.cif"" Chain information for fold_2025_05_14_18_58mxia1_model_0.cif #26 --- Chain | Description A | . > hide #26 models > show #26 models > ui tool show ""Side View"" > select add #26 5358 atoms, 5438 bonds, 686 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #26,1,0,0,135.58,0,1,0,-2.256e-13,0,0,1,290.29 > view P1 > view matrix models #26,1,0,0,224.75,0,1,0,201.52,0,0,1,332.43 > view matrix models #26,1,0,0,227.1,0,1,0,185.42,0,0,1,351.22 > hide #27.1 models > hide #27.2 models > hide #27.3 models > hide #27.4 models > hide #27.5 models > hide #27.9 models > hide #27.8 models > hide #27.7 models > hide #27.6 models > hide #27.10 models > hide #!27 models > show #!27 models > show #27.1 models > hide #27.1 models > show #27.2 models > hide #!27 models > show #!27 models > matchmaker #26 to #27 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 combination, chain A (#27) with fold_2025_05_14_18_58mxia1_model_0.cif, chain A (#26), sequence alignment score = 1659.8 RMSD between 262 pruned atom pairs is 0.900 angstroms; (across all 295 pairs: 1.890) > close #26 > select add #27 22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 > select #27/A-C:363 24 atoms, 21 bonds, 3 residues, 1 model selected > select #27/A-C:363-365 72 atoms, 69 bonds, 9 residues, 1 model selected > select #27/F,I:686 16 atoms, 14 bonds, 2 residues, 1 model selected > select #27/F,I:675-686 196 atoms, 196 bonds, 24 residues, 1 model selected > select #27/F,I:356 16 atoms, 14 bonds, 2 residues, 1 model selected > select #27/F,I:356-358 40 atoms, 38 bonds, 6 residues, 1 model selected > select #27/F,I:356 16 atoms, 14 bonds, 2 residues, 1 model selected > select #27/F,I:356-366 164 atoms, 164 bonds, 22 residues, 1 model selected > select #27/E,H:357 12 atoms, 10 bonds, 2 residues, 1 model selected > select #27/E,H:357-363 100 atoms, 100 bonds, 14 residues, 1 model selected > open ""/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA- > project/Data_Images/07072025/fold_2025_06_25_11_12mxian9/fold_2025_06_25_11_12mxian9_model_0.cif"" Chain information for fold_2025_06_25_11_12mxian9_model_0.cif #26 --- Chain | Description A B C D E F G H I | . > select clear > select add #26 23454 atoms, 23841 bonds, 3096 residues, 1 model selected > view matrix models #26,1,0,0,146.86,0,1,0,151.64,0,0,1,307.37 > hide sel atoms > show sel cartoons > view matrix models #26,1,0,0,251.22,0,1,0,311.07,0,0,1,372.74 > ui mousemode right ""rotate selected models"" > view matrix models > #26,0.88671,-0.1247,0.4452,254.1,0.36009,0.79023,-0.49585,304.06,-0.28998,0.59999,0.7456,376.86 > matchmaker #26 to #27 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 combination, chain A (#27) with fold_2025_06_25_11_12mxian9_model_0.cif, chain A (#26), sequence alignment score = 81.9 Fewer than 3 residues aligned; cannot match combination, chain A with fold_2025_06_25_11_12mxian9_model_0.cif, chain A > view matrix models > #26,0.60949,-0.15384,0.77772,257.26,0.74455,0.44806,-0.49486,300.01,-0.27233,0.88067,0.38763,376.41 > ui mousemode right ""translate selected models"" > view matrix models > #26,0.60949,-0.15384,0.77772,285.96,0.74455,0.44806,-0.49486,246.82,-0.27233,0.88067,0.38763,406.33 > view matrix models > #26,0.60949,-0.15384,0.77772,274.92,0.74455,0.44806,-0.49486,246.93,-0.27233,0.88067,0.38763,406.52 > view matrix models > #26,0.60949,-0.15384,0.77772,273.03,0.74455,0.44806,-0.49486,246.95,-0.27233,0.88067,0.38763,406.94 > ui mousemode right ""rotate selected models"" > view matrix models > #26,0.62253,-0.2226,0.75027,272.12,0.73187,0.50512,-0.4574,247.84,-0.27716,0.83385,0.47737,407.28 > view matrix models > #26,0.9126,0.08348,0.40023,271.4,0.25148,0.65721,-0.71051,248.11,-0.32235,0.74907,0.57878,407.44 > ui mousemode right ""translate selected models"" > view matrix models > #26,0.9126,0.08348,0.40023,271.28,0.25148,0.65721,-0.71051,250.69,-0.32235,0.74907,0.57878,407.22 > view matrix models > #26,0.9126,0.08348,0.40023,265.43,0.25148,0.65721,-0.71051,250.09,-0.32235,0.74907,0.57878,407.91 > view matrix models > #26,0.9126,0.08348,0.40023,260.97,0.25148,0.65721,-0.71051,250.94,-0.32235,0.74907,0.57878,408.4 > mlp sel Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_A SES surface"": minimum -27.73, mean -0.7528, maximum 23.91 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_B SES surface"": minimum -27.06, mean -0.7287, maximum 23.08 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_C SES surface"": minimum -27.17, mean -0.7259, maximum 23.76 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_D SES surface"": minimum -27.79, mean -0.6774, maximum 23.47 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_E SES surface"": minimum -27.83, mean -0.6658, maximum 23.42 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_F SES surface"": minimum -27.05, mean -0.7118, maximum 23.14 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_G SES surface"": minimum -28.03, mean -0.7055, maximum 23.34 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_H SES surface"": minimum -28.28, mean -0.728, maximum 23.46 Map values for surface ""fold_2025_06_25_11_12mxian9_model_0.cif_I SES surface"": minimum -27.24, mean -0.7021, maximum 23.39 To also show corresponding color key, enter the above mlp command and add key true > show #!9 models > view P1 > ui mousemode right ""rotate selected models"" > view matrix models > #26,0.93635,0.02058,0.35046,259.9,0.25148,0.65721,-0.71051,250.94,-0.24495,0.75342,0.61021,408.47 > view matrix models > #26,0.93421,0.014723,0.35641,259.9,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,408.47 > ui mousemode right ""translate selected models"" > view matrix models > #26,0.93421,0.014723,0.35641,258.25,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,412.5 > turn x 90 > view matrix models > #26,0.93421,0.014723,0.35641,256.64,0.24097,0.71067,-0.66097,262.97,-0.26303,0.70337,0.66037,412.5 > volume #312 region 0,0,0,120,120,200 No volumes specified > volume #9 region 0,0,0,120,120,200 > view matrix models > #26,0.93421,0.014723,0.35641,255.67,0.24097,0.71067,-0.66097,257.12,-0.26303,0.70337,0.66037,412.5 > show #!35 models > view orient > view matrix models > #26,0.93421,0.014723,0.35641,255.72,0.24097,0.71067,-0.66097,257.87,-0.26303,0.70337,0.66037,412.5 > volume #9 region 0,60,0,120,120,200 > view P1 > color #26 #d26968ff > select add #27 45696 atoms, 46299 bonds, 33 pseudobonds, 5841 residues, 12 models selected > show sel surfaces > save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs > includeMaps true ——— End of log from Tue Jul 8 20:43:49 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J000E1LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 2 days, 6 hours Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Q24i-10: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported ASUS PA279: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX