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#15919 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Window Toolkit	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        macOS-12.7.5-x86_64-i386-64bit
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

Current thread 0x000000010af02600 (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.surface._surface, 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.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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 125)


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{
  "uptime" : 330000,
  "procLaunch" : "2024-09-06 14:45:12.4012 +0200",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "procStartAbsTime" : 220003817226629,
  "coalitionID" : 19423,
  "osVersion" : {
    "train" : "macOS 12.7.5",
    "build" : "21H1222",
    "releaseType" : "User"
  },
  "captureTime" : "2024-09-10 12:35:26.0330 +0200",
  "incident" : "9961A723-A8E1-437D-94FC-E6EF0D99E979",
  "bug_type" : "309",
  "pid" : 16867,
  "procExitAbsTime" : 334386888070179,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2B2EB31E-8EA2-5C18-BFB4-79C2833878CA","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "785BE7DC-8148-7A79-AB25-C878A6F8DC27",
  "wakeTime" : 5,
  "bridgeVersion" : {"build":"21P5077","train":"8.5"},
  "sleepWakeUUID" : "0B925A66-3111-44D4-A5C1-94F32A83EA10",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4331266048\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10229e000-1022a2000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4331266048\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10229e000-1022a2000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA2.cxs

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Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #30.1, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #30.2, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #30.3, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #30.4, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #30.5, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 5 as #30.6, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 6 as #30.7, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Log from Fri Sep 6 13:13:45 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.00805, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0125, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #30.1, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #30.2, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #30.3, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #30.4, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #30.5, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 5 as #30.6, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 6 as #30.7, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Log from Tue Sep 3 14:38:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #30.1, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #30.2, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #30.3, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #30.4, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #30.5, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 5 as #30.6, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 6 as #30.7, grid
size 248,248,248, pixel 0.837, shown at level 0.0086, step 1, values float32  
Log from Thu Aug 29 14:44:39 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Tue Aug 27 10:43:20 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Mon Aug 26 17:49:42 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Sun Aug 25 17:46:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Sat Aug 24 21:20:57 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.0126, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0118, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.01, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.0081, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Sat Aug 24 11:29:55 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0136, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.0105, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0122, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Fri Aug 23 12:47:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0136, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.0105, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0115, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 0 as #21.1, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 1 as #21.2, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 2 as #21.3, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 3 as #21.4, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc 4 as #21.5, grid
size 248,248,248, pixel 0.837, shown at level 0.015, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00231, step 1, values float32  
Log from Fri Aug 23 11:48:49 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0136, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #18, grid size
248,248,248, pixel 0.837, shown at level 0.0105, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0115, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00518, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #14, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc as #20, grid size
248,248,248, pixel 0.837, shown at level 0.00609, step 1, values float32  
Log from Thu Aug 22 17:18:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0136, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1_postprocess.mrc as #12, grid size
248,248,248, pixel 0.837, shown at level 0.0135, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0105, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #14, grid size
248,248,248, pixel 0.837, shown at level 0.0115, step 1, values float32  
Log from Tue Aug 20 16:41:19 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0136, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1_postprocess.mrc as #12, grid size
248,248,248, pixel 0.837, shown at level 0.0135, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess.mrc as #14, grid size
248,248,248, pixel 0.837, shown at level 0.0134, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0142, step 1, values float32  
Log from Fri Aug 16 16:43:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs
> format session

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.00645, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00869, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.0084, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00992, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.0129, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state1_postprocess.mrc as #12, grid size
248,248,248, pixel 0.837, shown at level 0.0135, step 1, values float32  
Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess.mrc as #14, grid size
248,248,248, pixel 0.837, shown at level 0.0139, step 1, values float32  
Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.0142, step 1, values float32  
Log from Fri Aug 16 14:59:40 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_MESpH55.pdb

Chain information for NhaA-nd-6F9-K_MESpH55.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_MESpH55_postprocess_B60.mrc

Opened NhaA-nd-6F9-K_MESpH55_postprocess_B60.mrc as #2, grid size 248,248,248,
pixel 0.837, shown at level 0.0048, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH63_plugged.pdb

Chain information for NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc

Opened NhaA-nd-6F9-K_BTPpH63_plugged_postprocess_B90.mrc as #4, grid size
248,248,248, pixel 0.837, shown at level 0.00469, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH63_unplugged.pdb

Chain information for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc

Opened NhaA-nd-6F9-K_BTPpH63_unplugged_postprocess_B100.mrc as #6, grid size
248,248,248, pixel 0.837, shown at level 0.00469, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_plugged.pdb

Chain information for NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc

Opened NhaA-nd-6F9-K_BTPpH75_plugged_postprocess_B50.mrc as #8, grid size
248,248,248, pixel 0.837, shown at level 0.00605, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_unplugged.pdb

Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc

Opened NhaA-nd-6F9-K_BTPpH75_unplugged_postprocess_B50.mrc as #10, grid size
248,248,248, pixel 0.837, shown at level 0.00606, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH85_state1.pdb

Chain information for NhaA-nd-6F9-K_BTPpH85_state1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH85_state1_postprocess.mrc

Opened NhaA-nd-6F9-K_BTPpH85_state1_postprocess.mrc as #12, grid size
248,248,248, pixel 0.837, shown at level 0.00682, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH85_state2.pdb

Chain information for NhaA-nd-6F9-K_BTPpH85_state2.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH85_state2_postprocess.mrc

Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess.mrc as #14, grid size
248,248,248, pixel 0.837, shown at level 0.00768, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-Na_BTPpH85.pdb

Chain information for NhaA-nd-6F9-Na_BTPpH85.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-Na_BTPpH85_postprocess_B70.mrc

Opened NhaA-nd-6F9-Na_BTPpH85_postprocess_B70.mrc as #16, grid size
248,248,248, pixel 0.837, shown at level 0.00542, step 1, values float32  

> volume #2 level 0.006447

> volume #4 level 0.008687

> volume #6 level 0.008398

> volume #8 level 0.00992

> volume #10 level 0.01289

> volume #12 level 0.01353

> volume #14 level 0.01389

> volume #16 level 0.01415

> name /A:1-85,181-274 dimer

"dimer": invalid atom specifier  

> name /A:86-180,275-388 core

"core": invalid atom specifier  

> name /A:11-30,59-85,181-199,205-218,223-236,247-271 dimer_TM

"dimer_TM": invalid atom specifier  

> name dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271

> name core /A:86-180,275-388

> name dimer /A:1-85,181-274

> mmaker #3&dimer_TM to #1/A bring #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH63_plugged.pdb, chain A (#3), sequence alignment score = 618.1  
RMSD between 119 pruned atom pairs is 0.243 angstroms; (across all 119 pairs:
0.243)  
  

> mmaker #5&dimer_TM to #1/A bring #6

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 NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH63_unplugged.pdb, chain A (#5), sequence alignment score = 618.1  
RMSD between 119 pruned atom pairs is 0.281 angstroms; (across all 119 pairs:
0.281)  
  

> mmaker #7&dimer_TM to #1/A bring #8

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 NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH75_plugged.pdb, chain A (#7), sequence alignment score = 618.1  
RMSD between 119 pruned atom pairs is 0.249 angstroms; (across all 119 pairs:
0.249)  
  

> mmaker #9&dimer_TM to #1/A bring #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9), sequence alignment score = 614.5  
RMSD between 119 pruned atom pairs is 0.231 angstroms; (across all 119 pairs:
0.231)  
  

> mmaker #11&dimer_TM to #1/A bring #12

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 NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH85_state1.pdb, chain A (#11), sequence alignment score = 610.9  
RMSD between 119 pruned atom pairs is 0.311 angstroms; (across all 119 pairs:
0.311)  
  

> mmaker #13&dimer_TM to #1/A bring #14

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 NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-K_BTPpH85_state2.pdb, chain A (#13), sequence alignment score = 603.7  
RMSD between 113 pruned atom pairs is 0.603 angstroms; (across all 119 pairs:
1.089)  
  

> mmaker #15&dimer_TM to #1/A bring #16

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 NhaA-nd-6F9-K_MESpH55.pdb, chain A (#1) with NhaA-
nd-6F9-Na_BTPpH85.pdb, chain A (#15), sequence alignment score = 604.3  
RMSD between 113 pruned atom pairs is 0.601 angstroms; (across all 119 pairs:
1.087)  
  

> mmaker #15&dimer_TM to #9/A bring #16

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 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-Na_BTPpH85.pdb, chain A (#15), sequence alignment score = 603.7  
RMSD between 114 pruned atom pairs is 0.606 angstroms; (across all 119 pairs:
1.065)  
  

> mmaker #13&dimer_TM to #9/A bring #14

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 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_BTPpH85_state2.pdb, chain A (#13), sequence alignment score = 609.7  
RMSD between 114 pruned atom pairs is 0.595 angstroms; (across all 119 pairs:
1.058)  
  

> mmaker #11&dimer_TM to #9/A bring #12

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 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_BTPpH85_state1.pdb, chain A (#11), sequence alignment score = 610.3  
RMSD between 119 pruned atom pairs is 0.222 angstroms; (across all 119 pairs:
0.222)  
  

> mmaker #7&dimer_TM to #9/A bring #8

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 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_BTPpH75_plugged.pdb, chain A (#7), sequence alignment score = 617.5  
RMSD between 119 pruned atom pairs is 0.104 angstroms; (across all 119 pairs:
0.104)  
  

> mmaker #5&dimer_TM to #9/A bring #6

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 NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_BTPpH63_unplugged.pdb, chain A (#5), sequence alignment score = 617.5  
RMSD between 119 pruned atom pairs is 0.216 angstroms; (across all 119 pairs:
0.216)  
  

> mmaker #3&dimer_TM to #9/A bring #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_BTPpH63_plugged.pdb, chain A (#3), sequence alignment score = 617.5  
RMSD between 119 pruned atom pairs is 0.167 angstroms; (across all 119 pairs:
0.167)  
  

> mmaker #1&dimer_TM to #9/A bring #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#9) with NhaA-
nd-6F9-K_MESpH55.pdb, chain A (#1), sequence alignment score = 614.5  
RMSD between 119 pruned atom pairs is 0.231 angstroms; (across all 119 pairs:
0.231)  
  

> hide #11 models

> show #11 models

> hide #15 models

> hide #13 models

> hide #11 models

> hide #7 models

> hide #5 models

> hide #3 models

> hide #1 models

> hide #9 cartoons

> show #9 atoms

> show #9 cartoons

> setattr #9/A:2-9 res is_helix 1

Assigning is_helix attribute to 8 items  

> hide #9 atoms

> show #!8 models

> hide #!8 models

> show #7 models

> hide #9 models

> show #7 atoms

> hide #7 cartoons

> hide #7 models

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_plugged.pdb

Chain information for NhaA-nd-6F9-K_BTPpH75_plugged.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> dssp #17

> show #7 models

> hide #7,17 atoms

> show #7,17 cartoons

> mmaker #17 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NhaA-nd-6F9-K_BTPpH75_plugged.pdb, chain A (#7) with NhaA-
nd-6F9-K_BTPpH75_plugged.pdb, chain A (#17), sequence alignment score = 1994.6  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

[deleted to fit within ticket limits]

> select add #26.2/A:74@C

728 atoms, 1 pseudobond, 113 residues, 5 models selected  

> select clear

> view list

Named views: N-term_density_top, binding_site, core_inner_side,
core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
mono_back_, mono_front, pH-sensing, plug_side  

> view mono_back_

> hide #!26 models

> select ~sel & ##selected

Nothing selected  

> turn x 50

> turn x 5

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #23.1 models

> ui mousemode right distance

> distance #7/A:81@NH1 #7/A:252@OE1

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A ARG 81 NH1 and GLU 252
OE1: 3.594Å  

> distance #7/A:81@NH1 #7/A:252@OE1

Distance already exists; modify distance properties with 'distance style'  

> ~distance #7/A:81@NH1 #7/A:252@OE1

> ui mousemode right translate

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> transparency #26 30 target s

> transparency #26 80 target s

> hide #!26 models

> show #!26 models

> select #7

4736 atoms, 4840 bonds, 2 pseudobonds, 614 residues, 2 models selected  

> select clear

> hide #26 target c

> transparency ##name="cap near" 100

> clip front 0.4 position ##26.1/A:253;

Invalid "position" argument: Expected 3 floats or object specifier  

> clip front 0.4 position #26.1/A:253;

Invalid "position" argument: Center argument no objects specified  

> clip front 0.4 position #26.2/A:253

> clip front 1 position #26.2/A:253

> clip front 5 position #26.2/A:253

> clip front -5 position #26.2/A:253

> clip front -4 position #26.2/A:253

> clip front -2 position #26.2/A:253

> clip front -3 position #26.2/A:253

> clip front -4 position #26.2/A:253

> select #26.2.1.1

1 model selected  

> ~clip

> save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true

> select #26.2.1.1

1 model selected  

> transparency sel 100

> select clear

> save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true

> hide #!7 models

> transparency #26.2 0

> select #26.2.1.1

1 model selected  

> select clear

> save NhaA-pH75-plugged-top_surf.png supersample 3 transparentBackground true

> transparency #26.2 80 target s

> select #26.2.1.1

1 model selected  

> transparency sel 100

> select clear

> show #!7 models

> hide #!23 models

> save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true

> show #!23 models

> hide #23.1 models

> hide #!26 models

> hide #7 target c

> hide #!7 atoms

> show #7/A:4-9,78,81,82,252,253,256&sidechain target a

> hide ##name="chain trace"

> graphics silhouettes width 6

> graphics selection color lime

> color sel dark gray target p

> select clear

> save NhaA-pH75-plugged-top_res.png supersample 3 transparentBackground true

> color #1,3,7,11&core indian red

> color #1,3,7,11&dimer pink

> color /A:1-10 medium purple

> color #!7 byhetero

> save NhaA-pH75-plugged-top2_res.png supersample 3 transparentBackground true

> show #7/A target c

> graphics silhouettes width 2

> show #!26 models

> hide #!23 models

> save NhaA-pH75-plugged-top2.png supersample 3 transparentBackground true

> hide #!26 models

> transparency 30 target c

> save NhaA-pH75-plugged-top2_ribbon.png supersample 3 transparentBackground
> true

> transparency 0 target c

> show #!26 models

> hide #!7 models

> show #26.2 target c

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18174 of
299176 triangles, cap near, 427 of 2861 triangles, cap far, 2100 of 9790
triangles, 43 residues  

> select clear

> view list

Named views: N-term_density_top, binding_site, core_inner_side,
core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
mono_back_, mono_front, pH-sensing, plug_side  

> view name plug_top

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 14417 of
299176 triangles, cap near, 149 of 2861 triangles, cap far, 1561 of 9790
triangles, 26 residues  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 9886 of
299176 triangles, cap near, 76 of 2861 triangles, cap far, 1005 of 9790
triangles, 15 residues  

> transparency #26.2 0tar s

Missing or invalid "percent" argument: Expected a number  

> transparency #26.2 0 target s

> select clear

> view list

Named views: N-term_density_top, binding_site, core_inner_side,
core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2,
dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back,
mono_back_, mono_front, pH-sensing, plug_side, plug_top  

> view plug_top

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18824 of
299176 triangles, cap near, 374 of 2861 triangles, cap far, 2165 of 9790
triangles, 42 residues  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 24350 of
299176 triangles, cap far, 2652 of 9790 triangles, 53 residues  

> select #26.2/A:258@NE1

1 atom, 1 residue, 1 model selected  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18302 of
299176 triangles, cap far, 2010 of 9790 triangles, 40 residues  

> select add #26.2/A:370@CG1

296 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:370@CG1

295 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CD2

294 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CD1

293 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CB

292 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@O

291 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CA

290 atoms, 40 residues, 3 models selected  

> select add #26.2/A:143@O

291 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@O

290 atoms, 40 residues, 3 models selected  

> select add #26.2/A:143@CB

291 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CB

290 atoms, 40 residues, 3 models selected  

> select add #26.2/A:143@O

291 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@O

290 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@C

289 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:136@CZ

288 atoms, 40 residues, 3 models selected  

> select add #26.2/A:143@CD2

289 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:143@CD2

288 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:136@CE1

287 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:136@CE2

286 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@O

285 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CE1

284 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CD1

283 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CD2

282 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CB

281 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CG

280 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@C

279 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:261@CA

278 atoms, 40 residues, 3 models selected  

> select subtract #26.2/A:257@O

277 atoms, 40 residues, 3 models selected  

> select add #26.2/A:13@OG

278 atoms, 41 residues, 3 models selected  

> select add #26.2/A:261@CE1

279 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:264@CB

278 atoms, 41 residues, 3 models selected  

> show #!7 models

> select subtract #26.2/A:155@CD1

277 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:155@CB

276 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:155@CA

275 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:154@CG2

274 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:155@N

273 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:151@O

272 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:151@CB

271 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:151@N

270 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:150@N

269 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:150@CB

268 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:154@CB

267 atoms, 41 residues, 3 models selected  

> select subtract #26.2/A:151@CA

266 atoms, 41 residues, 3 models selected  

> select add #26.2/A:82@OE1

267 atoms, 42 residues, 3 models selected  

> select add #26.2/A:82@CD

268 atoms, 42 residues, 3 models selected  

> select add #26.2/A:82@CG

269 atoms, 42 residues, 3 models selected  

> select add #26.2/A:81@CB

270 atoms, 43 residues, 3 models selected  

> select add #26.2/A:81@CG

271 atoms, 43 residues, 3 models selected  

> select add #26.2/A:81@CD

272 atoms, 43 residues, 3 models selected  

> select add #26.2/A:252@OE2

273 atoms, 44 residues, 3 models selected  

> select add #26.2/A:252@CD

274 atoms, 44 residues, 3 models selected  

> select add #26.2/A:252@CG

275 atoms, 44 residues, 3 models selected  

> select add #26.2/A:81@NH1

276 atoms, 44 residues, 3 models selected  

> select add #26.2/A:81@NH2

277 atoms, 44 residues, 3 models selected  

> select add #26.2/A:81@NE

278 atoms, 44 residues, 3 models selected  

> select add #26.2/A:81@CZ

279 atoms, 44 residues, 3 models selected  

> select add #26.2/A:252@CB

280 atoms, 44 residues, 3 models selected  

> select add #26.2/A:253@N

281 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@CA

282 atoms, 45 residues, 3 models selected  

> select add #26.2/A:252@C

283 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@CD2

284 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@CB

285 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@ND1

286 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@NE2

287 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@CG

288 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@CE1

289 atoms, 45 residues, 3 models selected  

> select add #26.2/A:253@O

290 atoms, 45 residues, 3 models selected  

> select add #26.2/A:252@O

291 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:263@CD1

290 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:263@CG1

289 atoms, 45 residues, 3 models selected  

> hide #26.2&~sel target s

> select subtract #26.2/A:140@CG2

288 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:140@CG1

287 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:139@CA

286 atoms, 45 residues, 3 models selected  

> select add #26.2/A:139@CA

287 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:140@CA

286 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:139@O

285 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:143@CG

284 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:140@N

283 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:139@C

282 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:139@CA

281 atoms, 45 residues, 3 models selected  

> select add #26.2/A:139@CA

282 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:136@CD1

281 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:15@CA

280 atoms, 45 residues, 3 models selected  

> select add #26.2/A:15@CA

281 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:15@C

280 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:12@O

279 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:12@CB

278 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:71@CE2

277 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:71@CD2

276 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:264@CD2

275 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:133@OD2

274 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:134@N

273 atoms, 45 residues, 3 models selected  

> select add #26.2/A:133@OD2

274 atoms, 45 residues, 3 models selected  

> select add #26.2/A:134@N

275 atoms, 45 residues, 3 models selected  

> select add #26.2/A:264@CD2

276 atoms, 45 residues, 3 models selected  

> select add #26.2/A:71@CE2

277 atoms, 45 residues, 3 models selected  

> select add #26.2/A:71@CD2

278 atoms, 45 residues, 3 models selected  

> hide #26.2&~sel target s

> select subtract #26.2/A:257@C

277 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:161@CG2

276 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:161@CB

275 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:161@CD1

274 atoms, 45 residues, 3 models selected  

> select add #26.2/A:161@CD1

275 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:158@CA

274 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:158@CB

273 atoms, 45 residues, 3 models selected  

> select subtract #26.2/A:82@CG

272 atoms, 45 residues, 3 models selected  

> select add #26.2/A:82@CG

273 atoms, 45 residues, 3 models selected  

> hide #26.2&~sel target s

> select subtract #26.2/A:158@O

272 atoms, 45 residues, 3 models selected  

> hide #26.2&~sel target s

> select clear

> view plug_top

> select add #26.2/A:81@CD

1 atom, 1 residue, 1 model selected  

> select subtract #26.2/A:81@CD

1 model selected  

> select add #26.2/A:77@CB

1 atom, 1 residue, 1 model selected  

> select add #26.2/A:252@CB

2 atoms, 2 residues, 2 models selected  

> select add #26.2/A:77@O

3 atoms, 2 residues, 2 models selected  

> select add #26.2/A:77@CA

4 atoms, 2 residues, 2 models selected  

> select add #26.2/A:81@CB

5 atoms, 3 residues, 2 models selected  

> select subtract #26.2/A:81@CB

4 atoms, 2 residues, 2 models selected  

> hide sel target s

> select #26.2/A:12@C

1 atom, 1 residue, 1 model selected  

> hide sel target s

> select clear

> view plug_top

> transparency #26.2 80 target s

> save NhaA-pH75-plugged-top_surf-partial.png supersample 3
> transparentBackground true

> hide #!26 models

> save NhaA-pH75-plugged-top_sribbon_no-trans.png supersample 3
> transparentBackground true

> show #!26 models

> hide #!7 models

> show #!7 models

> hide #26.2 target c

> save NhaA-pH75-plugged-top_surf-partial.png supersample 3
> transparentBackground true

> hide #!26 models

> save NhaA-pH75-plugged-top_sribbon_no-trans.png supersample 3
> transparentBackground true

> hide #!7 models

> show #!26 models

> transparency #26.2 0 target s

> save NhaA-pH75-plugged-top_surf-partial_bg.png supersample 3
> transparentBackground true

> hide #!26 models

> show #!7 models

> view plug_top

> show #!9 models

> hide #!9 models

> show #!9 models

> show #9/A:78,81,82,252,253,256&sidechain target a

> hide #9 target c

> hide ##name="chain trance"

> hide ##name="chain trace"

> hide #9 target a

> show #9/A:78,81,82,252,253,256&sidechain target a

> hide ##name="chain trace"

> transparency #7/A:1-10 30 target a

> transparency #7/A:1-10 50 target a

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> ui mousemode right distance

> distance #9/A:252@OE1 #9/A:81@NE

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 252 OE1 and ARG
81 NE: 2.960Å  

> distance #9/A:81@NE #9/A:252@OE1

Distance already exists; modify distance properties with 'distance style'  

> show #!23 models

> show #23.1 models

> distance #9/A:81@NH1 #9/A:82@OE1

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ARG 81 NH1 and GLU
82 OE1: 3.128Å  

> distance #7/A:256@NE2 #7/A:78@OE2

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A HIS 256 NE2 and GLU 78
OE2: 3.336Å  

> distance #9/A:252@OE2 #9/A:81@NH2

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 252 OE2 and ARG
81 NH2: 2.826Å  

> ~distance #1/A:81@NE #1/A:252@OE1

> ~distance #9/A:252@OE1 #9/A:81@NE

> hide #23.1 models

> color sel dark gray

> select clear

> view plug_top

> hide #!9 models

> transparency #7/A:1-10 0 target a

> graphics silhouettes width 6

> hide #7 target c

> hide ##name="chain trace"

> save NhaA-pH75-plugged-top2_res.png supersample 3 transparentBackground true

> show #7/A target c

> graphics silhouettes width 2

> show #!9 models

> hide #!23 models

> transparency #7/A:1-10 50 target a

> transparency 30 target c

> size #7/A:1-10 stickRadius 0.1

Changed 93 bond radii  

> transparency #7/A:1-10 0 target a

> transparency #7/A:1-10 50 target a

> transparency #7/A:1-10 0 target a

> transparency #7/A:1-10 10 target a

> transparency #7/A:1-10 30 target a

> save NhaA-pH75-plugged-top_compare.png supersample 3 transparentBackground
> true

> show #!23 models

> hide sel

> select clear

> hide target c

> hide #7/A:1-10 target a

> hide ##name="chain trace"

> lighting full

> lighting shadows false

> graphics silhouettes width 6

> graphics silhouettes width 8

> save NhaA-pH75-plugged-top_compare_res.png supersample 3
> transparentBackground true

> hide #!23 models

> graphics silhouettes width 2

> show #7/A target c

> show #7/A:4-9 target a

> save NhaA-pH75-plugged-top_compare.png supersample 3 transparentBackground
> true

> show #!23 models

> hide #!23 models

> hide #7 target c

> hide ##name="chain trace"

> hide #7/A:1-10 target a

> show #!23 models

> graphics silhouettes width 8

> transparency 0 target ap

> transparency 100 target ap

> save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3
> transparentBackground true

> transparency 1 target p

> save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3
> transparentBackground true

> transparency 0 target ap

> distance #7/A:252@OE1 #7/A:81@NH1

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 252 OE1 and ARG 81
NH1: 3.594Å  

> show #23.1 models

> hide #23.1 models

> ~distance #7/A:252@OE1 #7/A:81@NH1

> ~distance #7/A:256@NE2 #7/A:78@OE2

> ui mousemode right translate

> view plug_top

> transparency 100 target a

> transparency 1 target p

> save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3
> transparentBackground true

> view name plug_top_zoom

> hide #!23 models

> transparency 0 target ap

> view cutaway

> ~clip

> hide #!7,9 atoms

> show #!1 models

> show #!3 models

> show #!5 models

> show #!11 models

> show #!13 models

> show #!15 models

> show #!17 models

> hide #!17 models

> hide #!1 models

> hide #!5 models

> hide #!15 models

> hide #!3,7,9,11,13 atoms

> show /A:163,164 target a

> hide #!3,7,9,11,13 atoms

> show /A:163,164&sidechain target a

> hide ##name="chain trace"

> color #!3,7,9,11,13 byhetero

> hide #!11 models

> hide #!9 models

> hide #!7 models

> hide #!13 models

> size tick 0.4

Expected a keyword  

> size stickRadius 0.4

Changed 168624 bond radii  

> size stickRadius 0.5

Changed 168624 bond radii  

> graphics silhouettes 2

Expected true or false or a keyword  

> graphics silhouettes width 2

> lighting full

> lighting shadows false

> lighting full multiShadow 1024 shadows false

> save NhaA-K-pH63-plugged_cutaway_res.png supersample 3 transparentBackground
> true

> show #!5 models

> hide #!3 models

> hide #!5 models

> show #!7 models

> save NhaA-K-pH75-plugged_cutaway_res.png supersample 3 transparentBackground
> true

> hide #!7 models

> show #!11 models

> save NhaA-K-pH85-state1-plugged_cutaway_res.png supersample 3
> transparentBackground true

> hide #!11 models

> show #!9 models

> save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3
> transparentBackground true

> size stickRadius 0.6

Changed 168624 bond radii  

> save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3
> transparentBackground true

> size stickRadius 0.7

Changed 168624 bond radii  

> save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3
> transparentBackground true

> hide #!9 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> save NhaA-K-pH63-plugged_cutaway_res.png supersample 3 transparentBackground
> true

> show #!1 models

> hide #!3 models

> hide #!1 atoms

> show /A:163,164&sidechain target a

> hide ##name="chain trace"

> color #!1 byhetero

> save NhaA-K-pH55-plugged_cutaway_res.png supersample 3 transparentBackground
> true

> hide #!1 models

> show #!7 models

> save NhaA-K-pH75-plugged_cutaway_res.png supersample 3 transparentBackground
> true

> hide #!7 models

> show #!11 models

> save NhaA-K-pH85-state1-plugged_cutaway_res.png supersample 3
> transparentBackground true

> hide #!11 models

> show #!5 models

> hide #!5 models

> show #!13 models

> color #13&core orange

> color #13&dimer khaki

> color #!13 byhetero

> save NhaA-K-pH85-state1-unplugged_cutaway_res.png supersample 3
> transparentBackground true

> hide #!13 models

> show #!15 models

> color #15&deep sky bluie;col #15&dimer light blue;

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #15&core deep sky blue

> color #15&dimer light blue

> hide #!15 atoms

> show /A:163,164&sidechain target a

> hide ##name="chain trace"

> show /A:163,164&sidechain target a

> hide ##name="chain trace"

> color #!15 byhetero

> select #15/A:164@CA

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> graphics selection color black

> graphics selection color black width 6

> graphics selection color black width 8

> graphics selection color black width 10

> save NhaA-K-pH85-state2_cutaway_res.png supersample 3 transparentBackground
> true

> graphics selection color black width 20

> graphics selection color black width 2

> graphics selection color ;ime wid 2

Invalid "color" argument: Invalid color name or specifier  

> graphics selection color lime width 2

> select clear

> size stickRadius 0.3

Changed 168624 bond radii  

> show #!17 models

> hide #!15,17 atoms

> show /A target c

> color #17&core dodger blue

> color #17&dimer light sky blue

> cartoon style modeHelix tube radius 1.4 sides 24

> color #17 dodger blue

> color #15 light blue

> color #17 dodger blue

> color #15 deep sky blue

> color #17 dodger blue

> color #15 light blue

> color #17 dodger blue

> color #15 light sky blue

> color #17 dodger blue

> color #15 light blue

> view mono_back_

> view mono_back

> view mono_back_

> save NhaA-pH85-Na-vs-K-superpose.png supersample 3 transparentBackground
> true

> transparency 0 target c

> save NhaA-pH85-Na-vs-K-superpose.png supersample 3 transparentBackground
> true

> cartoon style modeHelix default width 1.0 thickness 0.3

> view core_inner_side2

> hide dimer target c

> show /A:164,132 target a

> color #!15,17 byhetero

> hide #!17 models

> show #!17 models

> hide #!15 models

> show #!33 models

> hide #!17,33 atoms

> color #17 dodger blue

> color #33 light sky blue

> color #17 dodger blue

> color #33 light blue

> show /A:164,132 target a

> color #!17,33 byhetero

> size stickRadius 0.3

Changed 168624 bond radii  

> size stickRadius 0.4

Changed 168624 bond radii  

> select #17,33/A:130-144,150-174

580 atoms, 582 bonds, 1 pseudobond, 80 residues, 3 models selected  

> graphics selection color black width 4

> graphics selection color black width 6

> graphics selection color black width 4

> transparency #17,33/A&~:130-144,150-174 30 target c

> save NhaA-Na-pH85_vs_K-pH85_inside_TM4c-5.png supersample 3
> transparentBackground true

> select clear

> show /A target c

> transparency 0 target c

> view binding_site

> size stickRadius 0.3

Changed 168624 bond radii  

> show #17&(binding_site_res&sidechain

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #17&(binding_site_res&sidechain)

> show #17,33&(binding_site_res&sidechain)

> show #!23 models

> hide #!23 models

> transparency 30 target c

> save NhaA-Na-pH85_vs_K-pH85_binding-site.png supersample 3
> transparentBackground true

> show #!23 models

> show #23.1 models

> ui mousemode right distance

> distance #33/A:300@NZ #33/A:163@OD1

Distance already exists; modify distance properties with 'distance style'  

> show #23 target p

> hide :NA,HOH

> distance #17/A:164@OD1 #17/A:132@O

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 164 OD1 and THR 132 O:
4.183Å  

> ui mousemode right rotate

> color sel dodgerblue

> select clear

> hide #23.1 models

> hide target ac

> transparency #23 1 target p

> graphics silhouettes width 6

> show #17,33&(binding_site_res&sidechain|:132) target a

> transparency #17,33/A 0 target a

> transparency #23 0 target p

> graphics silhouettes width 6

> hide sel

> select clear

> save NhaA-Na-pH85_vs_K-pH85_binding-site_sil.png supersample 3
> transparentBackground true

> show /A target c

> show /A target cgra sil wid 2

Invalid "target" argument: Target option can only include letters a = atoms, b
= bonds, p = pseudobonds, c = cartoons, r = cartoons, s = surfaces, m =
models, got g  

> graphics silhouettes width 2

> hide #!23 models

> transparency 0 target a

> transparency 100 target a

> save NhaA-Na-pH85_vs_K-pH85_binding-site2.png supersample 3
> transparentBackground true

> view binding_site

> save NhaA-Na-pH85_vs_K-pH85_binding-site2.png supersample 3
> transparentBackground true

> transparency 0 target ac

> view cutaway

> hide #!17 models

> hide #!33 models

> show #!29 models

> hide #!29 models

> show #!29 models

> show #!28 models

> hide #!28 models

> hide #!29 models

> show #!26 models

> show #!26.1 models

> select add #26.2

2921 atoms, 2979 bonds, 380 residues, 1 model selected  

> coulombic sel

Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface
#26.2.1: minimum, -15.57, mean -0.06, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide target c

> select clear

> lighting soft multiShadow 1024

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> save NhaA-K-pH75-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> hide #!26 models

> show #!27 models

> show #!28 models

> show #!29 models

> show #27,28,29 target s

Cell requested for row 27 is out of bounds for table with 54 rows! Resizing
table model.  

> select add #27.2

2978 atoms, 3036 bonds, 380 residues, 2 models selected  

> select add #28.2

5900 atoms, 6016 bonds, 760 residues, 5 models selected  

> show #!29.2 models

> select add #29.2

8819 atoms, 8993 bonds, 1140 residues, 8 models selected  

> coulombic sel

Coulombic values for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 2_A SES
surface #27.2.1: minimum, -16.15, mean -0.11, maximum 16.64  
Coulombic values for NhaA-nd-6F9-K-MESpH55_plugged_split 2_A SES surface
#29.2.1: minimum, -15.70, mean -0.04, maximum 13.35  
Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split 2_A SES surface
#28.2.1: minimum, -17.21, mean 0.03, maximum 15.32  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> select clear

> hide #!28 models

> hide #!29 models

> save NhaA-K-pH85-state1-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> show #!28 models

> hide #!27 models

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> save NhaA-K-pH63-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> show #!29 models

> hide #!28 models

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> hide #!29 models

> show #!28 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!28 models

> show #!28 models

> hide #!29 models

> show #!29 models

> hide #!28 models

> view cutaway

> show #!28 models

> hide #!28 models

> save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> clip front 0.4 position #17:NA

> color ##name="cap front" black target s

> transparency 0 target s

> select #29.1.1.1

1 model selected  

> color sel medium purple

> select clear

> select #29.1.1.1

1 model selected  

> color sel medium purple

> transparency sel 1

> select clear

> save NhaA-K-pH55-plugged_cutaway.png supersample 3 transparentBackground
> true

> hide #!29 models

> show #!28 models

> select #28.2.1.1

1 model selected  

> color sel black

> select #28.1.1.1

1 model selected  

> color sel medium purple

> transparency sel 1

> select clear

> save NhaA-K-pH63-plugged_cutaway.png supersample 3 transparentBackground
> true

> show #!27 models

> hide #!28 models

> select #27.2.1.1

1 model selected  

> select #27.2.1.1

1 model selected  

> color sel black

> select #27.1.1.1

1 model selected  

> color sel medium purple

> transparency sel 1

> select clear

> save NhaA-K-pH85-state1-plugged_cutaway.png supersample 3
> transparentBackground true

> show #!26 models

> hide #!27 models

> select #26.2.1.1

1 model selected  

> select up

2828 atoms, 378 residues, 3 models selected  

> select down

1 model selected  

> color sel black

> select #26.1.1.1

1 model selected  

> color sel medium purple

> transparency sel 1

> select clear

> save NhaA-K-pH75-plugged_cutaway.png supersample 3 transparentBackground
> true

> hide #!26 models

> show #!29 models

> size #29 atomRadius default

Changed 2982 atom radii  

> hide #!29.1.1 models

> show #29.1.1 models

> close #29.1.1

> select add #29.1

63 atoms, 65 bonds, 7 residues, 1 model selected  

> show sel surfaces

> select clear

> select #29.2.1.1

1 model selected  

> select up

2828 atoms, 378 residues, 3 models selected  

> select down

1 model selected  

> color sel black

> select #29.1.1.1

1 model selected  

> color sel medium purple

> transparency sel 1

> select clear

> save NhaA-K-pH55-plugged_cutaway.png supersample 3 transparentBackground
> true

> transparency 30 target s

> color ##name="cap front" white transparency 100 target s

> save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3
> transparentBackground true

> view mono_back_

> hide #!29 models

> show #!17 models

> show #!17 cartoons

> lighting simple

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #44 models

> show #44#!17 cartoons

> show #45 models

> hide #44 models

> show #45#!17 cartoons

> show #46 models

> show #45-46#!17 cartoons

> show #!1 models

> show #45-46#!1,17 cartoons

> hide /B,C target c

> hide #45 models

> hide #46 models

> show #!48 models

> hide #!48 models

> show #47 models

> show /A target c

> hide #47 models

> show #47 models

> hide #47 models

> show #44 models

> show #45 models

> hide #44 models

> show #46 models

> show #47 models

> hide #47 models

> show #44 models

> hide #44 models

> show #43 models

> show #44 models

> show #47 models

> hide #43 models

> hide #44 models

> hide #45 models

> hide #46 models

> hide #47 models

> show #!1,17 atoms

> hide #!1,17 cartoons

> ui mousemode right distance

> distance #17/A:162@N #1/A:162@N

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ILE 162 N and NhaA-
nd-6F9-K_MESpH55.pdb #1/A ILE 162 N: 1.777Å  

> show #!23 models

> show #23.1 models

> distance #17/A:159@N #1/A:159@N

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A LEU 159 N and NhaA-
nd-6F9-K_MESpH55.pdb #1/A LEU 159 N: 1.621Å  

> hide #!23 models

> hide #!1 models

> hide #!17 atoms

> coulombic #!17

Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_A SES surface #17.1: minimum,
-15.88, mean 0.07, maximum 15.24  
Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_B SES surface #17.2: minimum,
-20.11, mean -1.82, maximum 11.17  
Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_C SES surface #17.3: minimum,
-14.41, mean -2.05, maximum 16.84  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!17 surfaces

> show #!17 cartoons

> show /A:ASP,GLU,LYS,ARG,HIS target a

> distance #17/A:225@CE1 #17/A:65@OD1

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A HIS 225 CE1 and ASP 65 OD1:
3.136Å  

> show #!23 models


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: 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: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
      OS Loader Version: 540.120.3~37

Software:

    System Software Overview:

      System Version: macOS 12.7.5 (21H1222)
      Kernel Version: Darwin 21.6.0
      Time since boot: 11 days 16:09

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        DELL U3821DW:
          Resolution: 6400 x 2666
          UI Looks like: 3200 x 1333 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: H5YZZ63     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
          Television: Yes


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

Change History (2)

comment:1 by Eric Pettersen, 14 months ago

Component:	Unassigned → Window Toolkit
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Tom Goddard, 14 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Qt 6.6 crash in displayConfigFinalizedProc, either from connecting or disconnecting external displays or waking from sleep.

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