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Opened 14 months ago

Last modified 14 months ago

#15919 closed defect

ChimeraX bug report submission — at Initial Version

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

Description

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)


{"app_name":"ChimeraX","timestamp":"2024-09-10 12:35:31.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.7.5 (21H1222)","incident_id":"9961A723-A8E1-437D-94FC-E6EF0D99E979","name":"ChimeraX"}
{
  "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,
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    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.8.0.0"
  },
  {
    "source" : "P",
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    "size" : 442368,
    "uuid" : "10c8ed27-59df-36b5-ab45-7a381b384783",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4478705664,
    "size" : 66404352,
    "uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
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    "arch" : "x86_64",
    "base" : 140703556481024,
    "size" : 364544,
    "uuid" : "a372724f-4642-369b-a01b-28e1f5e83ff1",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
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    "size" : 66076672,
    "uuid" : "40ef249b-28c0-36a0-a2c7-4f023a84cc12",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
    "name" : "libopenblas.0.dylib"
  },
  {
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    "arch" : "x86_64",
    "base" : 140703554248704,
    "size" : 245760,
    "uuid" : "dba8e82f-0557-37e8-ace0-173a9d0dce7f",
    "path" : "\/usr\/lib\/system\/libxpc.dylib",
    "name" : "libxpc.dylib"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140712564355072,
    "size" : 20480,
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    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCoreVMClient.dylib",
    "name" : "libCoreVMClient.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
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    "size" : 12288,
    "uuid" : "5070c64b-8a1f-3b86-b79d-349540bb0af8",
    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCVMSPluginSupport.dylib",
    "name" : "libCVMSPluginSupport.dylib"
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],
  "sharedCache" : {
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},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=142.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=142.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               768K        6 \nActivity Tracing                   256K        1 \nCG backing stores                 18.0M        5 \nCG image                           648K       50 \nColorSync                          232K       28 \nCoreAnimation                     2844K      104 \nCoreGraphics                        16K        3 \nCoreServices                       624K        2 \nCoreUI image data                 5156K       41 \nFoundation                          36K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                           139.5G     1893 \nMALLOC guard page                   48K       11 \nMALLOC_MEDIUM (reserved)           1.1G       12         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        272K       68 \nStack                            177.5M       69 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      850.8M     1030 \nVM_ALLOCATE (reserved)           352.0M        4         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            54.7M      789 \n__DATA_CONST                      42.4M      404 \n__DATA_DIRTY                      1778K      229 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       685.7M      229 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           969.0M      778 \n__UNICODE                          592K        1 \ndyld private memory               1064K        3 \nmapped file                      515.6M       92 \nshared memory                     2984K       29 \n===========                     =======  ======= \nTOTAL                            144.5G     5902 \nTOTAL, minus reserved VM space   142.9G     5902 \n",
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},
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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

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 0.0102, 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 0.013, 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 0.0125, 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 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)  
  

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

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> show #7 models

> hide #17 models

> show #17 models

> hide #7 models

> show #7 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #1 models

> show #3 models

> show #5 models

> show #9 models

> show #11 models

> show #13 models

> show #15 models

> color #1&core indian red

> color #1&dimer pink

> color #3,5&core orange

> color #3,5&dimer khaki

> hide #15 models

> hide #13 models

> hide #11 models

> hide #9 models

> hide #7 models

> hide #1 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #5 models

> show #5 models

> color #7,9&core medium sea green

> color #7,9&dimer pale green

> hide #3 models

> hide #5 models

> show #7 models

> show #9 models

> hide #9 models

> lighting soft

> graphics silhouettes true

> hide #7 models

> show #7 models

> show #!4 models

> hide #!4 models

> show #5 models

> hide #7 models

> show #7 models

> hide #5 models

> color #7,9&core sea green

> color #7,9&dimer pale green

> show #5 models

> hide #7 models

> show #7 models

> hide #7 models

> hide #5 models

> show #7 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #11 models

> color #11,13,15&core dodger blue

> color #11,13,15&dimer light sky blue

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> color /B,C gray

> color /B,C light gray

> color /B,C silver

> hide /B,C

> hide /B,C target c

> hide #7 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #!8 models

> hide #!8 models

> show #7 models

> hide #7 models

> show #9 models

> setattr #9/A:145-147 res is_helix 0

Assigning is_helix attribute to 3 items  

> show #9 atoms

> hide #9 cartoons

> color #9 byhetero

> show #9 cartoons

> setattr #9/A:285 res is_helix 1

Assigning is_helix attribute to 1 item  

> setattr #9/A:286 res is_helix 1

Assigning is_helix attribute to 1 item  

> setattr #9/A:286 res is_helix 0

Assigning is_helix attribute to 1 item  

> hide #9 atoms

> show #7 models

> hide #9 models

> show #9 models

> hide #7 models

> show #7 models

> hide #9 models

> cartoon style modeHelix tube radius 1.8 sides 24

> show #9 models

> hide #7 models

> show #7 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #7 models

> hide #9 models

> show #7 models

> cartoon style modeHelix default width 1.8 thickness 0.3

> setattr #7/A:11 res is_helix 0

Assigning is_helix attribute to 1 item  

> show #9 models

> hide #7 models

> show #7 models

> hide #9 models

> show #9 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> setattr #7/A:145-147 res is_helix 0

Assigning is_helix attribute to 3 items  

> hide #7 models

> show #7 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

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> show #9 models

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> show #7 models

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> show #7 models

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> show #9 models

> hide #9 models

> show #9 models

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> show #7 models

> hide #9 models

> show #9 models

> hide #7 models

> hide #9 models

> show #7 models

> show #5 models

> hide #5 models

> show #3 models

> mcopy #7/A toAtoms #3/A settings h

> hide #3 models

> show #13 models

> setattr #7/A:58,45 res is_strand 0

Assigning is_strand attribute to 2 items  

> hide #13 models

> setattr #7/A:45 res is_strand 1

Assigning is_strand attribute to 1 item  

> setattr #7/A:58 res is_strand 1

Assigning is_strand attribute to 1 item  

> show #13 models

> hide #13 models

> mcopy #7/A toAtoms #1,3/A settings h

> show #5 models

> hide #5 models

> hide #7 models

> show #5 models

> show #11 models

> mcopy #9/A toAtoms #5,11,13,15/A settings h

> show #13 models

> hide #13 models

> hide #11 models

> show #11 models

> hide #5 models

> show #11 atoms

> color #11 byhetero

> hide #11 cartoons

> show #13 models

> hide #13 models

> show #9 models

> show #9,11 atoms

> hide #9,11 cartoons

> show #9,11 cartoons

> hide #9,11 atoms

> show #9,11 atoms

> hide #9 models

> show #9 models

> hide #9,11 atoms

> hide #9 models

> show #13 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #13 atoms

> hide #13 cartoons

> color #13 byhetero

> show #13 cartoons

> setattr #13/A:223-226 res is_helix 0

Assigning is_helix attribute to 4 items  

> hide #13 cartoons

[Repeated 1 time(s)]

> show #13 cartoons

> setattr #13/A:223-226 res is_helix 1

Assigning is_helix attribute to 4 items  

> setattr #13/A:223-225 res is_helix 1

Assigning is_helix attribute to 3 items  

> setattr #13/A:223-225 res is_helix 0

Assigning is_helix attribute to 3 items  

> show #13 atoms

> hide #13 cartoons

> show #13 cartoons

> hide #13 cartoons

> setattr #13/A:223-226 res is_helix 0

Assigning is_helix attribute to 4 items  

> show #13 cartoons

> setattr #15/A:223-226 res is_helix 0

Assigning is_helix attribute to 4 items  

> show #15 models

> hide #13 models

> close #17

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #13 models

> show #11 models

> show #9 models

> show #7 models

> show #5 models

> show #3 models

> show #1 models

> hide /B,C target ac

> hide atoms

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Fri Aug 16 14:59:40 2024 ———

opened ChimeraX session  

> color #7,9&core forest green

> color #7,9&dimer pale green

> color #11,13&core light sea green

> color #11,13&dimer cyan

> hide #1 models

> hide #3 models

> hide #7 models

> hide #5 models

> hide #11 models

> hide #13 models

> hide #15 models

> show #11 models

> hide #9 models

> hide #11 models

> show #13 models

> show #15 models

> hide #13 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #15 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> color /A:1-10 orchid

> cartoon style modeHelix default width 1.8 thickness 0.3

> hide #11 models

> show #1 models

> show #3 models

> show #5 models

> show #7 models

> show #9 models

> show #11 models

> show #13 models

> show #15 models

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> hide #15 models

> hide #13 models

> hide #11 models

> show #11 models

> hide #11 models

> show #13 models

> hide #13 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> show #13 models

> hide #13 models

> hide #9 models

> show #9 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show :CDL,PTY target a

> show #11 models

> show #13 models

> show #15 models

> hide #1 models

> hide #3 models

> hide #5 models

> hide #7 models

> hide #9 models

> hide #15 models

> show #15 models

> hide #15 models

> hide #13 models

> show #!12 models

> hide #!12 models

> show #!12 models

> color #12 #ffb2b258 models

> color #12 #ffb2b26b models

> ui tool show "Side View"

> show #9 models

> hide #9 models

> show #9 models

> hide #!12 models

> select #11/A:401@C78

1 atom, 1 residue, 1 model selected  

> select add #11/A:401@C79

2 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C80

3 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C81

4 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C82

5 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C83

6 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C84

7 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C85

8 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C86

9 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C87

10 atoms, 1 residue, 1 model selected  

> delete sel

> select #11/A:401@C67

1 atom, 1 residue, 1 model selected  

> select add #11/A:401@C66

2 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C65

3 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C64

4 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C63

5 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C62

6 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C60

7 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C59

8 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C58

9 atoms, 1 residue, 1 model selected  

> delete sel

> select #11/A:401@C61

1 atom, 1 residue, 1 model selected  

> delete sel

> show #!12 models

> hide #!12 models

> select #11/A:401@C43

1 atom, 1 residue, 1 model selected  

> select add #11/A:401@C44

2 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C45

3 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C46

4 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C47

5 atoms, 1 residue, 1 model selected  

> delete sel

> show #!12 models

> hide #!12 models

> select #11/A:401@C19

1 atom, 1 residue, 1 model selected  

> select add #11/A:401@C20

2 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C21

3 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C22

4 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C23

5 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C24

6 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C25

7 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C26

8 atoms, 1 residue, 1 model selected  

> select add #11/A:401@C27

9 atoms, 1 residue, 1 model selected  

> delete sel

> show #!12 models

> hide #!12 models

> select #11/A:402@C17

1 atom, 1 residue, 1 model selected  

> select add #11/A:402@C18

2 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C19

3 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C20

4 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C21

5 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C22

6 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C23

7 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C24

8 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C25

9 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C26

10 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C27

11 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C28

12 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C29

13 atoms, 1 residue, 1 model selected  

> show #!12 models

> hide #!12 models

> delete sel

> show #!12 models

> hide #!12 models

> select #11/A:402@C44

1 atom, 1 residue, 1 model selected  

> select add #11/A:402@C43

2 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C42

3 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C41

4 atoms, 1 residue, 1 model selected  

> select add #11/A:402@C40

5 atoms, 1 residue, 1 model selected  

> delete sel

> show #!12 models

> hide #!12 models

> select #11/A:402@C39

1 atom, 1 residue, 1 model selected  

> select add #11/A:402@C38

2 atoms, 1 residue, 1 model selected  

> show #!12 models

> delete sel

> hide #!12 models

> hide #11 models

> show #11 models

> hide #11 models

> show #13 models

> show #!14 models

> color #14 #b2ffb250 models

> color #14 #b2ffb263 models

> volume #14 level 0.0155

> hide #!14 models

> select #13/A:401@C80

1 atom, 1 residue, 1 model selected  

> select add #13/A:401@C81

2 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C82

3 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C83

4 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C84

5 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C85

6 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C86

7 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C87

8 atoms, 1 residue, 1 model selected  

> delete sel

> show #!14 models

> hide #!14 models

> select #13/A:401@C55

1 atom, 1 residue, 1 model selected  

> select add #13/A:401@C56

2 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C57

3 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C58

4 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C59

5 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C60

6 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C61

7 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C62

8 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C63

9 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C64

10 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C65

11 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C66

12 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C67

13 atoms, 1 residue, 1 model selected  

> delete sel

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> volume #14 level 0.01343

> hide #!14 models

> select #13/A:401@C41

1 atom, 1 residue, 1 model selected  

> select add #13/A:401@C42

2 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C43

3 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C44

4 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C45

5 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C46

6 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C47

7 atoms, 1 residue, 1 model selected  

> delete sel

> show #!14 models

> hide #!14 models

> select #13/A:401@C17

1 atom, 1 residue, 1 model selected  

> select add #13/A:401@C18

2 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C19

3 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C20

4 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C21

5 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C22

6 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C23

7 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C24

8 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C25

9 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C26

10 atoms, 1 residue, 1 model selected  

> select add #13/A:401@C27

11 atoms, 1 residue, 1 model selected  

> delete sel

> show #!14 models

> select #13/A:402@C15

1 atom, 1 residue, 1 model selected  

> hide #!14 models

> select add #13/A:402@C16

2 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C17

3 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C18

4 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C19

5 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C20

6 atoms, 1 bond, 1 residue, 1 model selected  

> select add #13/A:402@C21

7 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C22

8 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C23

9 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C25

10 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C26

11 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C27

12 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C28

13 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C29

14 atoms, 1 residue, 1 model selected  

> delete sel

> select #13/A:402@C24

1 atom, 1 residue, 1 model selected  

> delete sel

> show #!14 models

> select #13/A:402@C41

1 atom, 1 residue, 1 model selected  

> select add #13/A:402@C42

2 atoms, 1 residue, 1 model selected  

> hide #!14 models

> select add #13/A:402@C43

3 atoms, 1 residue, 1 model selected  

> select add #13/A:402@C44

4 atoms, 1 residue, 1 model selected  

> show #!14 models

> select add #13/A:402@C40

5 atoms, 1 residue, 1 model selected  

> delete sel

> hide #!14 models

> hide #13 models

> show #13 models

> hide #13 models

> size stickRadius 0.3

Changed 38701 bond radii  

> style #9 ball

Changed 4737 atom styles  

> style #9 stick

Changed 4737 atom styles  

> style #9 ball

Changed 4737 atom styles  

> style #9 ball

Changed 4737 atom styles  

> style #9 stick

Changed 4737 atom styles  

> style #9 ball

Changed 4737 atom styles  

> style #9 stick

Changed 4737 atom styles  

> hide #9 models

> show #9 models

> show #!10 models

> volume #10 level 0.01355

> hide #!10 models

> camera ortho

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Fri Aug 16 16:43:58 2024 ———

opened ChimeraX session  

> close #13#14

> 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_B70.mrc

Opened NhaA-nd-6F9-K_BTPpH85_state2_postprocess_B70.mrc as #14, grid size
248,248,248, pixel 0.837, shown at level 0.00735, step 1, values float32  

> 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 = 603.7  
RMSD between 114 pruned atom pairs is 0.605 angstroms; (across all 119 pairs:
1.054)  
  

> hide #!14 models

> color #11,13&core light sea green

> color #11,13&dimer cyan

> hide #9 models

> show #9 models

> hide #9 models

> color /A:1-10 orchid

> color /B,C silver

> hide #13 atoms

> mcopy #15 toAtoms #13 settings h

> show #15 models

> hide #13,15 atoms

> hide /B,C

> hide /B,C target ac

> show :132,133,163,164,300 target a

> color #13,15 byhetero

> size stickRadius 0.3

Changed 38760 bond radii  

> show #!14 models

> transparency #14,16 40 target s

> volume #14 level 0.01445

> ui tool show "Side View"

> show :H2O target a

> show :O target a

> show :NA target a

> show #13,15 atoms

> lighting simple

> select #15/A:505@NA

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> select clear

> volume #14 level 0.01372

> show #!16 models

> volume #16 level 0.01314

> volume #16 level 0.01212

> volume #16 level 0.01172

> hide #13,15 cartoons

> show #13,15 cartoons

> hide #13,15 atoms

> show :132,133,163,164,300,HOH,NA target a

> hide /B,C target ac

> view name binding_site

> hide #!14 models

> hide #!16 models

> hide #13 models

> show #13 models

> hide #15 models

> show #15 models

> view list

Named views: binding_site  

> view binding_site

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #13 models

> show #!16 models

> volume #16 level 0.0105

> show #15 atoms

> show #13 models

> show #!14 models

> hide #15 models

> hide #!16 models

> hide #13 models

> hide #!14 models

> show #15 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> ui mousemode right distance

> distance #15/A:300@NZ #15/A:163@OD2

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A LYS 300 NZ and ASP 163 OD2:
3.986Å  

> hide #!17 models

> hide #17.1 models

> show #!17 models

> hide #15 models

> show #13 models

> show #!14 models

> hide #!14 models

> distance #13/A:300@NZ #13/A:163@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A LYS 300 NZ and ASP 163
OD2: 3.294Å  

> show #17.1 models

> show #!14 models

> show #15 models

> volume #14 level 0.01151

> hide #13,15 cartoons

> hide #!17 models

> show #!17 models

> hide #13 models

> hide #!14 models

> distance #15/A:132@O #15/A:164@OD1

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A THR 132 O and ASP 164 OD1:
4.183Å  

> distance #15/A:132@O #15/A:164@OD2

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #15/A THR 132 O and ASP 164 OD2:
4.787Å  

> hide #15 models

> show #13 models

> distance #13/A:132@O #13/A:164@OD1

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A THR 132 O and ASP 164
OD1: 5.033Å  

> distance #13/A:132@O #13/A:164@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #13/A THR 132 O and ASP 164
OD2: 6.181Å  

> show #15 models

> hide #13 models

> show #!16 models

> hide #!16 models

> hide #!17 models

> hide #15 models

> show #!14 models

> show #13 models

> show #15 models

> show #!16 models

> hide #!14 models

> show #!14 models

> hide #15 models

> hide #!16 models

> hide #!14 models

> show #15 models

> hide #13 models

> show #15 cartoons

> hide /B,C target ac

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Tue Aug 20 16:41:19 2024 ———

opened ChimeraX session  

> lighting soft

> lighting simple

> lighting soft

> hide #15 atoms

> close #17

> rename #15 id 17

> rename #16 id #18

> rename #14 id #16

> rename #13 id #15

> close #11#12

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

Chain information for NhaA-nd-6F9-K_BTPpH85_state1-plugged.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-unplugged_postprocess_B70.mrc

Opened NhaA-nd-6F9-K_BTPpH85_state1-unplugged_postprocess_B70.mrc as #12, grid
size 248,248,248, pixel 0.837, shown at level 0.00544, step 1, values float32  

> close #12

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH85_state1-plugged_postprocess_B70.mrc

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  

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

Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.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_state1-unplugged_postprocess_B70.mrc

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  

> hide #!12 models

> hide #!14 models

> mmaker #11 to #7 bring 12

> matchmaker #11 to #7 bring 12

Invalid "bring" argument: invalid models specifier  

> mmaker #11&dimer_TM to #7 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_plugged.pdb, chain A (#7) with NhaA-
nd-6F9-K_BTPpH85_state1-plugged.pdb, chain A (#11), sequence alignment score =
621.1  
RMSD between 119 pruned atom pairs is 0.160 angstroms; (across all 119 pairs:
0.160)  
  

> mmaker #13&dimer_TM to #7 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_plugged.pdb, chain A (#7) with NhaA-
nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#13), sequence alignment score
= 621.1  
RMSD between 119 pruned atom pairs is 0.167 angstroms; (across all 119 pairs:
0.167)  
  

> hide #17 models

> show #15 models

> hide #15 models

> hide #13 models

> hide #11 models

> show #11 models

> show #13 models

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> hide #13 models

> hide #11 models

> show #9 models

> color #7,9&core forest green

> color #7,9&dimer pale green

> color #7,9&core medium sea green

> color #7,9&dimer pale green

> show #11 models

> hide #11 models

> show #11 models

> color #7,9&core forest green

> color #7,9&dimer pale green

> hide #11 models

> color #7,9&core lime green

> color #7,9&dimer pale green

> cartoon style modeHelix default width 1.4 thickness 0.3

> cartoon style modeHelix default width 1.5 thickness 0.3

> cartoon style modeHelix default width 1.6 thickness 0.3

> cartoon style modeHelix default width 1.8 thickness 0.3

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> hide /B,C target ac

> color #7,9&core yellow green

> color #7,9&dimer pale green

> color #7,9&core olive drab

> color #7,9&dimer pale green

> show #11 models

> color #7,9&core forest green

> color #7,9&dimer pale green

> color #7,9&core olive drab

> color #7,9&dimer pale green

> color #7,9&core forest green

> color #7,9&dimer pale green

> color #7,9&core olive drab

> color #7,9&dimer pale green

> color #7,9&core lime green

> color #7,9&dimer pale green

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> color #11,13,15&core dark cyan

> color #11,13,15&dimer cyan

> hide #11 models

> show #11 models

> hide #9 models

> show #9 models

> hide #11 models

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> show #11 models

> hide #9 models

> show #9 models

> color #7,9&core forest green

> color #7,9&dimer pale green

> hide #11 models

> show #11 models

> hide #9 models

> hide target a

> color #11,13,15&core dark cyan

> color #11,13,15&dimer cyan

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> color #7,9&core forest green

> color #7,9&dimer pale green

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #11 models

> show #13 models

> hide #13 models

> show #15 models

> hide #9 models

> hide #15 models

> show #15 models

> show #9 models

> show #9,15 cartoons

> hide /B,C target ac

> show #17 models

> hide #9 models

> hide #17 models

> show #13 models

> hide #13 models

> show #9 models

> hide #9 models

> show #13 models

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_consensus.pdb

Chain information for NhaA-nd-6F9-K_BTPpH75_consensus.pdb #19  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C F | No description available  
  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_consensus_postprocess_B40.mrc

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  

> hide #13,15,19 atoms

> show #13,15,19 cartoons

> hide /B,C target ac

> hide #!20 models

> mmaker #19&dimer_TM to #9 bring #20

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_consensus.pdb, chain A (#19), sequence alignment score =
620.5  
RMSD between 119 pruned atom pairs is 0.103 angstroms; (across all 119 pairs:
0.103)  
  

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:11-85,181-274 pale green

> hide #19 models

> hide #15 models

> color #11,13,15&core light sea green

> color #11,13,15&dimer pale turquoise

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> color #11,13,15&core light sea green

> color #11,13,15&dimer pale turquoise

> show #15 models

> hide #15 models

> show #11 models

> hide #11 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> color #11,13,15&core light sea green

> color #11,13,15&dimer cyan

> color #11,13,15&core light sea green

> color #11,13,15&dimer pale turquoise

> color /A:1-10 orchid

> color /A,D:1-10 orchid

> show #11 models

> show #15 models

> hide #15 models

> hide #13 models

> show #13 models

> hide #13 models

> show #!10 models

> hide #!10 models

> show #9 models

> hide #9 models

> show #7 models

> mcopy #7 toAtoms #11 settings h

> hide #7 models

> show #9 models

> hide #9 models

> hide #11 models

> show #13 models

> mcopy #9 toAtoms #11,19 settings h

> mcopy #9 toAtoms #13,19 settings h

> show #11 models

> hide #13 models

> mcopy #7 toAtoms #11 settings h

> show #13 models

> hide #13 models

> hide #11 models

> show #7 models

> hide #7 models

> show #!8 models

> hide #!8 models

> show #17 models

> hide #17 models

> show #!16 models

> hide #!16 models

> show #15 models

> hide #15 models

> show #19 models

> mcopy #19/A-C toAtoms #19/D-F settings h

> mcopy #19/A toAtoms #19/D settings h

> mcopy #9 toAtoms #19/A settings h

> mcopy #9/A toAtoms #19/A settings h

> mcopy #9/A toAtoms #19/D settings h

> mcopy #9/A toAtoms #19/D settings h matchResidues false

> mcopy #9/B toAtoms #19/E settings h matchResidues false

> mcopy #9/C toAtoms #19/F settings h matchResidues false

> hide /B,C,E,F target ac

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> cartoon style modeHelix default width 1.8 thickness 0.3

> size stickRadius 0.3

Changed 53299 bond radii  

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Thu Aug 22 17:18:58 2024 ———

opened ChimeraX session  

> lighting soft multiShadow 1024

> show /B,C,E,F target c

> color /B,C,E,F silver

> view

> ui tool show "Side View"

> hide #19/A,D:1-10 target c

> show #19:CDL,PTY target a

> style #19:CDL,PTY ball

Changed 150 atom styles  

> view name dimer_view-all_front

> show #!20 models

> surface dust #20 size 1

> volume #20 level 0.006821

> view

> volume #20 level 0.007734

> volume #20 level 0.0081

> volume #20 level 0.008465

> view

> volume #20 level 0.008648

> view

[Repeated 1 time(s)]

> view name dimer_view-all_front

> transparency #20 60

> lighting simple

> select #19/A:401@C58

1 atom, 1 residue, 1 model selected  

> hide #!20 models

> select add #19/A:401@C59

2 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C60

3 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C61

4 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C62

5 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C63

6 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C64

7 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C65

8 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C66

9 atoms, 1 residue, 1 model selected  

> select add #19/A:401@C67

10 atoms, 1 residue, 1 model selected  

> show #!20 models

> select #19/A:401@C77

1 atom, 1 residue, 1 model selected  

> select add #19/A:401@C58

2 atoms, 1 residue, 1 model selected  

> volume #20 level 0.009561

> select add #19/A:401@C24

3 atoms, 1 residue, 1 model selected  

> select add #19/A:402@C16

4 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C37

5 atoms, 2 residues, 1 model selected  

> hide #!20 models

> select add #19/A:401@C59

6 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C60

7 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C61

8 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C62

9 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C63

10 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C64

11 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C65

12 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C66

13 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C67

14 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C78

15 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C79

16 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C80

17 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C81

18 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C82

19 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C83

20 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C84

21 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C85

22 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C86

23 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C87

24 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C25

25 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C26

26 atoms, 2 residues, 1 model selected  

> select add #19/A:401@C27

27 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C17

28 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C18

29 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C19

30 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C20

31 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C21

32 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C22

33 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C23

34 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C24

35 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C25

36 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C26

37 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C27

38 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C28

39 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C29

40 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C38

41 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C39

42 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C40

43 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C41

44 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C42

45 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C43

46 atoms, 2 residues, 1 model selected  

> select add #19/A:402@C44

47 atoms, 2 residues, 1 model selected  

> delete sel

> show #!20 models

> hide #!20 models

> view list

Named views: binding_site, dimer_view-all_front  

> view dimer_view-all_front

> lighting soft

> view name dimer_view-all_front

> lighting soft multiShadow 1024

> lighting gentle multiShadow 1024

> lighting soft multiShadow 1024

> show #!20 models

> transparency #20 0

> lighting soft

> lighting soft multiShadow 1024

> hide #!20 models

> view dimer_view-all_front

[Repeated 1 time(s)]

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

> hide #19 models

> show #1 models

> view dimer_view-all_front

> turn y 180

> turn y 10

> turn y -20

> turn y 10

> hide #1 models

> show #!8 models

> hide #!8 models

> show #7 models

> hide #7 models

> show #7 models

> show #9 models

> show #19 models

> view list

Named views: binding_site, dimer_view-all_front  

> view dimer_view-all_front

> turn y 180

[Repeated 13 time(s)]

> view dimer_view-all_front

> hide #9 models

> hide #7 models

> turn y 180

[Repeated 1 time(s)]

> show #7 models

> hide #7 models

> turn y 180

[Repeated 1 time(s)]

> turn z 1

> turn z -1

> turn z 0.05

> turn y 180

[Repeated 2 time(s)]

> view dimer_view-all_front

> turn z 0.1

> turn y 180

[Repeated 3 time(s)]

> view dimer_view-all_front

> turn z 0.04

> turn y 180

[Repeated 1 time(s)]

> view dimer_view-all_front

> turn z 0.06

> turn y 180

[Repeated 7 time(s)]

> view dimer_view-all_front

> turn z 0.08

> turn y 180

[Repeated 1 time(s)]

> view dimer_view-all_front

> turn x 0.08

> view dimer_view-all_front

> turn x -0.08

> turn y 180

[Repeated 1 time(s)]

> view dimer_view-all_front

> turn x -0.1

> turn y 180

[Repeated 7 time(s)]

> view dimer_view-all_front

> turn y 180

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

> view dimer_view-all_front

> show #1 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> view

> show #1/A:5-8 target a

> hide #1 atoms

> show #1/A:7-9 target a

> hide #1 atoms

> view list

Named views: binding_site, dimer_view-all_front  

> view dimer_view-all_front

> view

> show #5 models

> hide #5 models

> show #5 models

> hide #1 models

> show #1 models

> hide #5 models

> show #!4 models

> hide #!4 models

> show #5 models

> hide #1 models

> show #1 models

> hide #5 models

> view list

Named views: binding_site, dimer_view-all_front  

> view dimer_view-all_front

> view

> turn y 10

> turn y -10

> view name mono_front

> turn y 10

> view name mono_front

> turn y -10

> view name mono_front

> turn y 5

> turn y -5

[Repeated 2 time(s)]

> view list

Named views: binding_site, dimer_view-all_front, mono_front  

> view mono_front

[Repeated 1 time(s)]

> turn y 180

> turn y 5

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #!10 models

> hide #!10 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> view name mono_back

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_front  

> view mono_back

[Repeated 1 time(s)]

> view name mono_back

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

> graphics silhouettes width 2

> graphics silhouettes width 3

> graphics silhouettes width 2

> graphics silhouettes width 3

> graphics silhouettes width 2

> show #3 models

> hide #1 models

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

> show #!4 models

> hide #!4 models

> show #5 models

> hide #3 models

> lighting gentle multiShadow 1024

> lighting soft multiShadow 1024

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

> hide #5 models

> show #7 models

> save NhaA-K-pH75-plugged_model_back_6F9.png supersample 3
> transparentBackground true

> show #9 models

> hide #7 models

> save NhaA-K-pH75-unplugged_model_back_6F9.png supersample 3
> transparentBackground true

> hide #9 models

> show #11 models

> hide #11 models

> show #1 models

> hide /B,C target a

> hide /B,C target c

> view

> show #!4 models

> hide #!4 models

> show #3 models

> hide #3 models

> view

> view name mono_back_

> graphics silhouettes width 3

> graphics silhouettes width 2

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

> show #3 models

> hide #1 models

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

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> view name mono_back_

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

> show #1 models

> hide #3 models

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

> hide #1 models

> show #5 models

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

> show #7 models

> hide #5 models

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

> show #!8 models

> hide #!8 models

> hide #7 models

> show #9 models

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

> show #11 models

> hide #9 models

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

> show #13 models

> hide #11 models

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

> show #15 models

> hide #13 models

> save NhaA-K-pH85-state2-unplugged_model_back.png supersample 3
> transparentBackground true

> hide #15 models

> show #17 models

> save NhaA-Na-pH85-unplugged_model_back.png supersample 3
> transparentBackground true

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> view name mono_back_

> turn x 90

> turn x -90

> turn x -95

> turn x 95

[Repeated 1 time(s)]

> hide #17 models

> show #13 models

> hide #13 models

> show #7 models

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> turn x 90

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

> hide #7 atoms

> hide #7 models

> show #1 models

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

> show #3 models

> hide #1 models

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

> show #5 models

> hide #3 models

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

> show #7 models

> hide #5 models

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

> show #9 models

> hide #7 models

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

> show #11 models

> hide #9 models

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

> show #13 models

> hide #11 models

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

> show #15 models

> hide #13 models

> save NhaA-K-pH85-state2-unplugged_model_top.png supersample 3
> transparentBackground true

> show #17 models

> hide #15 models

> save NhaA-Na-pH85-unplugged_model_top.png supersample 3
> transparentBackground true

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view dimer_view-all_front

> hide #17 models

> show #19 models

> show #!20 models

> volume #20 level 0.01212

> volume #20 level 0.01376

> hide #!20 models

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:11-85,181-274 pale green

> color /B,C,E,F gray

> color /B,C,E,F silver

> color #20:CDL,PTY gray

> color #20:CDL,PTY gray target a

> color #19:CDL,PTY gray

> show #!20 models

> color zone #20 near #19

> color zone #20 near #19 distance 3

> color zone #20 near #19 distance 3.5

> volume #20 level 0.01358

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:1-85,181-274 pale green

> color zone #20 near #19 distance 3.5

> color zone #20 near #19

> volume #20 level 0.01504

> surface dust #20 size 5

> surface dust #20 size 4

> surface dust #20 size 3

> surface dust #20 size 4

> surface dust #20 size 10

> surface dust #20 size 1

> surface dust #20 size 4

> surface dust #20 size 3

> surface dust #20 size 4

> volume splitbyzone #20

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  

> hide #!21.1 models

> show #!21.1 models

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_consensus_lp6.mrc

Opened NhaA-nd-6F9-K_BTPpH75_consensus_lp6.mrc as #22, grid size 248,248,248,
pixel 0.837, shown at level 0.00427, step 1, values float32  

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-6F9-K_BTPpH75_consensus.pdb

Chain information for NhaA-nd-6F9-K_BTPpH75_consensus.pdb #23  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C F | No description available  
  

> mmaker #23 to #19 bring #22

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_consensus.pdb, chain A (#19) with NhaA-
nd-6F9-K_BTPpH75_consensus.pdb, chain A (#23), sequence alignment score =
1997.6  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

> hide #23 models

> volume #22 level 0.002198

> volume #22 level 0.002307

> transparency #22 1

> transparency #22 95

> color #22 snow

> transparency #22 99

> transparency #22 98

> transparency #22 95

> hide #19 models

> surface dust #21,22 size 4

> surface dust #21,22 size 3

> surface dust #21,22 size 4

> color #21.1 gray

> color #21.5 gainsboro

> color #21.1 dark gray

> color #21.1 gray

> color #21.1 dark gray

> graphics silhouettes false

> graphics silhouettes true

> transparency #22 100

> lighting soft multiShadow 1024

> lighting flat

> lighting soft

> lighting soft multiShadow 1024

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

> hide #!21 models

> close #23

> hide #!22 models

> show #19 models

> color #19 byhetero

> show #19 cartoons

> hide #19/A,D:1-10

> hide #19/A,D:1-10 target c

> color /B,C,E,F gainsboro

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view dimer_view-all_front

> hide #19 models

> show #19 models

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Fri Aug 23 11:48:49 2024 ———

opened ChimeraX session  

> hide #19 models

> show #17 models

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> show :NA target a

> style :NA ball

Changed 1 atom style  

> style :NA stick

Changed 1 atom style  

> style :NA sphere

Changed 1 atom style  

> color :NA byhetero target a

> ui tool show "Side View"

> select ~sel & ##selected

Nothing selected  

> lighting #17:NA shadows 0

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> lighting model #17:NA shadows false

> lighting model #17:NA shadows true

> lighting model #17:NA multishadows 0

Expected a keyword  

> lighting model #17:NA multiShadow false

> lighting model #17:NA multiShadow true

> lighting model #17:NA shadows true

> lighting model #17:NA shadows false

> color :NA orange red target a

> hide #17/A target c

> show #17/A target c

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> name /A:132,133,163,164,300,NA,HOH binding_site_res

"binding_site_res": invalid atom specifier  

> name binding_site_res /A:132,133,163,164,300,NA,HOH

"/A:132,133,163,164,300,NA,HOH ": contains extra trailing text  

> name binding_site_res /A:132,133,163,164,300,NA,HOH

> show #17&binding_site_res target a

> lighting simple

> lighting gentle multiShadow 1024

> lighting soft multiShadow 1024

> lighting soft

> lighting simple

> lighting soft multiShadow 1024

> color :NA orange target a

> color :NA gode tar a

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

> color :NA gold target a

> color :NA goldenrod target a

> color :NA tomato target a

> color :NA gold target a

> show #15 models

> show #17,15&binding_site_res target a

> color #15,17 byhetero

> show #13 models

> hide #13 models

> show #13 models

> hide #13 models

> show #13 models

> hide #13 models

> show #13 models

> show #17,15,13&binding_site_res target a

> hide #13 models

> hide #15 models

> hbonds #17 reveal true

6877 hydrogen bonds found  

> close #23

> hide #17 atoms

> show #17,15&binding_site_res target a

[Repeated 1 time(s)]

> cartoon #15,17/A:132 suppressBackboneDisplay false

> show #17,15&binding_site_res target a

> cartoon #15,17/A:132,133 suppressBackboneDisplay false

> cartoon #15,17/A:133 suppressBackboneDisplay true

> view name binding_site

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> lighting simple

> select #17/A:161

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target a

> cartoon sel suppressBackboneDisplay false

> hide sel target a

> cartoon sel suppressBackboneDisplay true

> select #17/A:160

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel target a

> cartoon sel suppressBackboneDisplay false

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

[Repeated 1 time(s)]

> select #17/A:505@NA

1 atom, 1 residue, 1 model selected  

> select clear

> style :NA stick

Changed 1 atom style  

> style :NA ball

Changed 1 atom style  

> style :NA stick

Changed 1 atom style  

> ui mousemode right distance

> distance #17/A:164@OD1 #17/A:505@NA

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 164 OD1 and NA 505 NA:
2.181Å  

> distance #17/A:163@OD1 #17/A:505@NA

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 163 OD1 and NA 505 NA:
3.219Å  

> close #23

> distance #17/A:505@NA #17/A:164@OD1

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ASP 164 OD1:
2.181Å  

> distance #17/A:505@NA #17/A:163@OD1

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ASP 163 OD1:
3.219Å  

> distance #17/A:505@NA #17/A:132@O

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and THR 132 O:
2.185Å  

> distance #17/A:505@NA #17/A:504@O

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and HOH 504 O:
2.987Å  

> distance #17/A:505@NA #17/A:160@O

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A NA 505 NA and ALA 160 O:
3.209Å  

> hide #23.1 models

> delete sel

> ui tool show Distances

> ~distance #17/A:505@NA #17/A:160@O

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> select #17/A:160

5 atoms, 4 bonds, 1 residue, 1 model selected  

> hide sel target a

> cartoon sel suppressBackboneDisplay true

> select clear

> view binding_site

> cartoon style modeHelix default width 1.0 thickness 0.3

> color #23 silver target p

> style :HOH ball

Changed 4 atom styles  

> style :HOH,NA ball

Changed 5 atom styles  

> style :NA sphere

Changed 1 atom style  

> show #!18 models

> color #18 snow

> transparency #18 70

> style :HOH,NA ball

Changed 5 atom styles  

> hide #!18 models

> hide #17 models

> show #!16 models

> show #!15 models

> hide #!15 models

> show #!18 models

> transparency #18 0

> color #18 bluw

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

> color #18 blue

> volume #16 level 0.01372

> volume #16 level 0.012

> volume #16 level 0.01225

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> hide #!16 models

> show #!16 models

> hide #!18 models

> show #!18 models

> hide #!16 models

> color #18 snow

> transparency #18 70

> show #17 models

> lighting soft multiShadow 1024

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Fri Aug 23 12:47:33 2024 ———

opened ChimeraX session  

> surface zone #18 nearAtoms #17&binding_site_res

> color #18 gainsboro

> color #18 whitesmoke

> color #18 snow

> color #18 whitesmoke

> color #18 gainsboro

> color #18 whitesmoke

> transparency #18 70

> transparency #18 60

> transparency #18 70

> transparency #17/A 80 target c

> hide #!23 models

> show #!23 models

> hide #!23 models

> transparency #17 100 target a

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

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

> hide #!18 models

> show #!18 models

> hide #!18 models

> cartoon tether #17 opacity 0

> cartoon tether #17/A:132 opacity 0

> cartoon tether #17/A:132 scale 0

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

> hide #17/A target ac

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

> transparency #17/A 100 target a

> transparency #23 100 target p

> show #!23 models

> hide sel

> graphics silhouettes width 6

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

> hide #17/A target ac

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

> transparency #17/A 0 target a

> transparency #23 100 target p

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

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> hide #!23 models

> show #!18 models

> show #17/A target c

> show #17&binding_site_res target a

> transparency #17 100 target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> hide #!18 models

> show #17/A target c

> transparency #17/A 70 target c

> show #17&binding_site_res target a

> transparency #17 100 target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

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

> show #!18 models

> color #18 gainsboro

> color #18 black

> color #18 gainsboro

> transparency #18 70

> transparency #18 50

> transparency #18 10

> transparency #18 0

> transparency #18 1

> transparency #17 0

> transparency #17 0 target ac

> transparency #18 60

> transparency #18 70

> transparency #18 80

> save NhaA-Na-pH85_binding-site_no-tra.png supersample 3
> transparentBackground true

> transparency #18 70

> save NhaA-Na-pH85_binding-site_no-tra.png supersample 3
> transparentBackground true

> hide #!18 models

> hide #17/A target ac

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

> transparency #17/A 100 target a

> transparency #23 0 target p

> graphics silhouettes width 6

> hide sel

> select clear

> show #!23 models

> transparency #23 1

> transparency #23 1 target p

> transparency #18 0 target a

> transparency #17 0 target a

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

> style :NA sphere

Changed 1 atom style  

> show #!18 models

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> volume #18 level 0.009684

> volume #18 level 0.009887

> volume #18 level 0.0098

> volume #18 level 0.01

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> style :NA ball

Changed 1 atom style  

> style :NA stick

Changed 1 atom style  

> color :NA gold

> hide #!23 models

> select ~sel & ##selected

Nothing selected  

> color :NA byhetero

> surface style #18 mesh

> surface style #18 mesh squaremesh false

Expected fewer arguments  

> surface style #18 solid

> volume #18 style mesh squareMesh false

> volume #18 style solid

> surface style #18 solid

> volume #18 style mesh squareMesh true

> surface style #18 solid

> color zone #18 near :NA distance 1

> color zone #18 near :NA distance 1.5

> transparency #18 60

> volume #18 style solid

> volume #18 style surface

> color :NA gold target a

> color zone #18 near :NA distance 1.5

> transparency #18 60

> color :NA byhetero target a

> color zone #18 near :NA distance 1.5

> transparency #18 60

> transparency #18 70

> color :NA byhetero transparency 80 target a

> color zone #18 near :NA distance 1.5

> color :NA byhetero target a

> color :NA byhetero transparency 0 target a

> lighting simple

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting soft multiShadow 1024

> color :NA byelement target a

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

> color zone #18 near :NA distance 1.5

> transparency #18 60

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

> hide #17/A target ac

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

> transparency #17/A 100 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> hide #!18 models

> hide sel

> hide #17/A target ac

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

> transparency #17/A 0 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> show #!22 models

> hide #!22 models

> show #!23 models

> select clear

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

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> hide #!23 models

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back

> view mono_back_

> hide #17 atoms

> show :NA target a

> style :NA sphere

Changed 1 atom style  

> cartoon style modeHelix default width 1.8 thickness 0.3

> combine #17

> hide #24 target c

> lighting model #24 multiShadow false

> hide #17:NA

> hide #17:NA target a

> lighting model #24 multiShadow true

> lighting model #24 shadows false

> lighting model #24 multiShadow false

> lighting model #24 shadows true

> ui tool show "Side View"

> lighting simple

> lighting full

> lighting soft

> lighting simple

> lighting soft multiShadow 1024

> lighting soft

> lighting simple

> hide #24 models

> show :NA target a

> transparency #17 100 target c

> transparency :NA 1 target a

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> save NhaA-Na-pH85_model_back_simple.png supersample 3 transparentBackground
> true

> lighting soft multiShadow 1024

> transparency #17 0 target c

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> show #24 models

> hide #24 models

> show #24 models

> select #17/A:505@NA

1 atom, 1 residue, 1 model selected  

> hide #17 models

> select clear

> select #24/A:505@NA

1 atom, 1 residue, 1 model selected  

> show sel surfaces

> hide #24 target a

> hide #!24 models

> close #24.1

> select clear

> show #24 models

> hide #24 models

> show #!18 models

> show #17 models

> hide #!18 models

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> style :NA stick

Changed 2 atom styles  

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> style :NA sphere

Changed 2 atom styles  

> style :NA stick

Changed 2 atom styles  

> style :NA ball

Changed 2 atom styles  

> style :NA stick

Changed 2 atom styles  

> cartoon style modeHelix default width 1.0 thickness 0.3

> lighting full

> lighting simple

> lighting full

> show #!18 models

> lighting simple

> lighting full

> lighting shadows false

> lighting full

> lighting shadows false

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

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

> hide #17/A target ac

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

> transparency #17/A 100 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> hide #!18 models

> hide sel

> select clear

> show #!23 models

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

> style :NA stick

Changed 2 atom styles  

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> transparency #17 0 target a

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> hide #!23 models

> view binding_site

> hide #17 models

> show #!15 models

> hide #!15 atoms

> style :NA stick

Changed 2 atom styles  

> show #15/A target c

> show #15&binding_site_res target a

> cartoon #15/A:132 suppressBackboneDisplay false

> cartoon tether #15/A:132 scale 0

> graphics silhouettes width 2

> lighting soft

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> show #!16 models

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> volume #18 change image level -0.001229,0 level 0.005411,0.8 level 0.07594,1

> volume #16 level 0.01176

> volume #16 level 0.01225

> ui mousemode right "mark center"

Enclosed volume for marked surface: 0.452  

> marker #25 position 117.7,81.62,99.72 color yellow radius 1

Enclosed volume for marked surface: 0.218  

> marker #25 position 116.7,82.14,101.9 color yellow radius 1

Enclosed volume for marked surface: 0.383  

> marker #25 position 115.9,80.84,101.2 color yellow radius 1

Enclosed volume for marked surface: 0.0893  

> marker #25 position 115.1,81.5,103.3 color yellow radius 1

Enclosed volume for marked surface: 0.103  

> marker #25 position 114.3,82.15,103.4 color yellow radius 1

> hide #25 models

> select clear

> show #25 models

> hide #25 models

> surface zone #16 nearAtoms #25|(#15&binding_site_res)

> color #16 gainsboro

> transparency #16 60

> surface unzone #16

Enclosed volume for marked surface: 2.23  

> marker #25 position 113.2,82.87,100.8 color yellow radius 1

> show #25 models

> hide #25 models

> select clear

> surface zone #16 nearAtoms #25|(#15&binding_site_res)

> color #16 gainsboro

> transparency #16 60

> view binding_site

> surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 2

> color #16 gainsboro

> transparency #16 60

> surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 1.8

> color #16 gainsboro

> transparency #16 60

> surface zone #16 nearAtoms #25|(#15&binding_site_res) distance 1.9

> color #16 gainsboro

> transparency #16 60

> surface zone #16 nearAtoms #25|(#15&binding_site_res)

> color #16 gainsboro

> transparency #16 60

> save NhaA-K-pH85-state2_binding-site_tra.png supersample 3
> transparentBackground true

> hide #15/A target ac

> show #15&(binding_site_res&sidechain|:132,NA,HOH) target a

> transparency #15/A 100 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> hide #!16 models

> hide sel

> save NhaA-K-pH85-state2_binding-site_sil.png supersample 3
> transparentBackground true

> hide #15/A target ac

> show #15&(binding_site_res&sidechain|:132,NA,HOH) target a

> transparency #15/A 0 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> save NhaA-K-pH85-state2_binding-site_sil.png supersample 3
> transparentBackground true

> hide #!15 models

> select clear

> show #17 models

> hide #17/A target ac

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

> transparency #17/A 0 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> hide sel

> show #!23 models

> transparency #23 0 target p

> color #23 gray target p

> color #23 dark gray target p

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

> hide #!23 models

> ui mousemode right distance

> 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  

> show #!23 models

> show #23.1 models

> hide #23.1 models

> show #23.1 models

> hide #!23 models

> show #!23 models

> hide #!17 models

> show #!15 models

> distance #15/A:164@OD1 #15/A:132@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A ASP 164 OD1 and THR
132 O: 5.033Å  

> show #!16 models

> lighting simple

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view binding_site

> hide #!16 models

> hide #23.1 models

> style :NA stick

Changed 2 atom styles  

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> style :NA stick

Changed 2 atom styles  

> show #15/A target c

> show #15&binding_site_res target a

> cartoon #15/A:132 suppressBackboneDisplay false

> cartoon tether #15/A:132 scale 0

> graphics silhouettes width 2

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back_

> hide #!23 models

> hide #15 models

> show #!7 models

> show #!8 models

> hide #!8 models

> hide #!7 atoms

> show #!9 models

> hide #7#!9 atoms

> select clear

> ui mousemode right translate

> ui mousemode right zoom

> view list

Named views: binding_site, dimer_view-all_front, mono_back, mono_back_,
mono_front  

> view mono_back

> view mono_back_

[Repeated 1 time(s)]

> turn x 90

> hide #9 models

> show #!8 models

> volume #8 level 0.01256

> surface dust #8 size 3

> surface dust #8 size 5

> surface dust #8 size 4

> surface dust #8 size 5

> surface dust #8 size 6

> surface dust #8 size 5

> surface dust #8 size 6

> show #9 models

> hide #!8 models

> show #!10 models

> show #!8 models

> volume #10 level 0.01179

> surface dust #8,10 size 6

> surface dust #8,10 size 7

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #7 models

> surface dust #8,10 size 0

> surface dust #8,10 size 1

> surface dust #8,10 size 0

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> color zone #10 near #8

color zone: No atoms specified.  

> color zone #10 near #9

> hide #!10 models

> hide #9 models

> show #19 models

> color :CDL,PTY gray target a

> hide #19 models

> show #9 models

> show #!10 models

> color zone #10 near #9

> color #10 snow

> color zone #10 near #9

> color #10 gainsboro

> color #10 silver

> color zone #10 near #9

> color zone #10 near #9 distance 3

> color zone #10 near #9 distance 2.5

> transparency #10 50

> transparency #10 60

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting shadows false

> transparency #10 60

> color zone #10 near #9 distance 2.5

> transparency #10 60

> color zone #10 near #9 distance 2.5

> transparency #10 60

> view name N-term_density_top

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting shadows false

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting gentle multiShadow 1024

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> lighting shadows false

> color #10 silver

> transparency #10 60

> color #10 dark gray

> color #10 gray

> lighting soft

> color #10 silver

> lighting soft

> lighting simple

> lighting full

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting simple

> lighting full

> lighting shadows false

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

[Repeated 1 time(s)]

> lighting shadows false

> hide #9 models

> show #9 models

> hide #!10 models

> hide #9 models

> show #9 models

> hide #9 models

> show #19 models

> hide #19 atoms

> show #!20 models

> color #20 gray

> color #20 silver

> transparency #20 60

> surface dust #20 0

Expected a keyword  

> surface dust #20 size 0

> show #!10 models

> hide #!10 models

> show #!10 models

> transparency #20 0

> volume #20 level 0.008648

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> volume #20 level 0.0081

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> transparency #20 60

> color zone #20 near #7,9:1-20

> color zone #20 near #7,9:1-10

> transparency #20 60

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting shadows false

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!20 models

> graphics silhouettes true

> graphics silhouettes 3

Expected true or false or a keyword  

> graphics silhouettes width 3

> save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #19 models

> show #!18 models

> hide #!18 models

> show #9 models

> save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #9 models

> show #7 models

> save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> show #!8 models

> hide #7 models

> hide #!8 models

> show #!10 models

> graphics silhouettes false

> color zone #10 near #9:1-10

> transparency #10 60

> save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!10 models

> show #!8 models

> color #8 silver

> color zone #8 near #7:1-10

> transparency #8 60

> save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> show #7 models

> transparency #8 60

> save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!8 models

> hide #7 models

> show #9 models

> show #!10 models

> save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> graphics silhouettes true

> graphics silhouettes false

> transparency #10 40

> save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!10 models

> show #!10 models

> hide #9 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!20 models

> hide #!10 models

> show #19 models

> color zone #20 near #7,9:1-10

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> transparency #20 40

> color zone #20 near #7,9:1-10

> transparency #20 40

> color zone #20 near #7,9:1-10

> transparency #20 30

> color zone #20 near #7,9:1-10

> save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!20 models

> graphics silhouettes true

> save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #19 models

> show #19 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #9 models

> hide #!10 models

> hide #19 models

> show #19 models

> hide #19 models

> hide #7,9:1-10 target c

> save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #9 models

> show #7 models

> save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> show #!8 models

> hide #7 models

> graphics silhouettes false

> transparency #8,10 30

> color zone #8 near #7:1-10

> transparency #8,10 30

> show #7 models

> color zone #8 near #7:1-10

> transparency #8 30

> color zone #8 near #7:1-10

> hide #!8 models

> show #!20 models

> hide #!20 models

> show #!8 models

> color #10 silver

> color #8 silver

> transparency #8 30

> color zone #8 near #7:1-10

> save NhaA-K-pH75-plugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!8 models

> hide #7 models

> show #9 models

> show #!10 models

> transparency #10 30

> color zone #10 near #9:1-10

> save NhaA-K-pH75-unplugged-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!10 models

> hide #9 models

> show #19 models

> show #!20 models

> color #20 gray

> transparency #20 30

> color #20 silver

> transparency #20 30

> color zone #20 near #7,9:1-10

> save NhaA-K-pH75-consensus-Nterm-density_no-sil.png supersample 3
> transparentBackground true

> hide #!20 models

> graphics silhouettes true

> graphics silhouettes width 4

> graphics silhouettes width 3

> graphics silhouettes width 4

> save NhaA-K-pH75-consensus-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #19 models

> show #9 models

> save NhaA-K-pH75-unplugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> hide #9 models

> show #7 models

> save NhaA-K-pH75-plugged-Nterm-density_ribbon.png supersample 3
> transparentBackground true

> view list

Named views: N-term_density_top, binding_site, dimer_view-all_front,
mono_back, mono_back_, mono_front  

> view name N-term_density_top

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Sat Aug 24 11:29:55 2024 ———

opened ChimeraX session  

> graphics silhouettes width 2

> view list

Named views: N-term_density_top, binding_site, dimer_view-all_front,
mono_back, mono_back_, mono_front  

> view mono_back_

> show /A:1-10 target c

> show #9 models

> hide #7 models

> hide #9 models

> show #!13 models

> hide #!13 atoms

> hide #13 models

> show #15 models

> show #17 models

> hide #15,17&dimer target c

> mmaker #17&dimer_TM to #15/A bring #18

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_BTPpH85_state2.pdb, chain A (#15) with NhaA-
nd-6F9-Na_BTPpH85.pdb, chain A (#17), sequence alignment score = 619.9  
RMSD between 119 pruned atom pairs is 0.146 angstroms; (across all 119 pairs:
0.146)  
  

> ui tool show "Side View"

> hide #15,17 atoms

> show #15,17/A:163,132 target a

> hide #15,17 atoms

> show #15,17/A:164,132 target a

> cartoon style modeHelix tube radius 1.8 sides 24

> cartoon style modeHelix default width 1.0 thickness 0.3

> cartoon style modeHelix default width 1.8 thickness 0.3

> cartoon style modeHelix default width 1.4 thickness 0.3

> cartoon style modeHelix default width 1.2 thickness 0.3

> show #15,17/A:164,132,133 target a

> hide #15,17 atoms

> show #15,17/A:164,132 target a

> lighting full

> lighting shadows false

> size stickRadius 0.5

Changed 58102 bond radii  

> size stickRadius 0.4

Changed 58102 bond radii  

> view name core_inner_side

> save NhaA-Na-pH85_vs_K-pH85_inside.png supersample 3 transparentBackground
> true

> show #15,17/A:150-274,130-144 target c

> hide #15,17&dimer target c

> show #15,17/A:150-174,130-144 target c

> hide #15,17 cartoons

> show #15,17/A:150-174,130-144 target c

> graphics silhouettes width 4

> graphics silhouettes width 6

> graphics silhouettes width 4

> graphics silhouettes width 6

> graphics silhouettes width 5

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

> cartoon style modeHelix default width 1 thickness 0.3

> cartoon style modeHelix default width 1.2 thickness 0.3

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Sat Aug 24 21:20:57 2024 ———

opened ChimeraX session  

> cartoon style modeHelix default width 1.0 thickness 0.3

> size stickRadius 0.3

Changed 58102 bond radii  

> graphics silhouettes 2

Expected true or false or a keyword  

> graphics silhouettes width 2

> show /A target c

> view list

Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
all_front, mono_back, mono_back_, mono_front  

> view binding_site

> show #15,17&binding_site_res target a

> hide :NA,HOH target a

> transparency #15,17 50 target c

> show #!23 models

> color #23 dark gray target p

> hide #17 models

> distance #15/A:163@OD2 #15/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A ASP 163 OD2 and LYS
300 NZ: 3.294Å  

> show #17 models

> hide #15 models

> distance #17/A:163@OD2 #17/A:300@NZ

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 163 OD2 and LYS 300 NZ:
3.986Å  

> show #15 models

> color #23 dark gray target p

> hide #!23 models

> transparency 100 target a

> transparency 0 target a

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

> hide #15,17 cartoons

> show #15,17 cartoons

> hide #15,17/A target ac

> show #15,17&(binding_site_res&sidechain|:132) target a

> transparency #15,17/A 0 target a

> transparency #23 1 target p

> graphics silhouettes width 6

> ui mousemode right translate

> hide sel

> select clear

> show #!16 models

> hide #!16 models

> show #!23 models

> transparency 0 target a

> transparency 100 target a

> transparency 0 target a

> color sel royal blue target p

> color sel blue target p

> color sel royal blue target p

> color sel deep sky blue target p

> color sel dodger blue target p

> color sel light sea green target p

> select clear

> show #23.1 models

> hide #23.1 models

> graphics silhouettes width 8

> hide #!23 models

> show #!23 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!17 models

> graphics silhouettes width 6

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

> show #23.1 models

> hide #!23 models

> style :NA stick

Changed 2 atom styles  

> show #17/A target c

> show #17&binding_site_res target a

> cartoon #17/A:132 suppressBackboneDisplay false

> cartoon tether #17/A:132 scale 0

> graphics silhouettes width 2

> hide :NA,HOH target a

> style :NA stick

Changed 2 atom styles  

> show #15,17/A target c

> show #15,17&binding_site_res target a

> cartoon #15,17/A:132 suppressBackboneDisplay false

> cartoon tether #15,17/A:132 scale 0

> graphics silhouettes width 2

> hide :NA,HOH target a

> transparency 100 target a

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

> transparency 0 target a

> hide /B,C,E,F target ac

> transparency 0 target c

> view list

Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
all_front, mono_back, mono_back_, mono_front  

> view mono_back_

> hide target a

> hide #17 models

> hide #15 models

> show #7 models

> show #!8 models

> hide #!8 models

> view mono_back_

> show /A:1-10 target a

> color #7 byhetero

> show #!8 models

> color #8 gray

> transparency #8 60

> color #8 silver

> hide #!8 models

> show #!8 models

> show /A:1-10,81,82,78,252,253,256 target a

> hide /A:1-10 target c

> show /A:1-10 target c

> hide /A:1-3 target a

> hide /A:1-4 target a

> hide /A:1-4,10 target a

> hide #!8 models

> ui mousemode right distance

> distance #7/A:82@OE1 #7/A:6@NH1

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 82 OE1 and ARG 6
NH1: 2.988Å  

> show #!23 models

> show #!8 models

> hide #!8 models

> distance #7/A:82@OE1 #7/A:6@NH2

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 82 OE1 and ARG 6
NH2: 3.052Å  

> ui tool show Distances

> ~distance #7/A:82@OE1 #7/A:6@NH2

> distance #7/A:6@NH2 #7/A:78@OE1

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A ARG 6 NH2 and GLU 78
OE1: 2.803Å  

> show #!8 models

> hide #!8 models

> 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  

> ui tool show Distances

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

> hide #7 models

> show #9 models

> color #9 byhetero

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

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

> show #!10 models

> hide #!10 models

> hide #9 models

> show #3 models

> color #3 byhetero

> distance #3/A:6@NH1 #3/A:82@OE2

Distance between NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3/A ARG 6 NH1 and GLU 82
OE2: 2.952Å  

> distance #3/A:6@NH2 #3/A:78@OE1

Distance between NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3/A ARG 6 NH2 and GLU 78
OE1: 2.641Å  

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #3 models

> distance #7/A:256@NE2 #7/A:252@OE2

Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A HIS 256 NE2 and GLU
252 OE2: 3.442Å  

> ui tool show Distances

> ~distance #7/A:256@NE2 #7/A:252@OE2

> show #5 models

> hide #7 models

> show #7 models

> hide #7 models

> color #5 byhetero

> distance #5/A:81@NH1 #5/A:82@OE2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ARG 81 NH1 and GLU
82 OE2: 3.215Å  

> show #9 models

> hide #9 models

> distance #5/A:252@OE2 #5/A:81@NH2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE2 and ARG
81 NH2: 2.623Å  

> distance #5/A:81@NH2 #5/A:78@OE1

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ARG 81 NH2 and GLU
78 OE1: 2.384Å  

> distance #5/A:252@OE1 #5/A:81@NE

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE1 and ARG
81 NE: 2.675Å  

> distance #5/A:252@OE2 #5/A:81@NE

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 252 OE2 and ARG
81 NE: 2.946Å  

> ui tool show Distances

> ~distance #5/A:252@OE1 #5/A:81@NE

> ~distance #5/A:252@OE2 #5/A:81@NE

> hide #5 models

> show #1 models

> color #1 byhetero

> show #!2 models

> hide #!2 models

> distance #1/A:81@NH1 #1/A:82@OE1

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH1 and GLU 82 OE1:
3.309Å  

> distance #1/A:81@NH2 #1/A:78@OE2

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH2 and GLU 78 OE2:
3.308Å  

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

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NE and GLU 252 OE1:
3.245Å  

> distance #1/A:81@NH2 #1/A:252@OE2

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ARG 81 NH2 and GLU 252 OE2:
3.627Å  

> show #3 models

> hide #3 models

> show #3 models

> hide #1 models

> hide #3 models

> show #1 models

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Sun Aug 25 17:46:16 2024 ———

opened ChimeraX session  

> view list

Named views: N-term_density_top, binding_site, core_inner_side, dimer_view-
all_front, mono_back, mono_back_, mono_front  

> view N-term_density_top

> view mono_back_

> hide #!23 models

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

Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #26  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #1 models

> show #13 models

> mmaker #26 to #13

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_BTPpH85_state1-unplugged.pdb, chain A (#13) with
NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#26), sequence alignment
score = 2000  
RMSD between 388 pruned atom pairs is 0.003 angstroms; (across all 388 pairs:
0.003)  
  

> mcopy #13 toAtoms #26 settings hscv

> cartoon style modeHelix default width 1.0 thickness 0.3

> cartoon style modeHelix default width 1.1 thickness 0.2

> cartoon style modeHelix default width 1.0 thickness 0.3

> hide #13 models

> close #13

> rename #26 id #13

> ui tool show "Side View"

> coulombic #13

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
#13.1: minimum, -16.52, mean 0.04, maximum 15.63  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
#13.2: minimum, -19.83, mean -1.80, maximum 8.49  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
#13.3: minimum, -13.89, mean -1.84, maximum 10.03  
To also show corresponding color key, enter the above coulombic command and
add key true  

> surface cap false

[Repeated 1 time(s)]

> show /A:163,164 target a

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> show #15 models

> hide #!13 models

> coulombic #15

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #15.1:
minimum, -17.07, mean 0.02, maximum 20.09  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #15.2:
minimum, -18.53, mean -1.82, maximum 10.93  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #15.3:
minimum, -14.51, mean -2.14, maximum 12.50  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #17 models

> coulombic #17

Using Amber 20 recommended default charges and atom types for standard
residues  
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 /B,C target cs

> show :NA target a

> show #!15 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!13 models

> hide #!15 models

> view name cutaway

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> show #11 models

> hide #!13 models

> coulombic #11

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_A SES surface
#11.1: minimum, -16.15, mean -0.06, maximum 16.72  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_B SES surface
#11.2: minimum, -19.94, mean -1.89, maximum 14.08  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb_C SES surface
#11.3: minimum, -13.83, mean -1.90, maximum 13.43  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!11 models

> show #9 models

> coulombic #9

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface #9.1:
minimum, -15.35, mean 0.08, maximum 15.24  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface #9.2:
minimum, -18.25, mean -1.97, maximum 8.02  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface #9.3:
minimum, -13.57, mean -1.87, maximum 9.81  
To also show corresponding color key, enter the above coulombic command and
add key true  

> show #!11 models

> hide #!9 models

> show #!9 models

> hide #!11 models

> show #!13 models

> hide #!9 models

> show #5 models

> hide #!13 models

> coulombic #5

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_A SES surface #5.1:
minimum, -15.26, mean 0.23, maximum 19.25  
Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_B SES surface #5.2:
minimum, -17.29, mean -2.01, maximum 8.10  
Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_C SES surface #5.3:
minimum, -13.33, mean -1.95, maximum 8.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!5 models

> show #!5 models

> show #!9 models

> hide #!5 models

> show #!5 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> hide #!9 models

> hide #!5 models

> show #!11 models

> show #!13 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!9 models

> hide #!9 models

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

Chain information for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #26  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #26 to #13

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_BTPpH85_state1-unplugged.pdb, chain A (#13) with
NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb, chain A (#26), sequence alignment
score = 2000  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

> mcopy #13 toAtoms #26 settings hscv

> cartoon style modeHelix default width 1.1 thickness 0.2

> cartoon style modeHelix default width 1.0 thickness 0.3

> hide #!13 models

> coulombic #26

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
#26.1: minimum, -16.52, mean 0.01, maximum 15.63  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
#26.2: minimum, -19.83, mean -1.80, maximum 8.49  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
#26.3: minimum, -13.89, mean -1.84, maximum 10.03  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!26 models

> show #!26 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!26 models

> hide #!9 models

> show #!13 models

> hide #!13 models

> close #13

> show #!26 models

> rename #26 id #13

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> show #!15 models

> hide #!13 models

> show #!13 models

> show #!17 models

> hide #!13 models

> hide #!15 models

> show #!13 models

> view cutaway

> hide #!17 models

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!13 models

> hide #!15 models

> show #!9 models

> hide #!13 models

> show #!5 models

> hide #!9 models

> show #!9 models

> hide #!5 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #19 models

> hide #19 models

> show #!17 models

> hide #!9 models

> show #!5 models

> hide #!17 models

> show #!17 models

> show #!9 models

> hide #!5 models

> hide /B,C target acs

> hide #!9 models

> show #!9 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> hide #!9 models

> show #!9 models

> hide #!17 models

> view cutaway

> show #!13 models

> hide #!9 models

> show #!17 models

> hide #!17 models

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!13 models

> hide #!15 models

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!15 models

> hide #!17 models

> show #!17 models

> show #!15 models

> hide #!15 models

> show #!13 models

> hide #!17 models

> show #!15 models

> hide #!15 models

> hide #!13 models

> show #!13 models

> show #!9 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!13 models

> show #!15 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> view name cutaway

> hide #!15 models

> clip near -0.8 position #9/A:164

> clip near -0.0 position #9/A:164

> clip near -1.5 position #9/A:164

> clip near -1.6 position #9/A:164

> clip near -2 position #9/A:164

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> clip near -2 position #17/A:164

> clip near -2 position #17/A:163

> clip near -3 position #17/A:163

> show #!9 models

> hide #!17 models

> clip near -3 position #9/A:163

> hide #!9 models

> show #!13 models

> clip near -3 position #13/A:163

> clip near -3 position #13/A:164@CG

> clip near 0 position #13/A:164@CG

> clip near -2 position #13/A:164@CG

> clip near -1 position #13/A:164@CG

> hide #!13 models

> show #!15 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!9 models

> hide #!15 models

> clip near -1 position #9/A:164@CG

> show #!17 models

> hide #!9 models

> show #!9 models

> hide #!17 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!13 models

> hide #!9 models

> show #!13 models

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!13 models

> hide #!15 models

> show #!15 models

> hide #!13 models

> show #!13 models

> hide #!15 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> show #!17 models

> hide #!17 models

> show #!9 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!15 models

> view name cutaway

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> surface cap true

[Repeated 1 time(s)]

> show #!15 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> hide #!15 models

> show #!13 models

> show #!9 models

> hide #!13 models

> show #!17 models

> hide #!9 models

> hide #!17 atoms

> hide #!17 cartoons

> color /A:NA,163,164 byhetero target a

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

[Repeated 1 time(s)]

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

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting soft multiShadow 1024

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Mon Aug 26 17:49:42 2024 ———

opened ChimeraX session  

> lighting soft multiShadow 1024

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

> save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground false

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> transparency ##name="cap near" 100

> transparency #17 70 target s

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

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

> transparency #17 70 target s

> view

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> ui tool show "Side View"

> clip front -0.8 position #17:NA

> clip front 0 position #17:NA

> clip front 1 position #17:NA

> clip front 0.5 position #17:NA

> clip front 0.4 position #17:NA

> hide #!17 models

> show #!11 models

> hide #!11 models

> show #!9 models

> show #!5 models

> hide #!9 models

> show #!9 models

> hide #!5 models

> hide #!9 models

> show #!17 models

> view name cutaway

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> transparency ##name="cap near" 100

> transparency #17 70 target s

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

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

> transparency #17 70 target s

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

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

> transparency #17 70 target s

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

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

> transparency #17 70 target s

> hide #!17 atoms

> save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground false

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

> transparency 0 target s

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

> transparency 0 target s

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

> transparency 0 target s

> save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground false

> hide #!17 models

> show #!15 models

> hide #!15 cartoons

> hide #!15 atoms

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

> transparency 0 target s

> save NhaA-K-pH85-state2_cutaway.png supersample 3 transparentBackground
> false

> show #!13 models

> hide #!15 models

> hide #!13 cartoons

> hide #!13 atoms

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

> transparency 0 target s

> save NhaA-K-pH85-state1-unplugged_cutaway.png supersample 3
> transparentBackground false

> show #!9 models

> hide #!13 models

> hide #!9 cartoons

> hide #!9 atoms

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

> transparency 0 target s

> save NhaA-K-pH75-unplugged_cutaway.png supersample 3 transparentBackground
> false

> hide #!9 models

> show #!5 models

> hide #!5 cartoons

> hide #!5 atoms

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

> transparency 0 target s

> save NhaA-K-pH63-unplugged_cutaway.png supersample 3 transparentBackground
> false

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

> transparency #17 70 target s

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

> transparency 70 target s

> save NhaA-K-pH63-unplugged_cutaway_surf.png supersample 3
> transparentBackground false

> show #!9 models

> hide #!5 models

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

> transparency 70 target s

> save NhaA-K-pH75-unplugged_cutaway_surf.png supersample 3
> transparentBackground false

> show #!13 models

> hide #!9 models

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

> transparency 70 target s

> save NhaA-K-pH85-state1-unplugged_cutaway_surf.png supersample 3
> transparentBackground false

> show #!15 models

> hide #!13 models

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

> transparency 70 target s

> save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
> false

> show #!17 models

> hide #!15 models

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

> transparency 70 target s

> save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground false

> hide #!17 models

> show #!17 models

> transparency 0 target s

> hide target s

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.4

Changed 58102 bond radii  

> graphics silhouettes 6;

Expected true or false or a keyword  

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.4

Changed 58102 bond radii  

> graphics silhouettes width 6

> ~clip

> clip model /A:NA,163,164 true

> lighting full

> lighting simple

> lighting full

> style :NA sphere

Changed 2 atom styles  

> hide sel

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.4

Changed 58102 bond radii  

> graphics silhouettes width 4

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.4

Changed 58102 bond radii  

> graphics silhouettes width 5

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.4

Changed 58102 bond radii  

> graphics silhouettes width 4

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 4

> clip model /A:NA,163,164 false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground false

> save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground true

> hide #!17 models

> show #!15 models

> hide sel

> save NhaA-K-pH85_cutaway_res.png supersample 3 transparentBackground true

> hide #!15 models

> show #!13 models

> select clear

> hide sel

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

> hide #!13 models

> show #!15 models

> hide #!15 models

> show #!9 models

> hide sel

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

> hide #!9 models

> show #!5 models

> hide sel

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

> hide #!5 models

> show #!5 models

> select clear

> show #!5 atoms

> hide #!5 atoms

> hide /A:NA,163,164 target a

> size stickRadius 0.3

Changed 58102 bond radii  

> graphics silhouettes width 2

> show #!9 models

> show #!13 models

> show #!15 models

> show #!17 models

> show #!5,9,13,15,17 surfaces

> hide #!17 models

> hide #!15 models

> hide #!13 models

> hide #!9 models

> hide #!5 models

> show #!5 models

> lighting soft

> lighting soft multiShadow 1024

> clip front 0.4 position #17:NA

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

> hide /B,C target asc

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

> show #!9 models

> hide #!5 models

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

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

> hide #!9 models

> show #!11 models

> hide #!11 models

> show #!13 models

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

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

> hide #!13 models

> show #!15 models

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

> save NhaA-K-pH85-state2_cutaway.png supersample 3 transparentBackground true

> hide #!15 models

> show #!17 models

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

> save NhaA-Na-pH85_cutaway.png supersample 3 transparentBackground true

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

> transparency 70 target s

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

> transparency 70 target s

> save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground true

> hide #!17 models

> show #!15 models

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

> transparency 70 target s

> save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
> true

> hide #!15 models

> show #!13 models

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

> transparency 70 target s

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

> hide #!13 models

> show #!9 models

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

> transparency 70 target s

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

> hide #!9 models

> show #!5 models

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

> transparency 70 target s

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

> transparency 0 target s

> hide #!5 models

> show #!5 models

> ~clip

> hide #5.1 models

> show #5.1 models

> hide target s

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> graphics silhouettes color white

> select up

4643 atoms, 1 pseudobond, 612 residues, 5 models selected  

> select down

1 pseudobond, 1 model selected  

> hide sel

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

> select up

1 pseudobond, 1 model selected  

> select clear

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> graphics silhouettes color black

> hide /A:NA,163,164 target a

> size stickRadius 0.3

Changed 58102 bond radii  

> graphics silhouettes width 2

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> lighting full

> lighting shadows false

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.6

Changed 58102 bond radii  

> graphics silhouettes width 5

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.6

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.8

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.7

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.7

Changed 58102 bond radii  

> graphics silhouettes width 2

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.7

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.7

Changed 58102 bond radii  

> graphics silhouettes width 2

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting shadows false

> select clear

> hide sel

> select clear

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

> hide #!5 models

> show #!17 models

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting soft

> lighting simple

> lighting full

> hide #!17 models

> show #!5 models

> hide #!5 models

> show #!9 models

> hide sel

> lighting shadows false

> lighting shadows true

> lighting shadows false

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

> hide #!9 models

> show #!13 models

> select clear

[Repeated 1 time(s)]

> hide sel

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

> hide #!13 models

> show #!15 models

> hide sel

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

> hide #!15 models

> show #!17 models

> select up

4643 atoms, 1 pseudobond, 612 residues, 5 models selected  

> select up

4749 atoms, 4850 bonds, 1 pseudobond, 617 residues, 5 models selected  

> select down

4643 atoms, 1 pseudobond, 612 residues, 5 models selected  

> select down

1 pseudobond, 1 model selected  

> hide sel

> save NhaA-Na-pH85_cutaway_res.png supersample 3 transparentBackground true

> hide /A:NA,163,164 target a

> size stickRadius 0.3

Changed 58102 bond radii  

> graphics silhouettes width 2

> clip front 0.4 position #17:NA

> transparency 70 target s

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

> show #!15 models

> show #!13 models

> show #!9 models

> show #!5 models

> show #!5,9,13,15,17 surfaces

> hide /B,C target s

> hide #!5 models

> hide #!9 models

> hide #!13 models

> hide #!15 models

> lighting soft

> lighting soft multiShadow 1024

> transparency 70 target s

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

> save NhaA-Na-pH85_cutaway_surf.png supersample 3 transparentBackground true

> hide #!17 models

> show #!15 models

> transparency 70 target s

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

> save NhaA-K-pH85-state2_cutaway_surf.png supersample 3 transparentBackground
> true

> hide #!15 models

> show #!13 models

> transparency 70 target s

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

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

> hide #!13 models

> show #!9 models

> transparency 70 target s

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

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

> hide #!9 models

> show #!5 models

> transparency 70 target s

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

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

> hide #!5 models

> show #7 models

> hide #7 models

> show #!9 models

> transparency 50 target s

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

> transparency 10 target s

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

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

> transparency 70 target s

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

> transparency 20 target s

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

> transparency 30 target s

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

> save NhaA-K-pH75-unplugged_cutaway_surf_30.png supersample 3
> transparentBackground true

> hide #!9 models

> show #!15 models

> transparency 30 target s

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

> save NhaA-K-pH85-state2_cutaway_surf_30.png supersample 3
> transparentBackground true

> hide #!15 models

> show #!17 models

> transparency 30 target s

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

> save NhaA-Na-pH85_cutaway_surf_30.png supersample 3 transparentBackground
> true

> hide #!17 models

> show #!14 models

> hide #!14 models

> show #!13 models

> transparency 30 target s

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

> save NhaA-K-pH85-state1-unplugged_cutaway_surf_30.png supersample 3
> transparentBackground true

> hide #!13 models

> show #!5 models

> transparency 30 target s

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

> save NhaA-K-pH63-unplugged_cutaway_surf_30.png supersample 3
> transparentBackground true

> hide target s

> ~clip

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 3

> hide #!5 models

> show #!13 models

> lighting full

> select clear

[Repeated 3 time(s)]

> hide sel

> select clear

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 4

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 5

> show :NA target a

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 58102 bond radii  

> graphics silhouettes width 2

> transparency 0 target a

> transparency 1000 target a

> transparency 100 target a

> graphics silhouettes 6

Expected true or false or a keyword  

> graphics silhouettes width 6

> graphics silhouettes width 8

> graphics silhouettes width 6

> graphics silhouettes width 8

> save NhaA-Na-pH85_cutaway_res_sil.png supersample 3 transparentBackground
> true

> hide #!13 models

> show #!15 models

> select clear

> hide sel

> save NhaA-K-pH85-state2_cutaway_res_sil.png supersample 3
> transparentBackground true

> graphics silhouettes width 15

> graphics silhouettes width 20

> save NhaA-K-pH85-state2_cutaway_res_sil.png supersample 3
> transparentBackground true

> select up

1 pseudobond, 1 model selected  

> select clear

> graphics silhouettes width 2

> transparency 0 target a

> lighting shadows false

> show #!13 models

> show #!11 models

> hide #!11 models

> show #!9 models

> show #7 models

> hide #7 models

> show #!5 models

> show /A target c

> hide #!5,9,13,15 atoms

> hide #!15 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide /A:NA,163,164 target a

> size stickRadius 0.3

Changed 58102 bond radii  

> graphics silhouettes width 2

> show #3 models

> hide #3 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #!11 models

> hide #!11 models

> show #7 models

> show #3 models

> show #1 models

> show #!11 models

> hide #1,3,7#!5,9,11,13 atoms

> show /A:144 target a

> ui mousemode right distance

> distance #1/A:144@CA #13/A:144@CA

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A LEU 144 CA and NhaA-
nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LEU 144 CA: 1.067Å  

> show /A:155 target a

> show /A:150 target a

> hide #3 models

> hide #!5 models

> distance #1/A:150@CA #13/A:150@CA

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A LEU 150 CA and NhaA-
nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LEU 150 CA: 0.906Å  

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view mono_back_

> combine #1,3,5,7,9,11,13,15 pH-superposition

Expected a keyword  

> combine #1,3,5,7,9,11,13,15 name pH-superposition

Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'D'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'E'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH63_plugged.pdb #3 to 'F'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'G'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'H'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5 to 'I'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'J'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'K'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7 to 'L'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'M'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'N'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9 to 'O'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'P'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'Q'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state1-plugged.pdb #11 to 'R'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
'S'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
'T'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13 to
'U'  
Remapping chain ID 'A' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'V'  
Remapping chain ID 'B' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'W'  
Remapping chain ID 'C' in NhaA-nd-6F9-K_BTPpH85_state2.pdb #15 to 'X'  

> hide #1 models

> hide #7 models

> hide #!9 models

> hide #!11 models

> hide #!13 models

> cartoon style modeHelix default width 1.0 thickness 0.3

> cartoon style modeHelix tube radius 1.8 sides 24

> cartoon style modeHelix default width 1.0 thickness 0.3

> size stickRadius 0.3

Changed 96905 bond radii  

> close #26

> show #1 models

> show #3 models

> show #!5 models

> show #7 models

> show #!9 models

> show #!11 models

> show #!13 models

> show #!15 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view mono_back_

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> view mono_back_

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Tue Aug 27 10:43:20 2024 ———

opened ChimeraX session  

> hide #1 models

> hide #3 models

> hide #!5 models

> hide #7 models

> hide #!9 models

> hide #!11 models

> hide #!13 models

> hide #!15 models

> show #!17 models

> show #17/A:163,164 target s

> show #17/A:163,164,132,133 target a

> show :NA target a

> show :NA target s

> hide :NA target a

> hide :NA target s

> show #17/A:163,164,132,133 target s

> show :NA target a

> hide :NA target a

> hide #17/A:163,164,132,133 target sa

> hide #!17 atoms

> hide #!17 models

> show #7 models

> show #!9 models

> hide #!9 models

> hide #7 models

> show #!9 models

> hide #!9 models

> show #7 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view cutaway

> clip front 0.4 position #17:NA

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

> coulombic #7

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_A SES surface #7.1:
minimum, -15.51, mean 0.31, maximum 15.23  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_B SES surface #7.2:
minimum, -18.75, mean -1.94, maximum 19.89  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged.pdb_C SES surface #7.3:
minimum, -13.67, mean -1.87, maximum 10.42  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #7/B,C target s

> clip model #7 false

> clip front 0.4 position #17:NA

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

> clip model #7 true

> ~clip

> combine #7 name NhaA-nd-6F9-K_BTPpH75_plugged_split

> delete #26/B,C

> hide #!7 models

> split #26 stoms :1-10

Expected a keyword  

> split #26 atoms :1-10

Split NhaA-nd-6F9-K_BTPpH75_plugged_split (#26) into 2 models  
Chain information for NhaA-nd-6F9-K_BTPpH75_plugged_split 1 #26.1  
---  
Chain | Description  
A | No description available  
  
Chain information for NhaA-nd-6F9-K_BTPpH75_plugged_split 2 #26.2  
---  
Chain | Description  
A | No description available  
  

> coulombic #26.1-2

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split
1_A SES surface #26.1.1: minimum, -4.18, mean 3.47, maximum 11.04  
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 #26 target ac

> clip front 0.4 position #17:NA

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

> select #26.1.1.1

1 model selected  

> color sel orchid target s

> select clear

> ~clip

> clip front 0.4 position #17:NA

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

> select #26.1.1.1

1 model selected  

> select up

90 atoms, 10 residues, 3 models selected  

> select down

1 model selected  

> select up

90 atoms, 10 residues, 3 models selected  

> color sel orchid target s

> select clear

> coulombic #!26.1-2

Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 1_A SES surface
#26.1.1: minimum, -4.18, mean 3.47, maximum 11.04  
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  

> clip front 0.4 position #17:NA

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

> select #26.1.1.1

1 model selected  

> color sel orchid target s

> select clear

> lighting soft multiShadow 1024

> select #26.1.1.1

1 model selected  

> transparency sel 1 target s

> select clear

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

> transparency 70 target s

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

> select #26.1.1.1

1 model selected  

> transparency sel 0 target s

> color sel orchid target s

> transparency sel 1 target s

> select clear

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

> hide #!26 models

> show #!7 models

> hide #!7 cartoons

> hide #!7 surfaces

> hide #!7 atoms

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 5

> ~clip

> hide sel

> select clear

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 2

> lighting full

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 3

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 2

> lighting simple

> lighting full

> lighting simple

> lighting full

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

> show #!9 models

> hide #!9 models

> show #3 models

> hide #!7 models

> hide #3 cartoons

> hide #!3 atoms

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 2

> hide sel

> lighting shadows false

> select clear

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

> hide #!3 models

> show #1 models

> hide #1 atoms

> hide #1 cartoons

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 2

> select up

4707 atoms, 4810 bonds, 1 pseudobond, 611 residues, 2 models selected  

> select down

1 pseudobond, 1 model selected  

> hide sel

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

> hide #!1 models

> show #!11 models

> hide #!11 atoms

> hide #!11 cartoons

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

> color /A:NA,163,164 byhetero target a

> size stickRadius 0.5

Changed 61174 bond radii  

> graphics silhouettes width 2

> hide sel

> select clear

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

> hide #!11 models

> combine #11 name NhaA-nd-6F9-K-BTPpH85_state1-plugged_split

> delete #28/B,C

> split #27 atoms :1-10

Split NhaA-nd-6F9-K-BTPpH85_state1-plugged_split (#27) into 2 models  
Chain information for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 1 #27.1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 2 #27.2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> combine #3 name NhaA-nd-6F9-K-BTPpH63_plugged_split

> delete #28/B,C

> delete #27/B,C

> combine #1 name NhaA-nd-6F9-K-MESpH55_plugged_split

> delete #29/B,C

> split #29 atoms :1-10

Split NhaA-nd-6F9-K-MESpH55_plugged_split (#29) into 2 models  
Chain information for NhaA-nd-6F9-K-MESpH55_plugged_split 1 #29.1  
---  
Chain | Description  
A | No description available  
  
Chain information for NhaA-nd-6F9-K-MESpH55_plugged_split 2 #29.2  
---  
Chain | Description  
A | No description available  
  

> hide #!28 models

> hide #!29 models

> show #!28 models

> show #!29 models

> show #!26 models

> hide #!26 models

> hide #27.1#29.1#!28#!27.2#!29.2 atoms

> hide #28 models

> show #28 models

> coulombic #28#27.1-2#29.1-2

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 4 time(s)]Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split_A
SES surface #28.1: minimum, -17.16, mean 0.42, maximum 15.73  
Coulombic values for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 1_A SES
surface #27.1.1: minimum, -4.22, mean 2.78, maximum 9.56  
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 1_A SES surface
#29.1.1: minimum, -4.09, mean 3.18, maximum 13.24  
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  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!28 models

> hide #!29 models

> lighting soft multiShadow 1024

> clip front 0.4 position #17:NA

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

> select #27.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> hide #!27 models

> show #!28 models

> select #28.1.1

1 model selected  

> select #28.1.1

1 model selected  

> select clear

> show #!29 models

> hide #!28 models

> show #!28 models

> hide #!29 models

> split #28 atoms :1-10

Split NhaA-nd-6F9-K-BTPpH63_plugged_split (#28) into 2 models  
Chain information for NhaA-nd-6F9-K-BTPpH63_plugged_split 1 #28.1  
---  
Chain | Description  
A | No description available  
  
Chain information for NhaA-nd-6F9-K-BTPpH63_plugged_split 2 #28.2  
---  
Chain | Description  
A | No description available  
  

> coulombic #28.1-2

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split
1_A SES surface #28.1.1: minimum, -4.62, mean 3.38, maximum 10.14  
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  

> clip front 0.4 position #17:NA

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

> select #28.1.1.1

1 model selected  

> color sel orchid target s

> select clear

> color sel orchid transparency 1 target s

> select #28.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> show #!29 models

> hide #!28 models

> clip front 0.4 position #17:NA

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

> color sel orchid transparency 1 target s

> select #29.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> hide #!29 models

> show #!29 models

> transparency 30 target s

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

> select #29.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> show #!28 models

> hide #!29 models

> transparency 30 target s

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

> select #28.1.1.1

1 model selected  

> select up

90 atoms, 10 residues, 3 models selected  

> select down

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> hide #!28 models

> show #!27 models

> transparency 30 target s

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

> select #27.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> hide #!27 models

> show #!26 models

> hide #!26.1-2 atoms

> transparency 30 target s

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

> select #26.1.1.1

1 model selected  

> color sel orchid transparency 1 target s

> select clear

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

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> hide #!26 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!5 models

> open /Users/tsweng/Documents/Projects/NhaA/Structures/hole_analysis/NhaA-
> nd-6F9-K_BTPpH63_unplugged_hole_out.sph

Unrecognized file suffix '.sph'  

> lighting full

> lighting shadows false

> hide #!5 models

> show #!20 models

> hide #!20 models

> show #19 models

> hide #19 atoms

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view dimer_view-all_front

> show #19:CDL,PTY target a

> size stickRadius 0.3

Changed 70360 bond radii  

> turn y -90

> view

> show #!21 models

> hide #!21.5 models

> hide #!21 models

> show #!20 models

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:11-85,181-274 pale green

> color :CDL,PTY gray target a

> color #19/D white

> color zone #20 near #19

> color #19/A,D:86-180,275-388 forest green target ac

> color #19/A,D:11-85,181-274 pale green target ac

> color :CDL,PTY gray target a

> color #19/D white

> color zone #20 near #19

> color #19/A,D:86-180,275-388 forest green target ac

> color #19/A,D:1-85,181-274 pale green target ac

> color :CDL,PTY gray target a

> color #19/D white

> color zone #20 near #19

> volume splitbyzone #20

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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, step 1, values float32  

> hide #!30.6 models

> hide #19/D target ac

> surface dust #30 size 5

> surface dust #30 size 6

> view name dimer_interface

> hide #!30.5 models

> hide #!30.3 models

> hide #!30.2 models

> volume #30 level 0.0085

> volume #30 level 0.009

> volume #30 level 0.0085

> volume #30 level 0.009

> volume #30 level 0.01

> view name dimer_interface2

> volume #30 level 0.008

> volume #30 level 0.0086

> volume #30 level 0.0085

> volume #30 level 0.0084

> volume #30 level 0.008

> transparency #30.4 50 target s

> color #19:CDL,PTY byhetero target a

> transparency #30.1 0 target s

> transparency #30.4 70 target s

> transparency #30.1 1 target s

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_view-all_front, mono_back,
mono_back_, mono_front  

> view dimer_interface2

> view name dimer_interface2

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:11-85,181-274 pale green

> show #19/D target c

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_view-all_front, mono_back,
mono_back_, mono_front  

> view dimer_view-all_front

> view

> turn x 90

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> turn x 5

> turn x -5

[Repeated 1 time(s)]

> open /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA-
> nd-Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb

Chain information for NhaA-nd-Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb
#31  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C F | No description available  
  

> mcopy #19 toAtoms #31 settings hsv

> mmaker #31 to #19

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_consensus.pdb, chain A (#19) with NhaA-nd-
Fv6F9-K_BTPpH75_consensus-map_dimer_CDL-PGT.pdb, chain A (#31), sequence
alignment score = 1997.6  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

> color #31/A,D:86-180,275-388 forest green

> color #19/A,D:1-85,181-274 pale green

> hide #31 target ac

> show #31:PGT target a

> style :PGT ball

Changed 51 atom styles  

> size stickRadius 0.3

Changed 80007 bond radii  

> hide #31 models

> view name dimer_interface_top

> volume #30 level 0.0084

> surface dust #30 size 5

> volume #30 level 0.0085

> volume #30 level 0.0086

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_interface_top, dimer_view-all_front,
mono_back, mono_back_, mono_front  

> view dimer_interface_top

> volume #30 level 0.0088

> volume #30 level 0.009

> view dimer_interface_top

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> volume #30 surfaceSmoothing true

> volume #30 level 0.0086

> view dimer_interface_top

> view dimer_interface2

> view dimer_interface

> view dimer_interface_top

> turn x 5

> select #19/A:250

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> show #19/A,D:ARG,TYR,LYS

> show #19/A,D:ARG,TYR,LYS target a

> style #19 stick

Changed 9389 atom styles  

> style :CDL,PTY,PGT ball

Changed 1801 atom styles  

> color #19 byhetero

> show #19/A,D:ARG,TYR,LYS,TRP target a

> show #19/A,D:204,245,250,258 target a

> hide #19 atoms

> show #19/A,D:204,245,250,258,CDL,PTY,PGT target a

> view dimer_interface_top

> select #30.1

4 models selected  

> select clear

> close #30

> color #19/A,D:86-180,275-388 forest green target ac

> color #19/A,D:1-85,181-274 pale green target ac

> color :CDL,PTY gray target a

> color #19/D white

> show #!20 models

> show #!9 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> combine #7

> mmaker #30 to #19/D

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_consensus.pdb, chain D (#19) with copy of
NhaA-nd-6F9-K_BTPpH75_plugged.pdb, chain A (#30), sequence alignment score =
1959.8  
RMSD between 378 pruned atom pairs is 0.151 angstroms; (across all 388 pairs:
2.825)  
  

> hide #!30 models

> show #!30 models

> show #30/A target c

> combine #7,30 name pH75_dimer_plug_dummy

Remapping chain ID 'A' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'D'  
Remapping chain ID 'B' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'E'  
Remapping chain ID 'C' in copy of NhaA-nd-6F9-K_BTPpH75_plugged.pdb #30 to 'F'  

> hide #30 models

> show #32/A target c

> select #32/A,D:1-10

180 atoms, 186 bonds, 20 residues, 1 model selected  

> select ~sel & ##selected

9292 atoms, 9494 bonds, 1208 residues, 1 model selected  

> delete sel

> color #19/A,D:86-180,275-388 forest green target ac

> color #19/A,D:1-85,181-274 pale green target ac

> color :CDL,PTY gray target a

> color #19/D white

> color #32 orchid

> close #30

> color zone #20 near #19,32

> delete #32/B,C,E,F

> color zone #20 near #19,32

> color #19/A,D:86-180,275-388 forest green target ac

> color #19/A,D:1-85,181-274 pale green target ac

> color :CDL,PTY gray target a

> color #19/D white

> color #32 orchid

> color #19/B,C,E,F gainsboro

> color zone #20 near #19,32

> volume splitbyzone #20

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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, 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 0.0081, step 1, values float32  

> hide #19 models

> show #19 models

> hide #!30.6 models

> show #!30.6 models

> hide #!30.5 models

> volume #30 level 0.86

> volume #30 level 0.086

> volume #30 level 0.0086

> surface dust #30 size 5

> hide #!30.3 models

> hide #!30.2 models

> hide #!30.6 models

> hide #!30.7 models

> hide #32 models

> volume #30 surfaceSmoothing true

> transparency #30.4 30

> color #19 byhetero

> transparency #30.4 60

> show #!30.3 models

> show #!30.2 models

> show #!30.5 models

> hide #!30.5 models

> show #!30.6 models

> lighting soft

> hide #!30.1 models

> show #!30.1 models

> hide #!30.2 models

> hide #!30.3 models

> hide #!30.4 models

> hide #!30.6 models

> show #!30.4 models

> coulombic #19

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_A SES surface #19.1:
minimum, -14.83, mean 0.05, maximum 16.17  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_B SES surface #19.2:
minimum, -18.31, mean -1.96, maximum 12.70  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_C SES surface #19.3:
minimum, -18.82, mean -1.78, maximum 9.24  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_D SES surface #19.4:
minimum, -19.90, mean 0.05, maximum 16.15  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_E SES surface #19.5:
minimum, -18.72, mean -1.97, maximum 12.71  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_consensus.pdb_F SES surface #19.6:
minimum, -19.23, mean -1.79, maximum 9.35  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #19/B,C,E,F target s

> hide #19 target s

> view dimer_interface_top

> turn x 5

> transparency #30.1 1

> color #30.1 gray

> lighting full

> lighting shadows false

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> color #30.1 dark gray

> graphics silhouettes false

> graphics silhouettes true

> cartoon style modeHelix default width 1.8 thickness 0.3

> gid #19/A,D:1-10 tar c

Unknown command: gid #19/A,D:1-10 tar c  

> hide #19/A,D:1-10 target c

> color #30.1 dark gray

> color #30.1 silver

> color #30.1 dark gray

> color #30.4 silver

> surface dust #30 size 6

> surface dust #30 size 5

> surface dust #30 size 6

> color #19/D antique white target c

> color #19/D antique white target ac

> color #!19 byhetero

> view name dimer_interface_top

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> lighting gentle multiShadow 1024

> lighting soft multiShadow 1024

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting shadows false

> color :CDL,PTY,PGT dim gray target a

> color :CDL,PTY,PGT dark slate gray target a

> color :CDL,PTY,PGT dim gray target a

> color #!19 byhetero

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

> turn z -90

> lighting soft multiShadow 1024

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> view name dimer_interface_top2

> view dimer_interface_top

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes width 2

> hide #!30 models

> hide #19/A,D target c

> hide #19/A,D target ac

> show #19/A,D(:204,245,250,258&sidechain)|(:CDL,PTY,PGT) tar a

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

> show #19/A,D((:204,245,250,258&sidechain)|(:CDL,PTY,PGT)) tar a

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

> show #19/A,D:204,245,250,258&sidechain target a

> show #19/A,D:CDL,PTY,PGT target a

> graphics silhouettes width 8

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

> graphics silhouettes width 2

> show #!30 models

> show #19/A,D target c

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view dimer_interface_top2

> save NhaA-K-pH75-consensus_interface_top2.png supersample 3
> transparentBackground true

> hide #!30 models

> hide #19/A,D target c

> graphics silhouettes width 6

> save NhaA-K-pH75-consensus_interface_top2_res.png supersample 3
> transparentBackground true

> view dimer_interface2

> graphics silhouettes width 2

> show #!30 models

> show #19/A,D target c

> surface dust #30 size 5

> color #30.1 silver

> view dimer_interface_top2

> cartoon style modeHelix default width 1.0 thickness 0.3

> save NhaA-K-pH75-consensus_interface_top2.png supersample 3
> transparentBackground true

> view dimer_interface2

> hide #19/D target c

> clip #19/D:258@CA

Expected a keyword  

> clip front 0.1 #19/D:258@CA

Expected a keyword  

> clip front 0.1 position #19/D:258@CA

> clip model #30.4 false

> clip model #30.4 true

> clip front 5 position #19/D:258@CA

> clip model #19 true

> clip model #19 false

> clip front 0 position #19/D:258@CA

> select #30.1

5 models selected  

> select clear

> ~clip

> clip front 0 position #19/D:258@CA

> clip front -1 position #19/D:258@CA

> clip front 0.5 position #19/D:258@CA

> clip front 0.1 position #19/D:258@CA

> size #19/A,D:204,245,250,258 stickRadius 0.4

Changed 90 bond radii  

> hide #19/A,D:1-10 target c

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

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

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view name dimer_interface2

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

> hide #!30 models

> hide #19/A target c

> graphics silhouettes width 4

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

> show #31 models

> hide #31 models

> show #31 models

> hide #31 models

> show #31 models

> select #31/A:402@C37

1 atom, 1 residue, 1 model selected  

> select add #31/A:402@C18

2 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C19

3 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C38

4 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C39

5 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C40

6 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C20

7 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C21

8 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C41

9 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C42

10 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C43

11 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C44

12 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C45

13 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C46

14 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C47

15 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C23

16 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C22

17 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C24

18 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C25

19 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C26

20 atoms, 1 residue, 1 model selected  

> select subtract #31/A:402@C47

19 atoms, 1 residue, 1 model selected  

> select add #31/A:402@C47

20 atoms, 1 residue, 1 model selected  

> delete sel

> hide #31 models

> show #31 models

> hide #31 models

> show #31 models

> hide #31 models

> show #31 models

> hide #31:CDL

> hide #19:PTY

> color #31#!19 byhetero

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

> graphics silhouettes width 2

> show #19/A target c

> show #!30 models

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

> view dimer_interface2

> view dimer_interface_top2

> show #19/D target c

> save NhaA-K-pH75-consensus_interface_top2_PGT.png supersample 3
> transparentBackground true

> hide #!30 models

> hide #19/A,D target c

> graphics silhouettes width 4

> save NhaA-K-pH75-consensus_interface_top2_PGT_res.png supersample 3
> transparentBackground true

> select #31/A:402@C48

1 atom, 1 residue, 1 model selected  

> delete sel

> view dimer_interface2

> show #19/A target s

> color #19/A pale green target s

> hide #31#!19 atoms

> show #19/D target s

> color #19/D pale green target s

> hide #19 target s

> show #31#!19 cartoons

> ~clip

> hide #31 models

> graphics silhouettes width 2

> view dimer_interface

> view dimer_view-all_front

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

> size #19/A,D:204,245,250,258 stickRadius 0.3

Changed 90 bond radii  

> show #19/A,D:204,245,250,258 target a

> hide #!30.4 models

> show #!30.4 models

> hide #!30.4 models

> show #!30.4 models

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Thu Aug 29 14:44:39 2024 ———

opened ChimeraX session  

> hide #!30 models

> show #!1 models

> hide #!1 models

> hide #!19 models

> show #!9 models

> show #!15 models

> hide #!9,15 atoms

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

> show #1 models

> hide #!9 models

> hide #!15 models

> show /A target c

> show #3 models

> hide #3 models

> show #!5 models

> hide #1 models

> show #!9 models

> show #!13 models

> show #!16 models

> hide #!16 models

> show #!15 models

> color #!5,9,13,15 byhetero

> hide #!5 models

> show #!5 models

> hide #!9 models

> hide #!13 models

> show #!23 models

> ui mousemode right distance

> distance #15/A:225@NE2 #15/A:65@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A HIS 225 NE2 and ASP 65
OD2: 3.587Å  

> hide #!15 models

> distance #5/A:65@OD2 #5/A:57@NZ

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 65 OD2 and LYS
57 NZ: 1.745Å  

> show #!15 models

> show #!13 models

> hide #!15 models

> distance #13/A:65@OD1 #13/A:57@NZ

Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 65 OD1
and LYS 57 NZ: 2.308Å  

> show #!15 models

> hide #!13 models

> ~distance #13/A:65@OD1 #13/A:57@NZ

> distance #15/A:57@NZ #15/A:65@OD1

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 57 NZ and ASP 65
OD1: 4.109Å  

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume #16 level 0.01249

> show #16 target s

> transparency #16 30 target s

> surface unzone #16

> hide #!5 models

> hide #!16 models

> show #!5 models

> distance #15/A:57@NZ #5/A:39@ND1

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 57 NZ and NhaA-
nd-6F9-K_BTPpH63_unplugged.pdb #5/A HIS 39 ND1: 18.994Å  

> distance #5/A:39@ND1 #5/A:43@OE2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A HIS 39 ND1 and GLU
43 OE2: 4.744Å  

> hide #!5 models

> hide #!15 models

> show #!17 models

> view list

Named views: N-term_density_top, binding_site, core_inner_side, cutaway,
dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2,
dimer_view-all_front, mono_back, mono_back_, mono_front  

> view binding_site

> show :HOH,NA target a

> show #!18 models

> view binding_site

[Repeated 1 time(s)]

> hide #!18 models

> hide #!17 models

> show #!15 models

> show #!13 models

> show #!11 models

> hide #!15 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!11 models

> show #!9 models

> show #!5 models

> hide #!9 models

> hide #!13 models

> distance #5/A:163@OD2 #5/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 163 OD2 and LYS
300 NZ: 3.848Å  

> show #!9 models

> hide #!5 models

> distance #9/A:163@OD2 #9/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ASP 163 OD2 and LYS
300 NZ: 3.109Å  

> show #!5 models

> show #!13 models

> hide #!9 models

> hide #!5 models

> distance #13/A:163@OD2 #13/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 163 OD2
and LYS 300 NZ: 2.957Å  

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!9 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!9 models

> show #!9 models

> hide #!7 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> show #!5 models

> hide #!5 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #!9 models

> hide #!13 models

> show #!5 models

> hide #3 models

> hide #!5 models

> show #!5 models

> show #!9 models

> show #3 models

> show #1 models

> hide #3 models

> hide #!5 models

> hide #!9 models

> ~distance #15/A:163@OD2 #15/A:300@NZ

> hide #!23 models

> show #!23 models

> ~distance #13/A:163@OD2 #13/A:300@NZ

> distance #1/A:163@OD2 #1/A:300@NZ

Distance between NhaA-nd-6F9-K_MESpH55.pdb #1/A ASP 163 OD2 and LYS 300 NZ:
3.533Å  

> show #3 models

> hide #1 models

> show #1 models

> hide #1 models

> show #!5 models

> hide #3 models

> show #!7 models

> hide #!5 models

> show #!9 models

> hide #!7 models

> show #!11 models

> hide #!9 models

> show #!13 models

> hide #!11 models

> show #!15 models

> hide #!13 models

> show #!13 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> view binding_site

> show #!15 models

> show #!11 models

> hide #!11 models

> show #!9 models

> show #!5 models

> style :NA stick

Changed 2 atom styles  

> show /A target c

> show binding_site_res target a

> cartoon /A:132 suppressBackboneDisplay false

> cartoon tether /A:132 scale 0

> graphics silhouettes width 2

> color #!5,9,13,15 byhetero

> hide #!5 models

> show #!5 models

> view binding_site

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> show #!16 models

> hide #!16 models

> show #!14 models

> hide #!15 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> show #!16 models

> hide #!16 models

> hide #!5 models

> hide #!9 models

> view binding_site

> color #15 dark cyan target ac

> color #!13,15 byhetero

> color #13 medium aquamarine target ac

> color #!13,15 byhetero

> color #13 medium seagreen target ac

> color #13 light seagreen target ac

> color #15 teal target ac

> color #!13,15 byhetero

> hide #!13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> show #!11 models

> hide #!15 models

> show #!15 models

> show #!9 models

> hide #!9 models

> hide #!11 models

> show #!9 models

> show #!5 models

> hide #!5,9,13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> hide #!15 models

> hide #!13 models

> hide #!9 models

> distance #5/A:78@OE2 #5/A:256@NE2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 78 OE2 and HIS
256 NE2: 3.405Å  

> show #!9 models

> show #!13 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!13 models

> hide #!9 models

> coulombic #!5

Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_A SES surface #5.1:
minimum, -15.26, mean 0.23, maximum 19.25  
Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_B SES surface #5.2:
minimum, -17.29, mean -2.01, maximum 8.10  
Coulombic values for NhaA-nd-6F9-K_BTPpH63_unplugged.pdb_C SES surface #5.3:
minimum, -13.33, mean -1.95, maximum 8.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide /B,C target s

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!9 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5.1 models

> show #5.1 models

> hide #!5 models

> hide #9.1 models

> show #9.1 models

> show #9 target s

> coulombic #!9

Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface #9.1:
minimum, -15.35, mean 0.08, maximum 15.24  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface #9.2:
minimum, -18.25, mean -1.97, maximum 8.02  
Coulombic values for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface #9.3:
minimum, -13.57, mean -1.87, maximum 9.81  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!9 models

> show #!5 models

> show #!9 models

> hide #!5 models

> hide #!9 models

> show #!13 models

> coulombic #!13

Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_A SES surface
#13.1: minimum, -16.52, mean 0.01, maximum 15.63  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_B SES surface
#13.2: minimum, -19.83, mean -1.80, maximum 8.49  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb_C SES surface
#13.3: minimum, -13.89, mean -1.84, maximum 10.03  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide /B,C target s

> show #!9 models

> hide #!13 models

> show #!13 models

> hide #!9 models

> show #!15 models

> hide #!13 models

> coulombic #!15

Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #15.1:
minimum, -17.07, mean 0.02, maximum 20.09  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #15.2:
minimum, -18.53, mean -1.82, maximum 10.93  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #15.3:
minimum, -14.51, mean -2.14, maximum 12.50  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide /B,C target s

> show #!13 models

> hide #!15 models

> show #!15 models

> hide #!13 models

> show #!13 models

> hide #!15 models

> hide #!13 models

> show #!13 models

> hide #!13.1 models

> hide #9.1 models

> show #!9 models

> show #!5 models

> hide #!5.1 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #1 models

> hide #1 models

> show #!15 models

> hide #!15.1 models

> hide #!5,9,13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> show #3 models

> hide #3 models

> show #3 models

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #3 models

> show #3 models

> hide #3 models

> show #!6 models

> volume #6 level 0.005928

> volume #6 level 0.008046

> select clear

> hide #!6 models

> 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 #33  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #33 to #5

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_BTPpH63_unplugged.pdb, chain A (#5) with NhaA-
nd-6F9-K_BTPpH63_unplugged.pdb, chain A (#33), sequence alignment score =
1998.2  
RMSD between 388 pruned atom pairs is 0.011 angstroms; (across all 388 pairs:
0.011)  
  

> mcopy #5 toAtoms #33 settings chsv

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> cartoon style modeHelix default width 1.0 thickness 0.3

> cartoon style modeHelix default width 1.2 thickness 0.2

> cartoon style modeHelix default width 1.0 thickness 0.3

> size stickRadius 0.3

Changed 85069 bond radii  

> size stickRadius 0.2

Changed 85069 bond radii  

> size stickRadius 0.3

Changed 85069 bond radii  

> hide #33:CDL,PTY target a

> close #5

> rename #33 id #5

> show #!16 models

> show #!14 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!14 models

> show #!14 models

> hide #!16 models

> hide #!14 models

> distance #5/A:78@OE2 #5/A:256@NE2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A GLU 78 OE2 and HIS
256 NE2: 2.543Å  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #!7 models

> hide #!7 models

> show #!11 models

> hide #!11 models

> save
> /Users/tsweng/Documents/Projects/NhaA/Structures/chimerax_session/NhaA.cxs

——— End of log from Tue Sep 3 14:38:58 2024 ———

opened ChimeraX session  

> color #5 orange target ac

> color #9 forestgreen target ac

> color #13 light seagreen target ac

> color #15 teal target ac

> color #5#!9,13,15 byhetero

> ui mousemode right translate

> select clear

> hide #23.1 models

> ui mousemode right distance

> hide #!13 models

> hide #!9 models

> hide #5 models

> distance #15/A:252@OE1 #15/A:81@NE

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A GLU 252 OE1 and ARG 81
NE: 3.097Å  

> show #23.1 models

> hide #23.1 models

> show #!9 models

> show #!13 models

> show #5 models

> ui mousemode right translate

> transparency 50 target c

> hide #5 models

> hide #!9 models

> hide #!13 models

> ui mousemode right distance

> ~distance #1/A:81@NH2 #1/A:252@OE2

> distance #15/A:252@OE1 #15/A:81@NH2

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A GLU 252 OE1 and ARG 81
NH2: 3.074Å  

> show #23.1 models

> ui tool show Distances

> ~distance #15/A:252@OE1 #15/A:81@NE

> show #!13 models

> show #!9 models

> show #5 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> distance #17/A:11@OD2 #17/A:153@NZ

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 11 OD2 and LYS 153 NZ:
3.741Å  

> ui mousemode right translate

> ui tool show Distances

> ~distance #17/A:11@OD2 #17/A:153@NZ

> hide #!17 models

> hide #23.1 models

> show #23.1 models

> hide #23.1 models

> transparency 70 target c

> transparency 50 target c

> show #23.1 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #5 models

> hide #!13 models

> ui mousemode right distance

> distance #9/A:78@OE1 #9/A:256@ND1

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 78 OE1 and HIS
256 ND1: 4.195Å  

> ui tool show Distances

> ~distance #9/A:78@OE1 #9/A:256@ND1

> show #!11 models

> hide #!11 models

> show #!13 models

> show #!15 models

> show #5 models

> hide #23.1 models

> select clear

> ui mousemode right translate

> select #9/A:81@NE

1 atom, 1 residue, 1 model selected  

> select clear

> color sel gray target p

> color sel dark gray target p

> select clear

> hide #!23 models

> save NhaA-pH-sensing-superpose.png supersample 3 transparentBackground true

> hide target c

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> hide #5#!9,13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a

> hide sel

> select clear

> hide sel

[Repeated 1 time(s)]

> graphics silhouettes width 6

> show #!23 models

> graphics silhouettes width 8

> graphics silhouettes width 6

> save NhaA-pH-sensing-superpose_res.png supersample 3 transparentBackground
> true

> graphics silhouettes width 2

> hide #!23 models

> show /A target c

> transparency 50 target c

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> transparency 30 target c

> save NhaA-pH-sensing-superpose.png supersample 3 transparentBackground true

> hide target c

> ui tool show "Selection Inspector"

[Repeated 1 time(s)]

> setattr =sel p display false

Assigning display attribute to 9 items  

> hide sel target p

> select clear

> show /A target c

> view name pH-sensing

> view list

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

> view binding_site

> hide #5#!9,13,15 atoms

> name pH-sensing /A:11,78,81,82,243,249,250,252,253,256

> name list

binding_site_res /A:132,133,163,164,300,NA,HOH  
core /A:86-180,275-388  
core_TM /A:91-116,123-144,150-174,281-313,325-350,355-383  
dimer /A:1-85,181-274  
dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271  
pH-sensing /A:11,78,81,82,243,249,250,252,253,256  

> show binding_site_res&sidechain target a

> show /A:132 target a

> show #!23 models

> hide #!15 models

> ui mousemode right distance

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

> distance #13/A:132@O #13/A:164@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A THR 132 O
and ASP 164 OD2: 2.894Å  

> show #23.1 models

> show #!15 models

> distance #15/A:300@NZ #15/A:163@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #15/A LYS 300 NZ and ASP 163
OD2: 3.294Å  

> show #!16 models

> hide #!16 models

> show #!16 models

> show #15/A:161 target a

> 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 #33  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #33 to #15

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_BTPpH85_state2.pdb, chain A (#15) with NhaA-
nd-6F9-K_BTPpH85_state2.pdb, chain A (#33), sequence alignment score = 2000  
RMSD between 388 pruned atom pairs is 0.047 angstroms; (across all 388 pairs:
0.047)  
  

> mcopy #15 toAtoms #33 settings hsvc

> hide #!16 models

> cartoon style modeHelix default width 1.8 thickness 0.2

> cartoon style modeHelix default width 1.0 thickness 0.3

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> distance #33/A:164@OD1 #33/A:132@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD1 and THR
132 O: 6.188Å  

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

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 163 OD1 and LYS
300 NZ: 3.678Å  

> view list

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

> view binding_site

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!15 models

> hide #33 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #33 models

> hide #5 models

> hide #!9 models

> hide #!13 models

> coulombic #33

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_A SES surface #33.1:
minimum, -15.50, mean 0.05, maximum 21.16  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_B SES surface #33.2:
minimum, -18.13, mean -1.81, maximum 11.34  
Coulombic values for NhaA-nd-6F9-K_BTPpH85_state2.pdb_C SES surface #33.3:
minimum, -14.70, mean -2.15, maximum 10.81  
To also show corresponding color key, enter the above coulombic command and
add key true  

> view list

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

> view cutaway

> ~clip

> view cutaway

> hide #15,33/A:161 target a

> hide /B,C target s

> hide #!33 models

> show #!9 models

> hide #!9 models

> show #!9 models

> view cutaway

> show #9.1 models

> hide #!9.1 models

> show #9.1 models

> hide #!9.1 models

> show #9.1 models

> hide #!9.1 models

> hide #!9 models

> show #!17 models

> hide #17.1 models

> show #17.1 models

> 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 #!17.1 models

> show #17.1 models

> hide #!17.1 models

> hide #!17.3 models

> show #17.3 models

> hide #17.4 models

> show #17.4 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!13 models

> show #13.1 models

> hide #!13.1 models

> hide #!13 models

> show #!15 models

> show #15.1 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33.1 models

> view binding_site

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> view binding_site

> hide #23.1 models

> show #!15 models

> hide #!15 models

> show #!9 models

> show #!7 models

> hide #!7 models

> show #5 models

> show #!13 models

> select clear

> ui mousemode right translate

> color sel dark gray target p

> select clear

> color sel teal target p

> select clear

[Repeated 1 time(s)]

> show #23.1 models

> hide #23.1 models

> transparency 50 target c

> hide #!23 models

> hide /A:160-161 target c

> show /A:160-161 target c

> show /A:160 target c

> hide /A:160 target c

> view binding_site

> select #13/A:162

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> hide /A:160-161 target c

> save NhaA-K-binding-site-superpose.png supersample 3 transparentBackground
> true

> show #!23 models

> hide target c

> hide sel target p

> select clear

> graphics silhouettes width 6

> save NhaA-K-binding-site-superpose_res.png supersample 3
> transparentBackground true

> show #23.1 models

> hide #23.1 models

> hide sel target p

> color sel dark gray target p

> select clear

> save NhaA-K-binding-site-superpose_res.png supersample 3
> transparentBackground true

> hide #!23 models

> show /A target c

> hide #33/A:160-161 target c

> hide /A:160-161 target c

> graphics silhouettes width 2

> graphics silhouettes false

> transparency 100 target a

> save NhaA-K-binding-site-superpose_rib.png supersample 3
> transparentBackground true

> transparency 0 target a

> show #!23 models

> show #23.1 models

> hide #!23 models

> hide #!13 models

> hide #!9 models

> hide #5 models

> show :HOH target a

> show #!17 models

> hide #!17 models

> show #!23 models

> hide #!23 models

> ui mousemode right distance

> distance #33/A:300@NZ #33/A:506@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A LYS 300 NZ and HOH 506
O: 2.587Å  

> show #!23 models

> distance #33/A:163@OD1 #33/A:506@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 163 OD1 and HOH
506 O: 2.835Å  

> color sel dark gray target p

> select clear

> hide #23.1 models

> show #!16 models

> hide #!16 models

> show #23.1 models

> distance #33/A:164@OD2 #33/A:504@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD2 and HOH
504 O: 4.635Å  

> select #33/A:504@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> ui mousemode right translate

> hide #23.1 models

> graphics silhouettes true

> show #!16 models

> show #25 models

> hide #25 models

> surface zone #16 nearAtoms #25|#33/A:132,133,163,164,300,HOH

> transparency 0 target c

> transparency #16 50 target s

> transparency #16 70 target s

> transparency #16 50 target s

> view binding_site

> select ~sel & ##selected

4794 atoms, 4897 bonds, 5 pseudobonds, 615 residues, 2 models selected  

> select up

4795 atoms, 4897 bonds, 5 pseudobonds, 616 residues, 2 models selected  

> select down

4794 atoms, 4897 bonds, 5 pseudobonds, 615 residues, 5 models selected  

> select clear

> transparency #16 70 target s

> lighting simple

> lighting full

> lighting shadows false

> hide #!33 models

> show #!33 models

> hide #!23 models

> transparency #16 50 target s

> transparency #16 60 target s

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

> show #!23 models

> hide #!23 models

> graphics silhouettes false

> graphics silhouettes true

> hide #33 target c

> hide #!16 models

> hide sel

> select clear

> graphics silhouettes width 6

> show #!23 models

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

> graphics silhouettes width 2

> hide #!23 models

> show #33/A target c

> show #!16 models

> transparency 100 target a

> transparency 70 target c

> graphics silhouettes false

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

> show #!23 models

> show #23.1 models

> graphics silhouettes true

> transparency 0 target c

> transparency 0 target a

> hide #!16 models

> hide #!33 models

> show #!13 models

> show #!14 models

> show #!16 models

> volume #14 level 0.0125

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!14 models

> hide #!13 models

> show #!16 models

> show #!10 models

> volume #10 level 0.01289

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> volume #10 level 0.01642

> show #!16 models

> volume #10 level 0.01289

> transparency #10 0 target s

> volume #10 level 0.01179

> color #10 silver target s

> color #10 silver transparency 0 target s

> volume #10 level 0.01047

> volume #10 level 0.01333

> hide #!10 models

> show #!10 models

> volume #10 level 0.01289

> volume #10 level 0.013

> view binding_site

> hide #!16 models

> show #!16 models

> transparency #10 50 target s

> hide #!10 models

> show #!10 models

> hide #!16 models

> show #!16 models

> color #10 snow target s

> hide #!10 models

> show #!10 models

> color #10 gainsboro target s

> hide #!10 models

> show #!10 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!9 models

> surface zone #10 nearAtoms #9&binding-site-res

Invalid "nearAtoms" argument: only initial part "#9" of atom specifier valid  

> surface zone #10 nearAtoms #9&binding-site_res

Invalid "nearAtoms" argument: only initial part "#9" of atom specifier valid  

> name list

binding_site_res /A:132,133,163,164,300,NA,HOH  
core /A:86-180,275-388  
core_TM /A:91-116,123-144,150-174,281-313,325-350,355-383  
dimer /A:1-85,181-274  
dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271  
pH-sensing /A:11,78,81,82,243,249,250,252,253,256  

> surface zone #10 nearAtoms #9&binding_site_res

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!14 models

> hide #23.1 models

> show #23.1 models

> ui mousemode right distance

> hide #!10 models

> distance #9/A:164@OD2 #9/A:132@O

Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ASP 164 OD2 and THR
132 O: 2.815Å  

> show #!10 models

> color sel dark gray target p

> select clear

> hide #23.1 models

> show #!17 models

> distance #17/A:133@OD1 #17/A:504@O

Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 133 OD1 and HOH 504 O:
3.335Å  

> show #23.1 models

> hide #!9 models

> show #!9 models

> hide #!17 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!13 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15.1 models

> hide #!15 models

> show #!33 models

> show #5 models

> hide #23.1 models

> hide #33:HOH

> hide sel target p

[Repeated 1 time(s)]

> select clear

> hide target c

> select up

4643 atoms, 4 pseudobonds, 612 residues, 8 models selected  

> select down

4 pseudobonds, 4 models selected  

> hide sel target p

> select clear

> graphics silhouettes width 6

> save NhaA-K-binding-site-superpose_res.png supersample 3
> transparentBackground true

> view list

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

> view binding_site

> save NhaA-K-binding-site-superpose_res.png supersample 3
> transparentBackground true

> hide #!5 models

> hide #!9 models

> hide #!13 models

> show #!24 models

> hide #!24,33 atoms

> show /A:132,133,163,164,300&sidechain target a

> show /A:132 target a

> show :NA target a

> hide :NA target a

> hide sel

> hide #!23 models

> show #!23 models

> show #23 target p

> hide :HOH

> distance #24/A:164@OD1 #24/A:132@O

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 164 OD1 and THR
132 O: 4.183Å  

> color sel dodgerblue target p

> select clear

> hide sel target p

> show #23.1 models

> distance #33/A:164@OD2 #33/A:132@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A ASP 164 OD2 and THR
132 O: 6.349Å  

> ui tool show Distances

> ~distance #33/A:164@OD2 #33/A:132@O

> hide #23.1 models

> view binding_site

> select up

33 pseudobonds, 1 model selected  

> select down

1 pseudobond, 1 model selected  

> select clear

> save NhaA-Na-pH85_vs_K-pH85_binding-site_sil2.png supersample 3
> transparentBackground true

> hide #!23 models

> show #!23 models

> show #!15 models

> hide #!15 models

> hide #!33 models

> hide sel target p

> show :NA,HOH target a

> show #23.1 models

> hide #23.1 models

> show #23 target p

> select clear

> show :NA,HOH target a

> show #23 target p

> hide sel

> distance #24/A:505@NA #24/A:163@OD1

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and ASP
163 OD1: 3.219Å  

> ~distance #17/A:505@NA #17/A:164@OD1

> ~distance #15/A:164@OD1 #15/A:132@O

> distance #24/A:505@NA #24/A:164@OD1

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and ASP
164 OD1: 2.181Å  

> distance #24/A:505@NA #24/A:132@O

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and THR
132 O: 2.185Å  

> distance #24/A:505@NA #24/A:504@O

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A NA 505 NA and HOH
504 O: 2.987Å  

> distance #24/A:163@OD2 #24/A:506@O

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and HOH
506 O: 2.645Å  

> show #23.1 models

> ~distance #33/A:300@NZ #33/A:506@O

> distance #24/A:506@O #24/A:300@NZ

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A HOH 506 O and LYS
300 NZ: 2.344Å  

> distance #24/A:163@OD2 #24/A:300@NZ

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and LYS
300 NZ: 3.986Å  

> hide #!24 models

> show #!24 models

> view binding_site

> select clear

[Repeated 5 time(s)]

> select #24/A:504@O

1 atom, 1 residue, 1 model selected  

> select #24/A:504@O

1 atom, 1 residue, 1 model selected  

> select clear

> select #24/A:132@O

1 atom, 1 residue, 1 model selected  

> select clear

> hide sel pseudobonds

> ~distance #24/A:163@OD2 #24/A:300@NZ

> view binding_site

> hide #23.1 models

> ui mousemode right zoom

> ui mousemode right translate

Drag select of 1 pseudobonds  
[Repeated 5 time(s)]

> color sel dark gray target p

> select clear

> view binding_site

> save NhaA-Na-pH85_binding-site_simple_sil2.png supersample 3
> transparentBackground true

> show #23.1 models

> hide #23.1 models

> show #!33 models

> color #33&core light sea green

> color #33&dimer cyan

> color #!24,33 byhetero

Drag select of 1 pseudobonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 pseudobonds  
[Repeated 1 time(s)]

> select clear

> hide :HOH,NA

> show #23 target p

> hide :HOH,NA

> hide #!33 models

> ui mousemode right distance

> distance #24/A:163@OD2 #24/A:300@NZ

Distance between copy of NhaA-nd-6F9-Na_BTPpH85.pdb #24/A ASP 163 OD2 and LYS
300 NZ: 3.986Å  

> ui mousemode right translate

> select clear

Drag select of 1 pseudobonds  

> select ~sel & ##selected

37 pseudobonds, 1 model selected  

> select ~sel & ##selected

37 pseudobonds, 1 model selected  

> select clear

Drag select of 1 pseudobonds  

> color sel dodgerblue target p

> select clear

> show #!33 models

> select clear

> save NhaA-Na-pH85_vs_K-pH85_binding-site2_sil.png supersample 3
> transparentBackground true

[Repeated 1 time(s)]

> hide #!24 models

> show #!24 models

> hide #!23 models

> hide #!24 models

> show #!24 models

> hide #!24 models

> show #!24 models

> hide #!24 models

> show #!17 models

> show #!24 models

> hide #!24 models

> show /A target c

> graphics silhouettes width 2

> transparency 50 target c

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

> hide #!33 models

> show #!33 models

> hide #!17 models

> hide /A target c

> hide sel

> select clear

> show #!23 models

> show :HOH

> select #33/A:504@O

1 atom, 1 residue, 1 model selected  

> hide sel

> select clear

> ui mousemode right distance

> distance #33/A:300@NZ #33/A:506@O

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A LYS 300 NZ and HOH 506
O: 2.587Å  

> hide sel

> select clear

> color sel dark gray

> select clear

> graphics silhouettes width 2

> graphics silhouettes width 6

> color #33&core teal

> color #!33 byhetero

> save NhaA-K-pH85-binding-site_density_res2.png supersample 3
> transparentBackground true

> hide #!33 models

> show #!14 models

> hide #!14 models

> show #!13 models

> show #24 target p

> distance #13/A:163@OD2 #13/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A ASP 163 OD2
and LYS 300 NZ: 2.957Å  

> show #23.1 models

> hide ##name="chain trace"

> select clear

> color sel dark gray

> select clear

> hide #23.1 models

> save NhaA-K-pH85-state1-unplugged-binding-site_density_res.png supersample 3
> transparentBackground true

> hide #!13 models

> show #!9 models

> save NhaA-K-pH75-unplugged-binding-site_density_res.png supersample 3
> transparentBackground true

> hide #!9 models

> show #!5 models

> ~distance #24/A:505@NA #24/A:164@OD1

> ~distance #24/A:164@OD1 #24/A:132@O

> distance #5/A:132@O #5/A:164@OD2

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A THR 132 O and ASP
164 OD2: 2.705Å  

> show #23.1 models

> ~distance #33/A:300@NZ #33/A:506@O

> ~distance #24/A:506@O #24/A:300@NZ

> ~distance #13/A:163@OD2 #13/A:300@NZ

> distance #5/A:163@OD2 #5/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH63_unplugged.pdb #5/A ASP 163 OD2 and LYS
300 NZ: 3.848Å  

> show #!6 models

> volume #6 level 0.01158

> hide #!6 models

> show #1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #1 models

> show #1 models

> hide #!5 models

> show #!2 models

> view binding_site

> hide #!2 models

> show #!5 models

> hide #!5 models

> show #3 models

> hide #3 models

> show #!7 models

> hide #!7 models

> show #!11 models

> hide #!11 models

> hide #1 models

> show #!5 models

> show #!9 models

> hide #!9 models

> show #!13 models

> hide #!5 models

> distance #13/A:300@NZ #13/A:163@OD2

Distance between NhaA-nd-6F9-K_BTPpH85_state1-unplugged.pdb #13/A LYS 300 NZ
and ASP 163 OD2: 2.957Å  

> show #!9 models

> hide #!13 models

> show #!5 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!13 models

> hide #!9 models

> show #!9 models

> hide #!13 models

> hide #!9 models

> hide #23.1 models

> select clear

Drag select of 1 pseudobonds  

> select clear

Drag select of 1 pseudobonds  
[Repeated 1 time(s)]

> color sel dark gray

> select clear

> ui mousemode right translate

> view binding_site

> save NhaA-K-pH63-unplugged-binding-site_density_res.png supersample 3
> transparentBackground true

> hide #!5 models

> show #!5 models

> show /A target c

> hide /A:160-161 target c

> graphics silhouettes width 2

> transparency 50 target c

> hide #!23 models

> show #!6 models

> color #6 gainsboro

> transparency #6 50

> surface zone #6 nearAtoms #5&binding_site_res

> transparency 0 target c

> show #!9 models

> hide #!9 models

> show #!10 models

> volume #6 level 0.008222

> transparency #10 0

> volume #6 level 0.01034

> hide #!10 models

> volume #6 level 0.01

> volume #6 level 0.01035

> show #!10 models

> hide #!10 models

> volume #6 level 0.01212

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> volume #6 level 0.01018

> save NhaA-K-pH63-unplugged-binding-site_density.png supersample 3
> transparentBackground true

> hide #5 models

> hide #!6 models

> show #!9 models

> show #!10 models

> hide #!9 models

> show #!9 models

> show #!7 models

> hide #!7 models

> transparency #10 50

> save NhaA-K-pH75-unplugged-binding-site_density.png supersample 3
> transparentBackground true

> hide #!9 models

> hide #!10 models

> show #!13 models

> show #!14 models

> color #14 gainsboro

> transparency #14 50

> surface zone #14 nearAtoms #13&binding_site_res

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> save NhaA-K-pH85-state1-unplugged-binding-site_density.png supersample 3
> transparentBackground true

> show #!23 models

> show #23.1 models

> hide #!13 models

> hide #!14 models

> show #!9 models

> hide #!9 models

> show #5 models

> hide #5 models

> show #5 models

> view mono_front

> view mono_back_

> hide #!23 models

> hide #5 atoms

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

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

> color #5,9,13&core orange

> color #5,9,13&dimer khaki

> color #17&core dodger blue

> color #17&dimer light sky blue

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #5#!7 atoms

> show #3 models

> hide #3,5#!7 atoms

> show #1 models

> hide #1,3,5#!7 atoms

> show #!9 models

> show #!11 models

> show #!13 models

> show #!15 models

> show #!17 models

> hide #1,3,5#!7,9,11,13,15,17 atoms

> hide /B,C target s

> 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 skyblue bluie;col #15&dimer light blue;

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

> color #15&core deep sky blue

> color #15&dimer light blue

> hide #1 models

> hide #3 models

> hide #!7 models

> hide #!11 models

> hide #!17 models

> show /A target s

> hide /A target s

> hide /A target c

> show /A target c

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> cartoon style modeHelix default width 1.8 thickness 0.3

> cartoon style modeHelix default width 1.6 thickness 0.3

> color /A:1-10 orchid

> hide #!5 models

> hide #!9 models

> hide #!15 models

> hide #!13 models

> show #!1 models

> show #1/A:1-10 target s

> show #!29 models

> hide #!1#!29.1-2 atoms

> hidhow #1/A:1-10 tar s

Unknown command: hidhow #1/A:1-10 tar s  

> hide #1/A:1-10 target s

> hide #!29.2 models

> hide #29.1.1 models

> show #29.1.1 models

> show #29.1 target s

> hidow #29.1 tar c

Unknown command: hidow #29.1 tar c  

> hidow #29.1 tar ctra #29.1 30 tar s

Unknown command: hidow #29.1 tar ctra #29.1 30 tar s  

> transparency #29.1 30 target s

> transparency #29.1 50 target s

> view mono_back_

> lighting soft

> lighting full

> lighting shadows false

> lighting simple

> lighting full

> lighting shadows false

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

> transparency #29.1 30 target s

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

> color #29.1 medium purple

> transparency #29.1 30 target s

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

> transparency #29.1 0 target s

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

> hide #!29 models

> cartoon style #1/A:1-10 thickness 0.5

> cartoon style #1/A:1-10 thickness 0.3

> show #!29 models

> hide #29.1.1 models

> cartoon style #29.1 thickness 0.3

> cartoon style #29.1 thickness 0.5

> cartoon style #29.1 thickness 0.6

> cartoon style #29.1 thickness 0.7

> cartoon style xsection barbell

> cartoon style xsection rectangle

> cartoon style xsection oval

> cartoon style strand xsection rectangle

> cartoon style helix xsection barbell

> cartoon style #29.1 thickness 1

> open /Users/tsweng/Downloads/AF-P38264-F1-model_v4.pdb

AF-P38264-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for SRP-independent targeting protein 3
(P38264) [more info...]  
  
Chain information for AF-P38264-F1-model_v4.pdb #34  
---  
Chain | Description | UniProt  
A | SRP-independent targeting protein 3 | PHO88_YEAST 1-188  
  

> hide #!29 models

> hide #!1 models

> view

> mlp #34

Map values for surface "AF-P38264-F1-model_v4.pdb_A SES surface": minimum
-26.94, mean -2.806, maximum 22.98  
To also show corresponding color key, enter the above mlp command and add key
true  

> close #34

> show #!1 models

> view mono_back_

> select #1/A:10

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #1/A:9

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:1-10

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

> graphics selection width 8 color black

[Repeated 1 time(s)]

> view mono_back_

> select up

2891 atoms, 2954 bonds, 385 residues, 2 models selected  

> select up

2982 atoms, 3043 bonds, 387 residues, 2 models selected  

> select up

4707 atoms, 4810 bonds, 611 residues, 2 models selected  

> select down

2982 atoms, 3043 bonds, 387 residues, 2 models selected  

> select down

2891 atoms, 2954 bonds, 385 residues, 2 models selected  

> select down

63 atoms, 65 bonds, 7 residues, 2 models selected  

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

> graphics selection width 6 color black

> graphics selection width 5 color black

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

> graphics selection width 2 color lime

> select clear

> show #!29 models

> combine #1

> hide #!29 models

> hide #34 target c

> show #34/A:1-10 target c

> cartoon style #34 thickness 1

> cartoon style #34 thickness 1.5

> cartoon style #34 thickness 1.2

> show #34/A:1-11 target c

> show #34/A:1-12 target c

> hide #34/A:11-12 target c

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

> color #34 medium purple

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

> cartoon style #34 thickness 1.5

> cartoon style #34 thickness 2

> transparency #1 50 target c

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

> transparency #1 20 target c

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

> transparency #1 0 target c

> cartoon style #34 thickness 3

> cartoon style #34 thickness 2

> view mono_back_

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

> cartoon byattr bfactor #34

Expected an atoms specifier or a keyword  

> hide #!1 models

> ui tool show "Render by Attribute"

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

——— End of log from Fri Sep 6 13:13:45 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #34 models

> setattr #1 res bfactor 1 create true

Assigning bfactor attribute to 611 items  

> setattr #1 res bfactor 0 create true

Assigning bfactor attribute to 611 items  

> setattr #1/A:1-10 res bfactor 1 create true

Assigning bfactor attribute to 7 items  

> worm bfactor #1/A:1-10 min:0.3 max:3

609 residues, residue bfactor range 43.1 to 220  

> worm bfactor #1/A:1-10 min:0.15 max:3

609 residues, residue bfactor range 43.1 to 220  

> setattr #1 res thick_rad 0 create true

Assigning thick_rad attribute to 611 items  

> setattr #1/A:1-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad #1/A:1-10 min:0.15 max:3

609 residues, residue thick_rad range 0 to 1  

> worm thick_rad #1/A:1-10 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> ~worm

> show #34 models

> setattr #34 res thick_rad 0 create true

Assigning thick_rad attribute to 611 items  

> setattr #34/A:1-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> show #34/A:1-11 target c

> view list

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

> view mono_back_

> setattr #34/A:10 res thick_rad 0

Assigning thick_rad attribute to 1 item  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> hide #34 models

> show #34 models

> hide #34 models

> show #34 models

> setattr #34/A:4,10 res thick_rad 0

Assigning thick_rad attribute to 2 items  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> setattr #34/A:1-4,10 res thick_rad 0

Assigning thick_rad attribute to 2 items  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> setattr #34/A:1-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> setattr #34/A:1-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad #34 min:0.15 max:1

609 residues, residue thick_rad range 0 to 1  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> worm thick_rad #34 min:0.15 max:1.5

609 residues, residue thick_rad range 0 to 1  

> view mono_back_

> worm thick_rad #34 min:0.15 max:1.2

609 residues, residue thick_rad range 0 to 1  

> worm thick_rad #34 min:0.15 max:1.

609 residues, residue thick_rad range 0 to 1  

> hide #!1 models

> hide #34 models

> show #!5 models

> setattr #29.1/A:1-10 res thick_rad 1 create true

Assigning thick_rad attribute to 7 items  

> show #!29 models

> worm thick_rad #29.1 min:0.15 max:1.

7 residues, residue thick_rad range 1 to 1  

> worm thick_rad #29 min:0.15 max:1.

385 residues, residue thick_rad range 1 to 1  

> setattr #29 res thick_rad 0 create true

Assigning thick_rad attribute to 387 items  

> setattr #29/A:1-10 res thick_rad 1 create true

Assigning thick_rad attribute to 7 items  

> worm thick_rad #29 min:0.15 max:1.

385 residues, residue thick_rad range 0 to 1  

> combine #5

> hide #!29 models

> hide #35 target c

> show #35/A:1-10 target c

> setattr #35 res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr #35/A:1-10 res thick_rad 1 create true

Assigning thick_rad attribute to 10 items  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> show #35/A:1-11 target c

> view mono_back_

> color #35/A:1-10 medium purple

> setattr #35/A:1 res thick_rad 0 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> setattr #35/A:1 res thick_rad 0.5 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> setattr #35/A:1 res thick_rad 0.1 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> hide #5/A:1-10 target c

> setattr #35/A:1 res thick_rad 0.2 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> view mono_back_

> worm thick_rad #35 min:0.5 max:1.

612 residues, residue thick_rad range 0 to 1  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> setattr #35/A:1 res thick_rad 0.2 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> setattr #35/A:1 res thick_rad 0.1 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> setattr #35/A:1 res thick_rad 0.5 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #35 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> save test.png supersample 3 transparentBackground true

> hide #!5 models

> show #!1 models

> hide #35 models

> show #34 models

> setattr #34/A:1-4 res thick_rad 0.5 create true

Assigning thick_rad attribute to 1 item  

> worm thick_rad #34 min:0.15 max:1.

609 residues, residue thick_rad range 0 to 1  

> save test.png supersample 3 transparentBackground true

> hide #34 models

> hide #!29.1 models

> hide #!1 models

> show #!15 models

> combine #15

> hide #36 target c

> show #36/A:1-11 target c

> setattr #36 res thick_rad 0 create true

Assigning thick_rad attribute to 616 items  

> setattr #36 res thick_rad 0 create true

Assigning thick_rad attribute to 616 items  

> setattr #36/A:1 res thick_rad 0.5

Assigning thick_rad attribute to 1 item  

> setattr #36/A:2-10 res thick_rad 1

Assigning thick_rad attribute to 9 items  

> worm thick_rad #36 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> color #36/A:1-10 medium purple

> save test.png supersample 3 transparentBackground true

> hide #36 models

> hide #!15 models

> show #!17 models

> combine #17

> setattr #37 res thick_rad 0 create true

Assigning thick_rad attribute to 617 items  

> setattr #37/A:1 res thick_rad 0.5

Assigning thick_rad attribute to 1 item  

> setattr #37/A:2-10 res thick_rad 1

Assigning thick_rad attribute to 9 items  

> hide #37 target c

> show #37/A:1-11 target c

> worm thick_rad #37 min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> color #37/A:1-10 medium purple

> save test.png supersample 3 transparentBackground true

> cartoon style barScale 0.6

> cartoon style barScale 0.8

> cartoon style barScale 0.3

> cartoon style barScale 0.5

> cartoon style thickness 0.5

> cartoon style thickness 0.3

> cartoon style thickness 0.4

> cartoon style thickness 0.3

> hide #37 models

> show #!1 models

> hide #!17 models

> view mono_back_

> color #1/A:1-10 medium purple

> show #1/A:1-10 target a

> size stickRadius 0.5

Changed 104582 bond radii  

> size stickRadius 0.4

Changed 104582 bond radii  

> save test.png supersample 3 transparentBackground true

> size stickRadius 0.5

Changed 104582 bond radii  

> save test.png supersample 3 transparentBackground true

> show #34 models

> hide #34 models

> select ~sel & ##selected

Nothing selected  

> size stickRadius 0.3

Changed 104582 bond radii  

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

> show #29.1.1 models

> transparency #29.1 30 target s

> hide #29.1 30 tar c

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

> hide #29.1 target c

> size atomRadius -1

Cannot reduce atom radius to  size atomRadius -0.5

Changed 102380 atom radii  

> size atomRadius default

Changed 102380 atom radii  

> size atomRadius -0.5

Changed 102380 atom radii  

> close #29.1.1

> show #29.1 target s

> size atomRadius default

Changed 102380 atom radii  

> transparency #29.1 30 target s

> hide #29.1.1 models

> hide #!29 models

> show #!3 models

> hide #!1 models

> show #!4 models

> show #!3 atoms

> hide #!3 atoms

> show #!7 models

> hide #!7 models

> view mono_back_

> hide #!4 models

> show #!7 models

> hide #!7 models

> show #!4 models

> show #!3 atoms

> show #!8 models

> hide #!4 models

> hide #!3 models

> show #!7 models

> hide #!7 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!4 models

> hide #!8 models

> view mono_back_

> hide #!4 models

> hide #!3 atoms

> hide #3/A:1-3

> hide #3/A:1-3 target c

> combine #3

> name cwm #38

> hide ~cwm/A:1-10 tar c;setattr cwm res thick_rad 0 create 1;setattr
> cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
> thick_rad cwm min:0.15 max:1.

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

> name cwm #38

> hide ~(cwm/A:1-10) tar c;setattr cwm res thick_rad 0 create 1;setattr
> cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
> thick_rad cwm min:0.15 max:1.

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

> name cwm #38

> hide ~ (cwm/A:1-10) tar c;setattr cwm res thick_rad 0 create 1;setattr
> cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
> thick_rad cwm min:0.15 max:1.

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

> name cwm #38

> hide cwm&(~/A:1-10) target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm/A:1-4 res thick_rad 0.5;setattr cwm/A:5-10 res thick_rad 1;worm
> thick_rad cwm min:0.15 max:1.

Expected a keyword  

> setattr cwm/A:1-4 res thick_rad 0.5;

Expected a keyword  

> setattr cwm/A:1-4 res thick_rad 0.5 create 1;

Expected a keyword  

> setattr cwm/A:1-4 res thick_rad 0

Expected a keyword  

> setattr cwm res thick_rad 0

Assigning thick_rad attribute to 614 items  

> name cwm #38

> hide cwm&~/A:1-10 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.5

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> show cwm&/A:11 target c

> name cwm #38

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.2

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #38

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.3

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #38

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.5

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> view list

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

> view mono_back_

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

> name cwm #38

> color cwm&/A:1-10 premium purp tar c;hid cwm&~/A:1-11 tar c;setattr cwm res
> thick_rad 0 create 1;setattr cwm&/A:1-4 res thick_rad 0.5;setattr
> cwm&/A:5-10 res thick_rad 1;worm thick_rad cwm min:0.15 max:1.

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

> name cwm #38

> color cwm&/A:1-10 memium purp tar c;hid cwm&~/A:1-11 tar c;setattr cwm res
> thick_rad 0 create 1;setattr cwm&/A:1-4 res thick_rad 0.5;setattr
> cwm&/A:5-10 res thick_rad 1;worm thick_rad cwm min:0.15 max:1.

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

> name cwm #38

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.5

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

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

> hide #!3 models

> show #!7 models

> hide #38 models

> combine #7

> name cwm #39

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-4 res thick_rad 0.5

Assigning thick_rad attribute to 4 items  

> setattr cwm&/A:5-10 res thick_rad 1

Assigning thick_rad attribute to 6 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #39

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1 res thick_rad 0.5

Assigning thick_rad attribute to 1 item  

> setattr cwm&/A:2-10 res thick_rad 1

Assigning thick_rad attribute to 9 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #39

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-2 res thick_rad 0.5

Assigning thick_rad attribute to 2 items  

> setattr cwm&/A:3-10 res thick_rad 1

Assigning thick_rad attribute to 8 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #39

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-3 res thick_rad 0.5

Assigning thick_rad attribute to 3 items  

> setattr cwm&/A:4-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

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

> hide #39 models

> hide #!7 models

> show #!11 models

> combine #11

> name cwm #40

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 608 items  

> setattr cwm&/A:1-3 res thick_rad 0.5

Assigning thick_rad attribute to 0 items  

> setattr cwm&/A:4-10 res thick_rad 1

Assigning thick_rad attribute to 4 items  

> worm thick_rad cwm min:0.15 max:1.

606 residues, residue thick_rad range 0 to 1  

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

> hide #40 models

> hide #!11 models

> show #!9 models

> combine #9

> name cwm #41

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-3 res thick_rad 0.5

Assigning thick_rad attribute to 3 items  

> setattr cwm&/A:4-10 res thick_rad 1

Assigning thick_rad attribute to 7 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #41

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-2 res thick_rad 0.5

Assigning thick_rad attribute to 2 items  

> setattr cwm&/A:3-10 res thick_rad 1

Assigning thick_rad attribute to 8 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

> name cwm #41

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-1 res thick_rad 0.5

Assigning thick_rad attribute to 1 item  

> setattr cwm&/A:2-10 res thick_rad 1

Assigning thick_rad attribute to 9 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

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

> hide #!9 models

> show #!13 models

> hide #41 models

> combine #13

> name cwm #42

> color cwm&/A:1-10 medium purple target c

> hide cwm&~/A:1-11 target c

> setattr cwm res thick_rad 0 create true

Assigning thick_rad attribute to 614 items  

> setattr cwm&/A:1-1 res thick_rad 0.5

Assigning thick_rad attribute to 1 item  

> setattr cwm&/A:2-10 res thick_rad 1

Assigning thick_rad attribute to 9 items  

> worm thick_rad cwm min:0.15 max:1.

612 residues, residue thick_rad range 0 to 1  

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

> hide #42 models

> show #!15 models

> hide #!13 models

> show #15:NA target a

> hide #!15 models

> show #!17 models

> show #17:NA target a

> style :NA sphere

Changed 3 atom styles  

> view mono_back_

> show #37 models

> hide #37 models

> show #37 models

> transparency #17,37 100 target c

> transparency #17:NA 1 target a

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> select #17/A:505@NA

1 atom, 1 residue, 1 model selected  

> select #17/A:505@NA

1 atom, 1 residue, 1 model selected  

> select #17/A:98

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> graphics silhouettes true

> save NhaA-Na-pH85_back_worm_Na.png supersample 3 transparentBackground true

> transparency #17:NA 0 target a

> transparency #17,37 0 target c

> hide #37 models

> hide #!17 models

> show #!19 models

> view dimer_view-all_front

> show #19 target c

> hide #!19 atoms

> color #19/A,D:86-180,275-388 forest green

> color #19/A,D:11-85,181-274 pale green

> hide #19/A,D:1-10 target c

> save /Users/tsweng/Desktop/image192.png supersample 3

> save NhaA-K-pH75_consensus_front_2.png supersample 3 transparentBackground
> true

> show :CDL,PTY target a

> save NhaA-K-pH75_consensus_front_2_PTY.png supersample 3
> transparentBackground true

> hide :CDL,PTY

> show #!31 models

> hide #31 target ac

> show #31:CDL,PGT target a

> hide #31:CDL target a

> show #19:CDL target a

> save NhaA-K-pH75_consensus_front_2_PGT.png supersample 3
> transparentBackground true

> hide #!31 models

> hide #!19 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #39 models

> view N-term_density_top

> view mono_back_

> turn x 90

> ui tool show "Side View"

> select #7/A:48

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

49 atoms, 49 bonds, 6 residues, 2 models selected  

> select up

2918 atoms, 2982 bonds, 388 residues, 2 models selected  

> select clear

> save NhaA-K-pH75_plugged_top.png supersample 3 transparentBackground true

> hide #39 models

> show #41 models

> hide #!7 models

> show #!9 models

> save NhaA-K-pH75_unplugged_top.png supersample 3 transparentBackground true

> select #41/A:6

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #41/A:6

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> hide #!9 models

> show #!9 models

> hide #41 models

> color /A:1-10 medium purple target c

> show #!7 models

> hide #!7 models

> show #!5 models

> show #!13 models

> show #!15 models

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

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

> color #5&core dark orange

> color #9&core orange

> color #13&core gold

> color #13&core dark orange

> color #9&core orange

> color #5&core gold

> cartoon style modeHelix default width 1.0 thickness 0.3

> cartoon style modeHelix default width 1.8 thickness 0.3

> cartoon style modeHelix default width 1.6 thickness 0.3

> color #13 dark orange

> color #9 orange

> color #5 gold

> view mono_back_

> cartoon style modeHelix tube radius 1.8 sides 24

> color #15 deep skyblue bluie;

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

> color #15 deep sky blue

> lighting soft

> lighting full

> lighting shadows false

> lighting simple

> lighting full

> lighting shadows false

> lighting full multiShadow 1024

> lighting shadows false

> lighting full multiShadow 1024 shadows false

> cartoon style modeHelix tube radius 1.6 sides 24

> cartoon style modeHelix tube radius 1.4 sides 24

> cartoon style modeHelix default width 1.8 thickness 0.3

> cartoon style modeHelix tube radius 1.4 sides 24

> graphics silhouettes false

> graphics silhouettes true

> save NhaA-pH-superpose_back.png supersample 3 transparentBackground true

> color #5,9,13&dimer_TM snow transparency 50 target c

> color #5,9,13,15&dimer_TM snow transparency 50 target c

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 50 target c

> view list

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

> view mono_back_

> transparency 1 target c

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 50 target c

> save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c

> save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true

> transparency 0 target c

> color #5&core dark orange

> color #9&core orange

> color #13&core gold

> color #15 deep sky blue

> color #5 dark orange

> color #9 orange

> color #13 gold

> color #15 deep sky blue

> turn x 90

> turn x -5

> cartoon style modeHelix default width 1.0 thickness 0.3 xsection oval

> color #13 dark orange

> color #9 orange

> color #5 gold

> color #15 deep sky blue

> cartoon style strand xsection rectangle

> ui mousemode right zoom

> view mono_back_

> show #5/A:1-11 target c

> cartoon style modeHelix tube radius 1.4 sides 24

> save NhaA-pH-superpose_back.png supersample 3 transparentBackground true

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c

> transparency 1 target c

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c

> save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true

> transparency 100 target c

> color #5,9,13,15&(dimer&~/A:35-58) snow transparency 20 target c

> save NhaA-pH-superpose_back_tra.png supersample 3 transparentBackground true

> color #13 dark orange

> color #9 orange

> color #5 gold

> color #15 deep sky blue

> transparency 0 target c

> hide #!5 models

> hide #!9 models

> hide #!13 models

> open /Users/tsweng/Downloads/NhaA-6F9_pH85_Na_open.pdb

Chain information for NhaA-6F9_pH85_Na_open.pdb #43  
---  
Chain | Description  
A | No description available  
  

> lighting full

> lighting shadows false

> delete #43:SOL

> delete #43:BUF

> delete #43:CLA

> delete #43:POPC

> mmaker #43/A to #15/A

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_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH85_Na_open.pdb, chain A (#43), sequence alignment score = 1621.3  
RMSD between 184 pruned atom pairs is 1.220 angstroms; (across all 379 pairs:
2.698)  
  

> cartoon style modeHelix default width 1.0 thickness 0.3

> hide #!15 models

> show #!15 models

> close #43

> open /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb

Summary of feedback from opening
/Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb title:  
Protein t= 1174557.62500 step= 587278800 [more info...]  
  
Chain information for NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb #43  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb #43  
---  
ARGT — (ARGT)  
ASPT — (ASPT)  
BUF — (BUF)  
CLA — (CLA)  
GLUT — (glut)  
HSPT — (HSPT)  
LYST — (lyst)  
NA — (NA)  
POPC — (popc)  
SOD — (SOD)  
SOL — (SOL)  
  

> delete #43:POPC

> delete #43:SOL,BUF,POPC,CLA

> mmaker #43/A to #15/A

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_BTPpH85_state2.pdb, chain A (#15) with
NhaA_Fv6F9_Na_pH85_CDL_PTY_chainA.pdb, chain A (#43), sequence alignment score
= 1627.6  
RMSD between 231 pruned atom pairs is 1.276 angstroms; (across all 388 pairs:
2.521)  
  

> show #43 target a

> delete #43@H

> delete #43@H*

> open /Users/tsweng/Downloads/NhaA-6F9_pH85_Na_open.pdb

Chain information for NhaA-6F9_pH85_Na_open.pdb #44  
---  
Chain | Description  
A | No description available  
  

> open /Users/tsweng/Downloads/NhaA-6F9_pH40_Na_closed.pdb

Chain information for NhaA-6F9_pH40_Na_closed.pdb #45  
---  
Chain | Description  
A | No description available  
  

> delete #44,45:SOL,BUF,POPC,CLA

> delete #44,45@H*

> mmaker #44,45/A to #15/A

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_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH85_Na_open.pdb, chain A (#44), sequence alignment score = 1621.3  
RMSD between 184 pruned atom pairs is 1.220 angstroms; (across all 379 pairs:
2.698)  
  
Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH40_Na_closed.pdb, chain A (#45), sequence alignment score = 1632.1  
RMSD between 278 pruned atom pairs is 1.152 angstroms; (across all 379 pairs:
2.025)  
  

> hide #43 models

> hide #44 models

> show #44 models

> hide #45 models

> mmaker #44,45/A to #15&dimer_TM

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_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH85_Na_open.pdb, chain A (#44), sequence alignment score = 548  
RMSD between 84 pruned atom pairs is 1.025 angstroms; (across all 119 pairs:
1.894)  
  
Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH40_Na_closed.pdb, chain A (#45), sequence alignment score = 555.2  
RMSD between 111 pruned atom pairs is 0.935 angstroms; (across all 119 pairs:
1.258)  
  

> show #45 models

> hide #44 models

> show #!13 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #44 models

> hide #44 models

> show #44 models

> hide target a

> cartoon style modeHelix default width 1.0 thickness 0.3

> show #!15 models

> hide #!13 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #44 models

> hide #45 models

> view binding_site

> view mono_back_

> turn y 90

> show #!13 models

> show #!9 models

> show #!5 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide dimer target c

> view core_inner_side

> view name core_inner_side2

> select /A:150-174,130-144,338-350

11252 atoms, 11339 bonds, 6 pseudobonds, 1537 residues, 30 models selected  

> grs sel col black wid 6

Unknown command: grs sel col black wid 6  

> grs sel col black wid 6

Unknown command: grs sel col black wid 6  

> graphics selection color black width 6

> graphics selection color black width 5

> graphics selection color black width 4

> transparency 1 target c

> tar ~/A:150-174,130-144,338-350 30 tar c

Unknown command: tar ~/A:150-174,130-144,338-350 30 tar c  

> transparency ~/A:150-174,130-144,338-350 30 target c

> transparency 0 target c

> transparency ~/A:150-174,130-144,338-350 30 target c

> save NhaA-pH-superpose_core_inner_side.png supersample 3
> transparentBackground true

> select clear

> transparency 0 target c

> turn x 90

> view mono_back_

> turn x 90

> turn x -10

> turn x -5

> show /A target c

> turn x -5

> transparency dimer 30 target c

> transparency dimer 50 target c

> transparency dimer 70 target c

> turn x -5

> ui mousemode right translate

> select #15/A:150-174,130-144,338-350

388 atoms, 391 bonds, 53 residues, 1 model selected  

> select #15&core

1552 atoms, 1583 bonds, 1 pseudobond, 209 residues, 2 models selected  

> select clear

> save NhaA-pH-superpose_core_top.png supersample 3 transparentBackground true

> transparency 1 target c

> transparency dimer 70 target c

> save NhaA-pH-superpose_core_top2.png supersample 3 transparentBackground
> true

> transparency 0 target c

> transparency dimer 70 target c

> ui mousemode right zoom

> ui mousemode right translate

> view list

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

> view name core_top

> show /A:11,78,81,82,243,248,250,252,253,256 target a

> color #!5,9,13,15 byhetero

> select /A:11,78,81,82,243,248,250,252,253,256 tar a

Expected a keyword  

> select /A:11,78,81,82,243,248,250,252,253,256

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 30 models selected  

> select up

14979 atoms, 15284 bonds, 7 pseudobonds, 1858 residues, 47 models selected  

> select up

83928 atoms, 85754 bonds, 7 pseudobonds, 11176 residues, 47 models selected  

> select down

14979 atoms, 15284 bonds, 7 pseudobonds, 1858 residues, 47 models selected  

> select down

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected  

> select down

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected  

> select down

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected  

> select down

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected  

> select down

2668 atoms, 2523 bonds, 7 pseudobonds, 290 residues, 47 models selected  

> select clear

> select /A:11,78,81,82,243,248,250,252,253,256&sidechain

1798 atoms, 1595 bonds, 7 pseudobonds, 290 residues, 30 models selected  

> select clear

> select #15/A:11@OD2

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:11,78,81,82,243,248,250,252,253,256&sidechain

1798 atoms, 1595 bonds, 7 pseudobonds, 290 residues, 30 models selected  

> select clear

> hide #!5,9,13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256 target a

> hide #!5,9,13,15 atoms

> show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a

> transparency 30 target c

> transparency 0 target a

> transparency 1000 target a

> transparency core 70 target c

> transparency core 80 target c

> transparency core 70 target c

> save NhaA-pH-superpose_pH-sensing_top.png supersample 3
> transparentBackground true

> hide target c

> transparency 0 target a

> graphics silhouettes width 6

> hide target c

> transparency 0 target a

> graphics silhouettes width 6

> hide ##="chain trace";

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

> hide target c

> transparency 0 target a

> graphics silhouettes width 6

> hide ##name="chain trace"

> save NhaA-pH-superpose_pH-sensing_top_res.png supersample 3
> transparentBackground true

> show /A target c

> transparency 0 target a

> graphics silhouettes width 2

> 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  

> view core_top

> hide target a

> transparency 0 target c

> transparency dimer 70 target c

> save NhaA-pH-superpose_core_top2.png supersample 3 transparentBackground
> true

> transparency 0 target c

> view binding_site

> show binding_site_res&sidechain target a

> show /A:132 target a

> hide #!15 models

> hide #!9 models

> show #!9 models

> hide #!5 models

> hide #!13 models

> show #!13 models

> show #!5 models

> show #!17 models

> color #!5,9,13,17 byhetero

> hide /A:160-161 target c

> show #!23 models

> hide #23.1 models

> hide sel

> select clear

> hide sel

> color sel dark gray

> select clear

> transparency 30 target c

> hide #!23 models

> transparency 0 target a

> transparency 100 target a

> save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
> true

> transparency 0 target a

> hide target c

> hide ##name="chain trace"

> graphics silhouettes 6

Expected true or false or a keyword  

> transparency 0 target a

> hide target c

> hide ##name="chain trace"

> graphics silhouettes width 6

> show #23.1 models

> hide #23.1 models

> save NhaA-pH-superpose_binding_site_res.png supersample 3
> transparentBackground true

> hide #!17 models

> show #!15 models

> save NhaA-pH-superpose_binding_site_res.png supersample 3
> transparentBackground true

> transparency 100 target a

> show /A target c

> graphics silhouettes width 2

> hide #!15 models

> show #!15 models

> hide #!23 models

> save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
> true

> show #!33 models

> mcopy #15 toAtoms #33 settings c

> hide #!15 models

> hide /A:160-161 target c

> save NhaA-pH-superpose_binding_site.png supersample 3 transparentBackground
> true

> transparency 0 target a

> hide target c

> hide ##name="chain trace"

> graphics silhouettes width 6

> transparency 0 target a

> hide target c

> hide ##name="chain trace"

> graphics silhouettes width 6

> save NhaA-pH-superpose_binding_site_res.png supersample 3
> transparentBackground true

> show #!23 models

> hide #!23 models

> show #!23 models

> show #23 target p

> hide :HOH target a

> hide sel

> select clear

> hide sel

> select clear

> hide sel

> select clear

> hide sel

> select #33/A:300@NZ

1 atom, 1 residue, 1 model selected  

> select #33/A:300@NZ

1 atom, 1 residue, 1 model selected  

> select clear

> color sel drak gra

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

> color sel dark gray

> select clear

> select #33/A:164@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> select clear

> save NhaA-pH-superpose_binding_site_res.png supersample 3
> transparentBackground true

> hide #!23 models

> hide #!5 models

> hide #!9 models

> hide #!13 models

> show #33:HOH

> select #33/A:504@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select clear

> show #!23 models

> show #23 target p

> select clear

> select #33/A:504@O

1 atom, 1 residue, 1 model selected  

> select up

3070 atoms, 3130 bonds, 392 residues, 1 model selected  

> select down

1 atom, 1 residue, 2 models selected  

> hide sel target a

> hide sel target p

> ui mousemode right distance

> distance #33/A:506@O #33/A:300@NZ

Distance between NhaA-nd-6F9-K_BTPpH85_state2.pdb #33/A HOH 506 O and LYS 300
NZ: 2.587Å  

> select clear

> color sel dark gray

> select clear

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

> hide #!23 models

> show #!16 models

> graphics silhouettes 2

Expected true or false or a keyword  

> graphics silhouettes width 2

> show #31/A target c

> show #33/A target c

> transparency 0 target c

> transparency #33 100 target a

> transparency #33 0 target a

> transparency #33 100 target a

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

> transparency #33 0 target a

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

> show #!33 atoms

> hide #!33 atoms

> show #!13 models

> show #!9 models

> show #!5 models

> hide #!16 models

> show #!15 models

> hide #!5,9,13,15,33 atoms

> show /A target c

> 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  

> view core_top

> hide #!33 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> show /A:11,78,81,82,243,249,250,252,253,256&sidechain target a

> show #!23 models

> color sel dark gray

> select clear

> view core_top

> show #23.1 models

> hide #23.1 models

> show #23.1 models

> hide #23.1 models

> hide target c

> transparency 0 target a

> graphics silhouettes width 6

> hide ##name="chain trace"

> hide target c

> transparency 0 target a

> graphics silhouettes width 6

> hide ##name="chain trace"

> save NhaA-pH-superpose_pH-sensing_top_res2.png supersample 3
> transparentBackground true

> graphics silhouettes width 2

> show /A target c

> hide #!23 models

> hide #!5,9,13,15 atoms

> view mono_back_

> show #45 models

> hide #45 models

> show #45 models

> hide #45 models

> show #44 models

> hide #44 models

> show #44 models

> show #43 models

> hide #44 models

> show #44 models

> hide #44 models

> show #44 models

> hide #44 models

> show #44 models

> hide #44 models

> show #44 models

> show #45 models

> hide #43-45#!5,9,13,15 atoms

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

> hide #!15 models

> hide #!13 models

> hide #!9 models

> hide #!5 models

> show #!5 models

> show /A:GLUT,ASPT,HIST,LYST,ARGT target a

> show /A:GLUT,ASPT,HSPT,LYST,ARGT target a

> hide #!5 models

> show #!15 models

> show #!5 models

> hide #43 models

> hide #44 models

> hide #45 models

> show #!6 models

> hide #!6 models

> show #!20 models

> hide #!20 models

> show #!21 models

> hide #!5 models

> show #!5 models

> hide #!15 models

> lighting full

> lighting simple

> hide #!21 models

> show #!20 models

> hide #!20 models

> show #!20 models

> volume #20 level 0.007186

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> volume #20 level 0.0081

> hide #!20 models

> show #!15 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #23.1 models

> show #!5,15 atoms

> hide #!5,15 atoms

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

> view mono_back_

> show #43 models

> show #45 models

> hide #43 models

> show #43 models

> hide #45 models

> show #44 models

> hide #43 models

> hide #44 models

> show #43 models

> show #44 models

> show #45 models

> hide #43 models

> hide #44 models

> hide #45 models

> open /Users/tsweng/Downloads/NhaA-6F9_pH40_no-sodium.pdb

Chain information for NhaA-6F9_pH40_no-sodium.pdb #46  
---  
Chain | Description  
A | No description available  
  

> open /Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb

Summary of feedback from opening
/Users/tsweng/Downloads/NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb title:  
Protein t= 1193217.37500 step= 596608700 [more info...]  
  
Chain information for NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb #47  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb #47  
---  
ARGT — (ARGT)  
ASPT — (ASPT)  
BUF — (BUF)  
CL — (CL)  
CLA — (CLA)  
GLUT — (glut)  
HSPT — (HSPT)  
LYST — (lyst)  
POPC — (popc)  
SOD — (SOD)  
SOL — (SOL)  
  

> hide :POPC

> delete :SOL,CLA

> delete :SOL,CLA,BUF

> hide :SOD

> select ~sel & ##selected

Nothing selected  

> hide :CL

> mmaker #46,47/A to #15&dimer_TM

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_BTPpH85_state2.pdb, chain A (#15) with
NhaA-6F9_pH40_no-sodium.pdb, chain A (#46), sequence alignment score = 558.2  
RMSD between 108 pruned atom pairs is 0.891 angstroms; (across all 119 pairs:
1.334)  
  
Matchmaker NhaA-nd-6F9-K_BTPpH85_state2.pdb, chain A (#15) with
NhaA_Fv6F9_Na_pH40_CDL_PTY_chainA.pdb, chain A (#47), sequence alignment score
= 544.4  
RMSD between 109 pruned atom pairs is 0.990 angstroms; (across all 119 pairs:
1.303)  
  

> hide #!23 models

> show #!23 models

> hide #!15 models

> hide #!5 models

> hide #46-47 atoms

> show /A:GLUT,ASPT,HSPT,LYST,ARGT target a

> delete #46,47@H*

> show #!15 models

> show #!5 models

> hide #46 models

> hide #47 models

> hide #!5,15 cartoons

> show /A target c

> hide #!5,15 atoms

> hide #!5 models

> hide #!15 models

> show #!7 models

> show #!9 models

> hide #!7,9 atoms

> color /A:1-10 medium purple

> color #5,9,13&core orange

> color #5,9,13&dimer khaki

> color /A:1-10 medium purple

> hide #!9 models

> show #!9 models

> select #9/A:10

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #9/A:9

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #9/A:8

23 atoms, 21 bonds, 3 residues, 2 models selected  

> select clear

> select #9/A:1-10

90 atoms, 93 bonds, 10 residues, 1 model selected  

> mlp sel

Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface":
minimum -27.5, mean 0.3038, maximum 23.58  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> hide #9.1 models

> show #9.1 models

> hide #9.1 models

> show #9.1 models

> hide #9.1 models

> show #9.1 models

> hide #9.1 models

> show #41 models

> hide #41 models

> show #9.1 models

> transparency #9.1 30

> transparency #9.1 50

> transparency #9.1 30

> combine #9

> split #9 atoms /A:1-10

Split NhaA-nd-6F9-K_BTPpH75_unplugged.pdb (#9) into 2 models  
Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1 #9.1  
---  
Chain | Description  
A | No description available  
  
Chain information for NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 2 #9.2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #48 models

> show #48 models

> hide #48 models

> show #48 models

> hide #48 models

> show #48 models

> 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 #49  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #49 to #48

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 copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#48) with
NhaA-nd-6F9-K_BTPpH75_unplugged.pdb, chain A (#49), sequence alignment score =
1999.4  
RMSD between 388 pruned atom pairs is 0.000 angstroms; (across all 388 pairs:
0.000)  
  

> mcopy #13 toAtoms #49 settings hc

> hide #48 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> mcopy #13 toAtoms #49 settings v

> show #49 target c

> show #49 models

> mcopy #13 toAtoms #49 settings s

> cartoon style modeHelix default width 1.1 thickness 0.2

> cartoon style modeHelix default width 1.0 thickness 0.3

> hide #49#!7 atoms

> hide /B,C

> hide /B,C target c

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> close #9

> rename #49 #9

No name or id option specified for renaming  

> rename #49 id #9

> split #48 atoms /A:1-10

Split copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb (#48) into 2 models  
Chain information for copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1 #48.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 2 #48.2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #!48 models

> show #!48 models

> show #48.1 models

> select add #48.1

90 atoms, 93 bonds, 10 residues, 1 model selected  

> mlp sel

Map values for surface "copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1_A SES
surface": minimum -21.99, mean -0.3689, maximum 22.72  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> hide #48 target c

> transparency #48 30

> transparency #48 40

> show #9/A:2-9 target a

> hide #!48 models

> color #9#!7 byhetero

> show #!48 models

> lighting full multiShadow 1024

> lighting full multiShadow 1024 shadows false

> transparency #48 30

> transparency #48 20

> lighting simple

> lighting full multiShadow 1024 shadows false

> transparency #48 10

> transparency #48 0

> transparency #48 10

> transparency #48 20

> transparency #48 30

> hide #!48 models

> select #9/A:9

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show #!48 models

> hide #!48 models

> select #9/A:1-10

90 atoms, 93 bonds, 10 residues, 1 model selected  

> show #!48 models

> select clear

> select #9/A:1-10

90 atoms, 93 bonds, 10 residues, 1 model selected  

> select clear

> transparency #48 30

> transparency #48 50

> select #9/A:1-10

90 atoms, 93 bonds, 10 residues, 1 model selected  

> transparency #48 50

> transparency #48 80

> hide #!7 models

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> show #!7 models

> select up

2918 atoms, 2982 bonds, 388 residues, 1 model selected  

> select up

3012 atoms, 3074 bonds, 390 residues, 1 model selected  

> select down

2918 atoms, 2982 bonds, 388 residues, 1 model selected  

> select down

90 atoms, 93 bonds, 10 residues, 1 model selected  

> show /A:1-10 target a

> hide #48 target a

> show #7/A:1-10,78,81,82,252,253,256 target a

> ui mousemode right zoom

> ui mousemode right translate

> view name plug_side

> hide sel atoms

> select clear

> hide #!7 models

> show /A:2-9 target a

> hide #48 target a

> save test.png supersample 3 transparentBackground true

> hide #9 models

> transparency #48 0

> save test2.png supersample 3 transparentBackground true

> hide #!48 models

> show #!48 models

> transparency #48 80

> show #9 models

> select #9/A:1-10

90 atoms, 93 bonds, 10 residues, 1 model selected  

> save test.png supersample 3 transparentBackground true

> select clear

> hide #9 models

> hide #!48 models

> show #!5 models

> hide #!5 models

> show #!7 models

> transparency #7&core 0 target c

> transparency #7&core 100 target c

> transparency #7&core 80 target c

> transparency #7&core 100 target c

> transparency #7&dimer 1 target c

> transparency #7 0 target c

> 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 #!7 atoms

> show #9 models

> hide #9#!7 atoms

> show #39 models

> show #41 models

> hide #9,39,41#!7 atoms

> hide #41 models

> hide #39 models

> cartoon style modeHelix tube radius 1.4 sides 24

> color #9 orange

> color #7 indianred

> color /A:1-10 medium purple

> select #7,9/A:1-10

180 atoms, 186 bonds, 20 residues, 2 models selected  

> color #9 orange

> color #7 indianred

> graphics selection color medium purple

> graphics selection color medium purple width 6

> graphics selection color medium purple width 8

> graphics selection color medium purple width 6

> graphics selection color medium purple width 4

> graphics selection color black width 4

> graphics selection color black width 8

> select clear

> save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true

> select #7,9/A:1-10

180 atoms, 186 bonds, 20 residues, 2 models selected  

> select up

188 atoms, 194 bonds, 21 residues, 3 models selected  

> select down

180 atoms, 186 bonds, 20 residues, 3 models selected  

> save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true

> graphics selection color black width 6

> graphics selection color black width 4

> save NhaA-pH75-plug-superpose.png supersample 3 transparentBackground true

> transparency 80 target c

> transparency sel 1 target c

> select clear

> save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
> true

> transparency 50 target c

> transparency #7,9/A:1-10 1 target c

> save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
> true

> transparency 30 target c

> transparency #7,9/A:1-10 1 target c

> save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
> true

> select #7,9/A:1-10

180 atoms, 186 bonds, 20 residues, 2 models selected  

> select #9/A:1-10|#7/A:1-7,9

163 atoms, 167 bonds, 18 residues, 2 models selected  

> select #9/A:1-10|#7/A:1-6,8-9

163 atoms, 167 bonds, 18 residues, 2 models selected  

> select clear

> color ~#7,9/A:1-10 snow

> save NhaA-pH75-plug-superpose_tra.png supersample 3 transparentBackground
> true

> select #9/A:1-10|#7/A:1-6,8-9

163 atoms, 167 bonds, 18 residues, 2 models selected  

> select clear

> color #9 orange

> color #7 indianred

> transparency 0 target c

> cartoon style modeHelix default width 1.0 thickness 0.3

> turn y -90

> hide core target c

> hide #9 models

> hide #!7 models

> show #9 models

> color #7,9/A:1-10 medium purple

> show #!48 models

> select add #48

4737 atoms, 4840 bonds, 614 residues, 3 models selected  

> mlp sel & #!48.1

Map values for surface "copy of NhaA-nd-6F9-K_BTPpH75_unplugged.pdb 1_A SES
surface": minimum -21.99, mean -0.3689, maximum 22.72  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> hide #!48.1 models

> show #!48.1 models

> hide #!48 models

> show #!48 models

> hide #9 models

> hide #!48 models

> show #!7 models

> show #7/A:1-10,78,81,82,252,253,256 target a

> color #!7 byhetero

> show #9 models

> show #9/A:2-9 target a

> color #9#!7 byhetero

> view mono_back_

> turn y -90

> show #!48 models

> hide #!48 models

> hide #!48.1 models

> show #!48.1 models

> hide #!48 models

> show /A target c

> view mono_back_

> turn x 50

> lighting simple

> show #39 models

> hide #39 models

> show #39 models

> hide #39 models

> show #!26 models

> hide #!26.1 models

> show #!26.1 models

> hide #!26.1 models

> hide #!26.2 models

> select add #26.2.1

2828 atoms, 378 residues, 1 model selected  

> select subtract #26.2.1

1 model selected  

> select add #26.2

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

> mlp #9#!7

Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_A SES surface":
minimum -27.5, mean 0.3038, maximum 23.58  
Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_B SES surface":
minimum -24.66, mean -5.522, maximum 22.07  
Map values for surface "NhaA-nd-6F9-K_BTPpH75_unplugged.pdb_C SES surface":
minimum -26.11, mean -5.396, maximum 23.67  
Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_A SES surface":
minimum -27.56, mean 0.1673, maximum 23.61  
Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_B SES surface":
minimum -26.83, mean -5.72, maximum 22.56  
Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged.pdb_C SES surface":
minimum -25.35, mean -5.769, maximum 23.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> select subtract #26.2

1 model selected  

> hide #26.2.1 models

> show #26.2.1 models

> hide #!26 models

> show #!26 models

> hide #7,9 target s

> select add #26

3011 atoms, 3072 bonds, 390 residues, 3 models selected  

> mlp sel & #!26.2

Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface":
minimum -27.17, mean 0.3244, maximum 23.52  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #26

3011 atoms, 3072 bonds, 390 residues, 7 models selected  

> select subtract #26

2 models selected  

> hide #!26.2 models

> show #!26.2 models

> hide /B,C target s

> hide #26 target a

> hide #!26 models

> hide #!9 models

> hide #7/A:1-10

> show #7/A:4-9

> hide #23.1 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

> select #26.2/A:81@CG

1 atom, 1 residue, 1 model selected  

> select #26.2/A:82@OE1

1 atom, 1 residue, 1 model selected  

> select add #26.2/A:81@CG

2 atoms, 2 residues, 2 models selected  

> select add #26.2/A:81@NE

3 atoms, 2 residues, 2 models selected  

> select add #26.2/A:81@NH2

4 atoms, 2 residues, 2 models selected  

> select add #26.2/A:81@NH1

5 atoms, 2 residues, 2 models selected  

> select add #26.2/A:252@CB

6 atoms, 3 residues, 2 models selected  

> select add #26.2/A:253@CB

7 atoms, 4 residues, 2 models selected  

> select add #26.2/A:249@O

8 atoms, 5 residues, 2 models selected  

> select add #26.2/A:253@CA

9 atoms, 5 residues, 2 models selected  

> select clear

> hide #!7 models

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18801 of
299176 triangles, cap far, 2104 of 9688 triangles, cap near, 285 of 2384
triangles, 39 residues  

> select subtract #26.2/A:258@CZ2

290 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CH2

289 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CZ3

288 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@NE1

287 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CD2

286 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CD1

285 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CE2

284 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CE3

283 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CG

282 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@CA

281 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:257@CG

280 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:257@CB

279 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:257@O

278 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:258@N

277 atoms, 39 residues, 4 models selected  

> select subtract #26.2/A:257@C

276 atoms, 39 residues, 4 models selected  

> select add #26.2/A:142@CB

277 atoms, 40 residues, 4 models selected  

> select subtract #26.2/A:12@CB

276 atoms, 40 residues, 4 models selected  

> select subtract #26.2/A:12@C

275 atoms, 40 residues, 4 models selected  

> show #!7 models

> select subtract #26.2/A:257@CD

274 atoms, 40 residues, 4 models selected  

> select add #26.2/A:257@CD

275 atoms, 40 residues, 4 models selected  

> select add #26.2/A:253@O

276 atoms, 41 residues, 4 models selected  

> select add #26.2/A:253@CD2

277 atoms, 41 residues, 4 models selected  

> select add #26.2/A:253@NE2

278 atoms, 41 residues, 4 models selected  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 8 of
299176 triangles  

> hide #!7 models

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18787 of
299176 triangles, cap far, 2367 of 10109 triangles, cap near, 58 of 2444
triangles, 42 residues  

> select subtract #26.2/A:255@CD2

312 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:255@CD1

311 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:255@CG

310 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:70@CA

309 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:70@N

308 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:70@CG2

307 atoms, 42 residues, 4 models selected  

> select add #26.2/A:70@CG2

308 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:70@CG2

307 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:70@CG1

306 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:263@CD1

305 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:263@CG1

304 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CB

303 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CD1

302 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:255@CA

301 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@NE1

300 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CG

299 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CZ3

298 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CE3

297 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CD2

296 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CE2

295 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CH2

294 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CZ2

293 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@CA

292 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:257@O

291 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:257@C

290 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:258@N

289 atoms, 42 residues, 4 models selected  

> show #!7 models

> select subtract #26.2/A:265@CB

288 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:265@CG

287 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:265@O

286 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:265@C

285 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:136@CE2

284 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:136@CZ

283 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:136@CE1

282 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:136@CD1

281 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@CG2

280 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@CA

279 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@O

278 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:15@CA

277 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:139@CA

276 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:15@C

275 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@CG1

274 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@CD1

273 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:13@O

272 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:16@CB

271 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:13@CA

270 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:13@CB

269 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:12@CB

268 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:13@N

267 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:12@N

266 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:12@C

265 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:13@OG

264 atoms, 42 residues, 4 models selected  

> select add #26.2/A:139@CA

265 atoms, 42 residues, 4 models selected  

> select add #26.2/A:15@CA

266 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:151@CB

265 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:158@CB

264 atoms, 42 residues, 4 models selected  

> select subtract #26.2/A:154@CG2

263 atoms, 42 residues, 4 models selected  

> select add #26.2/A:82@OE1

264 atoms, 43 residues, 4 models selected  

> select add #26.2/A:82@CD

265 atoms, 43 residues, 4 models selected  

> select add #26.2/A:81@CG

266 atoms, 44 residues, 4 models selected  

> select add #26.2/A:81@CB

267 atoms, 44 residues, 4 models selected  

> select add #26.2/A:82@CG

268 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:81@CD

269 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:81@NH1

270 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:81@NH2

271 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:81@NE

272 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:81@CZ

273 atoms, 1 pseudobond, 44 residues, 5 models selected  

> select add #26.2/A:249@O

274 atoms, 1 pseudobond, 45 residues, 5 models selected  

> select subtract #26.2/A:151@CA

273 atoms, 1 pseudobond, 45 residues, 5 models selected  

> select subtract #26.2/A:151@N

272 atoms, 1 pseudobond, 45 residues, 5 models selected  

> select subtract #26.2/A:150@N

271 atoms, 1 pseudobond, 45 residues, 5 models selected  

> select add #26.2/A:142@CB

272 atoms, 1 pseudobond, 46 residues, 5 models selected  

> select add #26.2/A:142@CA

273 atoms, 1 pseudobond, 46 residues, 5 models selected  

> select add #26.2/A:154@CG2

274 atoms, 1 pseudobond, 46 residues, 5 models selected  

> select subtract #26.2/A:154@CG2

273 atoms, 1 pseudobond, 46 residues, 5 models selected  

> select add #26.2/A:154@CG2

274 atoms, 1 pseudobond, 46 residues, 5 models selected  

> select add #26.2/A:82@OE2

275 atoms, 1 pseudobond, 46 residues, 5 models selected  

> name sel pH-75-plugged-entrance

"sel" is reserved and cannot be redefined  

> name pH-75-plugged-entrance sel

> select clear

> hide #26 target s

> name list

binding_site_res /A:132,133,163,164,300,NA,HOH  
core /A:86-180,275-388  
cwm #42  
dimer /A:1-85,181-274  
dimer_TM /A:11-30,59-85,181-199,205-218,223-236,247-271  
pH-75-plugged-entrance sel  
pH-sensing /A:11,78,81,82,243,249,250,252,253,256  

> show pH-75-plugged-entrance target s

> hide #26 target c

> show #26.1/A target s

> select add #26

3011 atoms, 3072 bonds, 390 residues, 5 models selected  

> mlp sel & #!26.2

Map values for surface "NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface":
minimum -27.17, mean 0.3244, maximum 23.52  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> hide #!7 models

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 16068 of
299176 triangles, cap far, 1824 of 10660 triangles  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 19002 of
299176 triangles, cap far, 1748 of 10880 triangles, cap near, 229 of 3002
triangles  

> select #26.2/A:153@NZ

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 22916 of
299176 triangles, cap far, 1943 of 10880 triangles, cap near, 267 of 3002
triangles  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 1491 of
299176 triangles, cap far, 239 of 10832 triangles  

> select clear

> show #26.1 target c

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 14598 of
299176 triangles, cap far, 1196 of 10832 triangles  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 2963 of
299176 triangles, cap far, 319 of 10832 triangles  

> select clear

> select #26.2/A:134@CG2

1 atom, 1 residue, 1 model selected  

> select #26.2/A:134@CB

1 atom, 1 residue, 1 model selected  

> select #26.2/A:135@CA

1 atom, 1 residue, 1 model selected  

> select #26.2/A:134@CG2

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 6962 of
299176 triangles, cap far, 754 of 11866 triangles  

> select clear

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 32887 of
299176 triangles  

> select clear

> select #26.2/A:256@ND1

1 atom, 1 residue, 1 model selected  

> select add #26.2/A:256@CE1

2 atoms, 1 residue, 2 models selected  

> select add #26.2/A:78@OE2

3 atoms, 2 residues, 2 models selected  

> select clear

> select #26.2/A:256@CE1

1 atom, 1 residue, 1 model selected  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 23532 of
299176 triangles  

> select clear

> select #26.2/A:256@ND1

1 atom, 1 residue, 1 model selected  

> select add #26.2/A:256@CE1

2 atoms, 1 residue, 2 models selected  

> select add #26.2/A:260@CB

3 atoms, 2 residues, 2 models selected  

> select add #26.2/A:256@O

4 atoms, 2 residues, 2 models selected  

> select add #26.2/A:256@CB

5 atoms, 2 residues, 2 models selected  

> select add #26.2/A:256@CD2

6 atoms, 2 residues, 2 models selected  

> select add #26.2/A:256@CG

7 atoms, 2 residues, 2 models selected  

> select add #26.2/A:256@NE2

8 atoms, 2 residues, 2 models selected  

> select add #26.2/A:78@OE2

9 atoms, 3 residues, 2 models selected  

> select add #26.2/A:78@CD

10 atoms, 3 residues, 2 models selected  

> select add #26.2/A:157@SD

11 atoms, 4 residues, 2 models selected  

> select add #26.2/A:157@CB

12 atoms, 4 residues, 2 models selected  

> select add #26.2/A:138@CD1

13 atoms, 5 residues, 2 models selected  

> select add #26.2/A:157@CG

14 atoms, 5 residues, 2 models selected  

> select add #26.2/A:161@CD1

15 atoms, 6 residues, 2 models selected  

> select add #26.2/A:78@CB

16 atoms, 6 residues, 2 models selected  

> select add #26.2/A:78@CG

17 atoms, 6 residues, 2 models selected  

> select add #26.2/A:75@CA

18 atoms, 7 residues, 2 models selected  

> select add #26.2/A:75@N

19 atoms, 7 residues, 2 models selected  

> select add #26.2/A:74@C

20 atoms, 8 residues, 2 models selected  

> select add #26.2/A:74@CG

21 atoms, 8 residues, 2 models selected  

> select add #26.2/A:74@CB

22 atoms, 8 residues, 2 models selected  

> select add #26.2/A:75@CG2

23 atoms, 8 residues, 2 models selected  

> select subtract #26.2/A:75@CG2

22 atoms, 8 residues, 2 models selected  

> select add #26.2/A:75@CG2

23 atoms, 8 residues, 2 models selected  

> select add #26.2/A:71@CE1

24 atoms, 9 residues, 2 models selected  

> select add #26.2/A:71@CZ

25 atoms, 9 residues, 2 models selected  

> select add #26.2/A:134@CD1

26 atoms, 10 residues, 2 models selected  

> select add #26.2/A:161@CG1

27 atoms, 10 residues, 2 models selected  

> select add #26.2/A:134@CG2

28 atoms, 10 residues, 2 models selected  

> select add #26.2/A:134@CB

29 atoms, 10 residues, 2 models selected  

> select add #26.2/A:135@CA

30 atoms, 11 residues, 2 models selected  

> select add #26.2/A:135@N

31 atoms, 11 residues, 2 models selected  

> select add #26.2/A:134@O

32 atoms, 11 residues, 2 models selected  

> select add #26.2/A:135@CB

33 atoms, 11 residues, 2 models selected  

> select add #26.2/A:264@CD1

34 atoms, 12 residues, 2 models selected  

> select add #26.2/A:259@CG1

35 atoms, 13 residues, 2 models selected  

> select add #26.2/A:74@CD2

36 atoms, 13 residues, 2 models selected  

> select add #26.2/A:259@CB

37 atoms, 13 residues, 2 models selected  

> select add #26.2/A:256@CA

38 atoms, 13 residues, 2 models selected  

> select add #26.2/A:260@CA

39 atoms, 13 residues, 2 models selected  

> select add #26.2/A:260@N

40 atoms, 13 residues, 2 models selected  

> select add #26.2/A:135@O

41 atoms, 13 residues, 2 models selected  

> select add #26.2/A:139@N

42 atoms, 14 residues, 2 models selected  

> select add #26.2/A:14@C

43 atoms, 15 residues, 2 models selected  

> select add #26.2/A:14@CA

44 atoms, 15 residues, 2 models selected  

> select add #26.2/A:18@CD1

45 atoms, 16 residues, 2 models selected  

> select add #26.2/A:264@CB

46 atoms, 16 residues, 2 models selected  

> select add #26.2/A:18@CB

47 atoms, 16 residues, 2 models selected  

> select add #26.2/A:18@CD2

48 atoms, 16 residues, 2 models selected  

> select add #26.2/A:18@CG

49 atoms, 16 residues, 2 models selected  

> select add #26.2/A:14@O

50 atoms, 16 residues, 2 models selected  

> select add #26.2/A:265@CD

51 atoms, 17 residues, 2 models selected  

> select add #26.2/A:260@O

52 atoms, 17 residues, 2 models selected  

> select add #26.2/A:265@CG

53 atoms, 17 residues, 2 models selected  

> select add #26.2/A:138@CB

54 atoms, 17 residues, 2 models selected  

> select add #26.2/A:15@N

55 atoms, 18 residues, 2 models selected  

> select add #26.2/A:139@CA

56 atoms, 18 residues, 2 models selected  

> select add #26.2/A:15@CA

57 atoms, 18 residues, 2 models selected  

> select add #26.2/A:138@C

58 atoms, 18 residues, 2 models selected  

> select add #26.2/A:138@O

59 atoms, 18 residues, 2 models selected  

> select add #26.2/A:142@CB

60 atoms, 19 residues, 2 models selected  

> select add #26.2/A:11@CA

61 atoms, 20 residues, 2 models selected  

> select add #26.2/A:11@O

62 atoms, 20 residues, 2 models selected  

> select add #26.2/A:11@C

63 atoms, 20 residues, 2 models selected  

> select add #26.2/A:11@N

64 atoms, 20 residues, 2 models selected  

> select add #26.2/A:11@OD2

65 atoms, 20 residues, 2 models selected  

> select add #26.2/A:14@N

66 atoms, 20 residues, 2 models selected  

> select add #26.2/A:13@OG

67 atoms, 21 residues, 2 models selected  

> select add #26.2/A:11@CG

68 atoms, 21 residues, 2 models selected  

> select add #26.2/A:11@CB

69 atoms, 21 residues, 2 models selected  

> select add #26.2/A:261@CZ

70 atoms, 22 residues, 2 models selected  

> select add #26.2/A:261@CE1

71 atoms, 22 residues, 2 models selected  

> select add #26.2/A:261@OH

72 atoms, 22 residues, 2 models selected  

> select subtract #26.2/A:261@CE1

71 atoms, 22 residues, 2 models selected  

> show #!7 models

> hide #!7 models

> select add #26.2/A:257@CD

72 atoms, 23 residues, 2 models selected  

> select add #26.2/A:257@N

73 atoms, 23 residues, 2 models selected  

> select add #26.2/A:256@C

74 atoms, 23 residues, 2 models selected  

> select add #26.2/A:257@CA

75 atoms, 23 residues, 2 models selected  

> select add #26.2/A:261@CE2

76 atoms, 23 residues, 2 models selected  

> select add #26.2/A:257@CB

77 atoms, 23 residues, 2 models selected  

> select add #26.2/A:257@CG

78 atoms, 23 residues, 2 models selected  

> select add #26.2/A:261@CE1

79 atoms, 23 residues, 2 models selected  

> select add #26.2/A:253@NE2

80 atoms, 24 residues, 2 models selected  

> select add #26.2/A:253@O

81 atoms, 24 residues, 2 models selected  

> select add #26.2/A:253@CD2

82 atoms, 24 residues, 2 models selected  

> select add #26.2/A:252@CG

83 atoms, 25 residues, 2 models selected  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 41 of
299176 triangles  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 12439 of
299176 triangles  

> select clear

> ui mousemode right select

> ui mousemode right translate

> hide #26.2.1 models

> show #26.2 target c

> show #26.2.1 models

Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 27437 of
299176 triangles, 71 residues  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 24490 of
299176 triangles, 45 residues  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 4712 of
299176 triangles, 13 residues  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 2203 of
299176 triangles, 14 residues  

> select add #26.2/A:71@CE1

708 atoms, 96 residues, 2 models selected  

> select add #26.2/A:75@CG2

709 atoms, 97 residues, 2 models selected  

> select add #26.2/A:264@CD1

710 atoms, 98 residues, 2 models selected  

> select add #26.2/A:71@CZ

711 atoms, 98 residues, 2 models selected  

> select add #26.2/A:18@CD1

712 atoms, 99 residues, 2 models selected  

> select add #26.2/A:264@CB

713 atoms, 99 residues, 2 models selected  

> select add #26.2/A:18@CB

714 atoms, 99 residues, 2 models selected  

> select add #26.2/A:18@CD2

715 atoms, 99 residues, 2 models selected  

> select add #26.2/A:18@CG

716 atoms, 99 residues, 2 models selected  

> select add #26.2/A:11@OD2

717 atoms, 100 residues, 2 models selected  

> select add #26.2/A:11@OD1

718 atoms, 100 residues, 2 models selected  

> select add #26.2/A:11@CB

719 atoms, 100 residues, 2 models selected  

> select add #26.2/A:11@CG

720 atoms, 100 residues, 2 models selected  

> select add #26.2/A:11@N

721 atoms, 100 residues, 2 models selected  

> select add #26.2/A:11@CA

722 atoms, 100 residues, 2 models selected  

> select add #26.2/A:142@CB

723 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:363@CD2

722 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:363@CA

721 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:339@CE2

720 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:339@CD2

719 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:339@CZ

718 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:136@CZ

717 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:136@CE2

716 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:339@CE1

715 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:339@CB

714 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:136@CE1

713 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:136@CD1

712 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:139@CA

711 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CA

710 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CG2

709 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@O

708 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CG1

707 atoms, 101 residues, 2 models selected  

> select add #26.2/A:16@CG1

708 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CG1

707 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:15@CA

706 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:139@C

705 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:15@C

704 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CD1

703 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:12@CB

702 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:13@CA

701 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:13@O

700 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:16@CB

699 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:265@O

698 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:265@CB

697 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:265@C

696 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:261@O

695 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:265@CG

694 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:261@CB

693 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:261@CA

692 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:261@C

691 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CB

690 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@NE1

689 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CZ2

688 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CH2

687 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CZ3

686 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CD2

685 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CE3

684 atoms, 101 residues, 2 models selected  

> select add #26.2/A:258@CD2

685 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CG

684 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CE2

683 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CD2

682 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CD1

681 atoms, 101 residues, 2 models selected  

> select subtract #26.2/A:258@CA

680 atoms, 101 residues, 2 models selected  

> show #!7 models

> select add #26.2/A:252@OE2

681 atoms, 102 residues, 2 models selected  

> select add #26.2/A:252@CG

682 atoms, 102 residues, 2 models selected  

> select add #26.2/A:252@CD

683 atoms, 102 residues, 2 models selected  

> select add #26.2/A:81@CD

684 atoms, 103 residues, 2 models selected  

> select add #26.2/A:81@NH2

685 atoms, 103 residues, 2 models selected  

> select add #26.2/A:81@NE

686 atoms, 103 residues, 2 models selected  

> select add #26.2/A:81@NH1

687 atoms, 103 residues, 2 models selected  

> select add #26.2/A:81@CZ

688 atoms, 103 residues, 2 models selected  

> select add #26.2/A:249@O

689 atoms, 104 residues, 2 models selected  

> select add #26.2/A:252@CB

690 atoms, 104 residues, 2 models selected  

> select add #26.2/A:253@CA

691 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@N

692 atoms, 105 residues, 2 models selected  

> select add #26.2/A:252@C

693 atoms, 105 residues, 2 models selected  

> select add #26.2/A:252@O

694 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@O

695 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@NE2

696 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@CD2

697 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@CE1

698 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@CB

699 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@ND1

700 atoms, 105 residues, 2 models selected  

> select add #26.2/A:253@CG

701 atoms, 105 residues, 2 models selected  

> select add #26.2/A:81@CG

702 atoms, 105 residues, 2 models selected  

> select add #26.2/A:82@OE1

703 atoms, 106 residues, 2 models selected  

> select add #26.2/A:81@CB

704 atoms, 106 residues, 2 models selected  

> select add #26.2/A:82@CD

705 atoms, 106 residues, 2 models selected  

> select add #26.2/A:82@CG

706 atoms, 1 pseudobond, 106 residues, 3 models selected  

> select add #26.2/A:154@CG2

707 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:82@OE2

708 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:154@CA

709 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:154@CD1

710 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:154@CG1

711 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:154@N

712 atoms, 1 pseudobond, 107 residues, 3 models selected  

> select add #26.2/A:150@CD1

713 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:150@CD2

714 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:150@CB

715 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:150@CG

716 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:150@CA

717 atoms, 1 pseudobond, 108 residues, 3 models selected  

> hide #26.2&~sel target s

> show #26.2&~sel target s

> select add #26.2/A:139@CA

718 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:15@CA

719 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:265@CG

720 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:11@O

721 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:11@C

722 atoms, 1 pseudobond, 108 residues, 3 models selected  

> select add #26.2/A:267@CE1

723 atoms, 1 pseudobond, 109 residues, 3 models selected  

> select add #26.2/A:68@SD

724 atoms, 1 pseudobond, 110 residues, 3 models selected  

> select add #26.2/A:267@CZ

725 atoms, 1 pseudobond, 110 residues, 3 models selected  

> select add #26.2/A:267@CD1

726 atoms, 1 pseudobond, 110 residues, 3 models selected  

> select add #26.2/A:264@CD2

727 atoms, 1 pseudobond, 110 residues, 3 models selected  

> select add #26.2/A:68@CE

728 atoms, 1 pseudobond, 110 residues, 3 models selected  

> select add #26.2/A:71@CE2

729 atoms, 1 pseudobond, 110 residues, 3 models selected  
Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 8669 of
299176 triangles, 20 residues  

> hide #26.2&~sel target s

> select subtract #26.2/A:113@CB

736 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:113@O

735 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:113@C

734 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:113@CD2

733 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:113@CD1

732 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CD1

731 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CG

730 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@NE1

729 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CZ2

728 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CH2

727 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CZ3

726 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CD2

725 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CE3

724 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CE2

723 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:126@CB

722 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:161@CD1

721 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:157@CE

720 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select subtract #26.2/A:82@CG

719 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select add #26.2/A:82@CG

720 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select add #26.2/A:157@CE

721 atoms, 1 pseudobond, 112 residues, 5 models selected  

> select add #26.2/A:161@CD1

722 atoms, 1 pseudobond, 112 residues, 5 models selected  

> show #26.2&~sel target s

> select add #26.2/A:74@CD2

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

> select add #26.2/A:74@CB

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

> select add #26.2/A:74@CG

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

> select add #26.2/A:75@N

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

> select add #26.2/A:75@CA

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

> 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

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