id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15919 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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, 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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) [deleted to fit within ticket limits] > select add #26.2/A:74@C 728 atoms, 1 pseudobond, 113 residues, 5 models selected > select clear > view list Named views: N-term_density_top, binding_site, core_inner_side, core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing, plug_side > view mono_back_ > hide #!26 models > select ~sel & ##selected Nothing selected > turn x 50 > turn x 5 > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #23.1 models > ui mousemode right distance > distance #7/A:81@NH1 #7/A:252@OE1 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A ARG 81 NH1 and GLU 252 OE1: 3.594Å > distance #7/A:81@NH1 #7/A:252@OE1 Distance already exists; modify distance properties with 'distance style' > ~distance #7/A:81@NH1 #7/A:252@OE1 > ui mousemode right translate > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > transparency #26 30 target s > transparency #26 80 target s > hide #!26 models > show #!26 models > select #7 4736 atoms, 4840 bonds, 2 pseudobonds, 614 residues, 2 models selected > select clear > hide #26 target c > transparency ##name=""cap near"" 100 > clip front 0.4 position ##26.1/A:253; Invalid ""position"" argument: Expected 3 floats or object specifier > clip front 0.4 position #26.1/A:253; Invalid ""position"" argument: Center argument no objects specified > clip front 0.4 position #26.2/A:253 > clip front 1 position #26.2/A:253 > clip front 5 position #26.2/A:253 > clip front -5 position #26.2/A:253 > clip front -4 position #26.2/A:253 > clip front -2 position #26.2/A:253 > clip front -3 position #26.2/A:253 > clip front -4 position #26.2/A:253 > select #26.2.1.1 1 model selected > ~clip > save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true > select #26.2.1.1 1 model selected > transparency sel 100 > select clear > save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true > hide #!7 models > transparency #26.2 0 > select #26.2.1.1 1 model selected > select clear > save NhaA-pH75-plugged-top_surf.png supersample 3 transparentBackground true > transparency #26.2 80 target s > select #26.2.1.1 1 model selected > transparency sel 100 > select clear > show #!7 models > hide #!23 models > save NhaA-pH75-plugged-top.png supersample 3 transparentBackground true > show #!23 models > hide #23.1 models > hide #!26 models > hide #7 target c > hide #!7 atoms > show #7/A:4-9,78,81,82,252,253,256&sidechain target a > hide ##name=""chain trace"" > graphics silhouettes width 6 > graphics selection color lime > color sel dark gray target p > select clear > save NhaA-pH75-plugged-top_res.png supersample 3 transparentBackground true > color #1,3,7,11&core indian red > color #1,3,7,11&dimer pink > color /A:1-10 medium purple > color #!7 byhetero > save NhaA-pH75-plugged-top2_res.png supersample 3 transparentBackground true > show #7/A target c > graphics silhouettes width 2 > show #!26 models > hide #!23 models > save NhaA-pH75-plugged-top2.png supersample 3 transparentBackground true > hide #!26 models > transparency 30 target c > save NhaA-pH75-plugged-top2_ribbon.png supersample 3 transparentBackground > true > transparency 0 target c > show #!26 models > hide #!7 models > show #26.2 target c Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18174 of 299176 triangles, cap near, 427 of 2861 triangles, cap far, 2100 of 9790 triangles, 43 residues > select clear > view list Named views: N-term_density_top, binding_site, core_inner_side, core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing, plug_side > view name plug_top Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 14417 of 299176 triangles, cap near, 149 of 2861 triangles, cap far, 1561 of 9790 triangles, 26 residues > select clear Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 9886 of 299176 triangles, cap near, 76 of 2861 triangles, cap far, 1005 of 9790 triangles, 15 residues > transparency #26.2 0tar s Missing or invalid ""percent"" argument: Expected a number > transparency #26.2 0 target s > select clear > view list Named views: N-term_density_top, binding_site, core_inner_side, core_inner_side2, core_top, cutaway, dimer_interface, dimer_interface2, dimer_interface_top, dimer_interface_top2, dimer_view-all_front, mono_back, mono_back_, mono_front, pH-sensing, plug_side, plug_top > view plug_top Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18824 of 299176 triangles, cap near, 374 of 2861 triangles, cap far, 2165 of 9790 triangles, 42 residues > select clear Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 24350 of 299176 triangles, cap far, 2652 of 9790 triangles, 53 residues > select #26.2/A:258@NE1 1 atom, 1 residue, 1 model selected Drag select of NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface, 18302 of 299176 triangles, cap far, 2010 of 9790 triangles, 40 residues > select add #26.2/A:370@CG1 296 atoms, 41 residues, 3 models selected > select subtract #26.2/A:370@CG1 295 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CD2 294 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CD1 293 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CB 292 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@O 291 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CA 290 atoms, 40 residues, 3 models selected > select add #26.2/A:143@O 291 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@O 290 atoms, 40 residues, 3 models selected > select add #26.2/A:143@CB 291 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CB 290 atoms, 40 residues, 3 models selected > select add #26.2/A:143@O 291 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@O 290 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@C 289 atoms, 40 residues, 3 models selected > select subtract #26.2/A:136@CZ 288 atoms, 40 residues, 3 models selected > select add #26.2/A:143@CD2 289 atoms, 40 residues, 3 models selected > select subtract #26.2/A:143@CD2 288 atoms, 40 residues, 3 models selected > select subtract #26.2/A:136@CE1 287 atoms, 40 residues, 3 models selected > select subtract #26.2/A:136@CE2 286 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@O 285 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CE1 284 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CD1 283 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CD2 282 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CB 281 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CG 280 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@C 279 atoms, 40 residues, 3 models selected > select subtract #26.2/A:261@CA 278 atoms, 40 residues, 3 models selected > select subtract #26.2/A:257@O 277 atoms, 40 residues, 3 models selected > select add #26.2/A:13@OG 278 atoms, 41 residues, 3 models selected > select add #26.2/A:261@CE1 279 atoms, 41 residues, 3 models selected > select subtract #26.2/A:264@CB 278 atoms, 41 residues, 3 models selected > show #!7 models > select subtract #26.2/A:155@CD1 277 atoms, 41 residues, 3 models selected > select subtract #26.2/A:155@CB 276 atoms, 41 residues, 3 models selected > select subtract #26.2/A:155@CA 275 atoms, 41 residues, 3 models selected > select subtract #26.2/A:154@CG2 274 atoms, 41 residues, 3 models selected > select subtract #26.2/A:155@N 273 atoms, 41 residues, 3 models selected > select subtract #26.2/A:151@O 272 atoms, 41 residues, 3 models selected > select subtract #26.2/A:151@CB 271 atoms, 41 residues, 3 models selected > select subtract #26.2/A:151@N 270 atoms, 41 residues, 3 models selected > select subtract #26.2/A:150@N 269 atoms, 41 residues, 3 models selected > select subtract #26.2/A:150@CB 268 atoms, 41 residues, 3 models selected > select subtract #26.2/A:154@CB 267 atoms, 41 residues, 3 models selected > select subtract #26.2/A:151@CA 266 atoms, 41 residues, 3 models selected > select add #26.2/A:82@OE1 267 atoms, 42 residues, 3 models selected > select add #26.2/A:82@CD 268 atoms, 42 residues, 3 models selected > select add #26.2/A:82@CG 269 atoms, 42 residues, 3 models selected > select add #26.2/A:81@CB 270 atoms, 43 residues, 3 models selected > select add #26.2/A:81@CG 271 atoms, 43 residues, 3 models selected > select add #26.2/A:81@CD 272 atoms, 43 residues, 3 models selected > select add #26.2/A:252@OE2 273 atoms, 44 residues, 3 models selected > select add #26.2/A:252@CD 274 atoms, 44 residues, 3 models selected > select add #26.2/A:252@CG 275 atoms, 44 residues, 3 models selected > select add #26.2/A:81@NH1 276 atoms, 44 residues, 3 models selected > select add #26.2/A:81@NH2 277 atoms, 44 residues, 3 models selected > select add #26.2/A:81@NE 278 atoms, 44 residues, 3 models selected > select add #26.2/A:81@CZ 279 atoms, 44 residues, 3 models selected > select add #26.2/A:252@CB 280 atoms, 44 residues, 3 models selected > select add #26.2/A:253@N 281 atoms, 45 residues, 3 models selected > select add #26.2/A:253@CA 282 atoms, 45 residues, 3 models selected > select add #26.2/A:252@C 283 atoms, 45 residues, 3 models selected > select add #26.2/A:253@CD2 284 atoms, 45 residues, 3 models selected > select add #26.2/A:253@CB 285 atoms, 45 residues, 3 models selected > select add #26.2/A:253@ND1 286 atoms, 45 residues, 3 models selected > select add #26.2/A:253@NE2 287 atoms, 45 residues, 3 models selected > select add #26.2/A:253@CG 288 atoms, 45 residues, 3 models selected > select add #26.2/A:253@CE1 289 atoms, 45 residues, 3 models selected > select add #26.2/A:253@O 290 atoms, 45 residues, 3 models selected > select add #26.2/A:252@O 291 atoms, 45 residues, 3 models selected > select subtract #26.2/A:263@CD1 290 atoms, 45 residues, 3 models selected > select subtract #26.2/A:263@CG1 289 atoms, 45 residues, 3 models selected > hide #26.2&~sel target s > select subtract #26.2/A:140@CG2 288 atoms, 45 residues, 3 models selected > select subtract #26.2/A:140@CG1 287 atoms, 45 residues, 3 models selected > select subtract #26.2/A:139@CA 286 atoms, 45 residues, 3 models selected > select add #26.2/A:139@CA 287 atoms, 45 residues, 3 models selected > select subtract #26.2/A:140@CA 286 atoms, 45 residues, 3 models selected > select subtract #26.2/A:139@O 285 atoms, 45 residues, 3 models selected > select subtract #26.2/A:143@CG 284 atoms, 45 residues, 3 models selected > select subtract #26.2/A:140@N 283 atoms, 45 residues, 3 models selected > select subtract #26.2/A:139@C 282 atoms, 45 residues, 3 models selected > select subtract #26.2/A:139@CA 281 atoms, 45 residues, 3 models selected > select add #26.2/A:139@CA 282 atoms, 45 residues, 3 models selected > select subtract #26.2/A:136@CD1 281 atoms, 45 residues, 3 models selected > select subtract #26.2/A:15@CA 280 atoms, 45 residues, 3 models selected > select add #26.2/A:15@CA 281 atoms, 45 residues, 3 models selected > select subtract #26.2/A:15@C 280 atoms, 45 residues, 3 models selected > select subtract #26.2/A:12@O 279 atoms, 45 residues, 3 models selected > select subtract #26.2/A:12@CB 278 atoms, 45 residues, 3 models selected > select subtract #26.2/A:71@CE2 277 atoms, 45 residues, 3 models selected > select subtract #26.2/A:71@CD2 276 atoms, 45 residues, 3 models selected > select subtract #26.2/A:264@CD2 275 atoms, 45 residues, 3 models selected > select subtract #26.2/A:133@OD2 274 atoms, 45 residues, 3 models selected > select subtract #26.2/A:134@N 273 atoms, 45 residues, 3 models selected > select add #26.2/A:133@OD2 274 atoms, 45 residues, 3 models selected > select add #26.2/A:134@N 275 atoms, 45 residues, 3 models selected > select add #26.2/A:264@CD2 276 atoms, 45 residues, 3 models selected > select add #26.2/A:71@CE2 277 atoms, 45 residues, 3 models selected > select add #26.2/A:71@CD2 278 atoms, 45 residues, 3 models selected > hide #26.2&~sel target s > select subtract #26.2/A:257@C 277 atoms, 45 residues, 3 models selected > select subtract #26.2/A:161@CG2 276 atoms, 45 residues, 3 models selected > select subtract #26.2/A:161@CB 275 atoms, 45 residues, 3 models selected > select subtract #26.2/A:161@CD1 274 atoms, 45 residues, 3 models selected > select add #26.2/A:161@CD1 275 atoms, 45 residues, 3 models selected > select subtract #26.2/A:158@CA 274 atoms, 45 residues, 3 models selected > select subtract #26.2/A:158@CB 273 atoms, 45 residues, 3 models selected > select subtract #26.2/A:82@CG 272 atoms, 45 residues, 3 models selected > select add #26.2/A:82@CG 273 atoms, 45 residues, 3 models selected > hide #26.2&~sel target s > select subtract #26.2/A:158@O 272 atoms, 45 residues, 3 models selected > hide #26.2&~sel target s > select clear > view plug_top > select add #26.2/A:81@CD 1 atom, 1 residue, 1 model selected > select subtract #26.2/A:81@CD 1 model selected > select add #26.2/A:77@CB 1 atom, 1 residue, 1 model selected > select add #26.2/A:252@CB 2 atoms, 2 residues, 2 models selected > select add #26.2/A:77@O 3 atoms, 2 residues, 2 models selected > select add #26.2/A:77@CA 4 atoms, 2 residues, 2 models selected > select add #26.2/A:81@CB 5 atoms, 3 residues, 2 models selected > select subtract #26.2/A:81@CB 4 atoms, 2 residues, 2 models selected > hide sel target s > select #26.2/A:12@C 1 atom, 1 residue, 1 model selected > hide sel target s > select clear > view plug_top > transparency #26.2 80 target s > save NhaA-pH75-plugged-top_surf-partial.png supersample 3 > transparentBackground true > hide #!26 models > save NhaA-pH75-plugged-top_sribbon_no-trans.png supersample 3 > transparentBackground true > show #!26 models > hide #!7 models > show #!7 models > hide #26.2 target c > save NhaA-pH75-plugged-top_surf-partial.png supersample 3 > transparentBackground true > hide #!26 models > save NhaA-pH75-plugged-top_sribbon_no-trans.png supersample 3 > transparentBackground true > hide #!7 models > show #!26 models > transparency #26.2 0 target s > save NhaA-pH75-plugged-top_surf-partial_bg.png supersample 3 > transparentBackground true > hide #!26 models > show #!7 models > view plug_top > show #!9 models > hide #!9 models > show #!9 models > show #9/A:78,81,82,252,253,256&sidechain target a > hide #9 target c > hide ##name=""chain trance"" > hide ##name=""chain trace"" > hide #9 target a > show #9/A:78,81,82,252,253,256&sidechain target a > hide ##name=""chain trace"" > transparency #7/A:1-10 30 target a > transparency #7/A:1-10 50 target a > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > ui mousemode right distance > distance #9/A:252@OE1 #9/A:81@NE Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 252 OE1 and ARG 81 NE: 2.960Å > distance #9/A:81@NE #9/A:252@OE1 Distance already exists; modify distance properties with 'distance style' > show #!23 models > show #23.1 models > distance #9/A:81@NH1 #9/A:82@OE1 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A ARG 81 NH1 and GLU 82 OE1: 3.128Å > distance #7/A:256@NE2 #7/A:78@OE2 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A HIS 256 NE2 and GLU 78 OE2: 3.336Å > distance #9/A:252@OE2 #9/A:81@NH2 Distance between NhaA-nd-6F9-K_BTPpH75_unplugged.pdb #9/A GLU 252 OE2 and ARG 81 NH2: 2.826Å > ~distance #1/A:81@NE #1/A:252@OE1 > ~distance #9/A:252@OE1 #9/A:81@NE > hide #23.1 models > color sel dark gray > select clear > view plug_top > hide #!9 models > transparency #7/A:1-10 0 target a > graphics silhouettes width 6 > hide #7 target c > hide ##name=""chain trace"" > save NhaA-pH75-plugged-top2_res.png supersample 3 transparentBackground true > show #7/A target c > graphics silhouettes width 2 > show #!9 models > hide #!23 models > transparency #7/A:1-10 50 target a > transparency 30 target c > size #7/A:1-10 stickRadius 0.1 Changed 93 bond radii > transparency #7/A:1-10 0 target a > transparency #7/A:1-10 50 target a > transparency #7/A:1-10 0 target a > transparency #7/A:1-10 10 target a > transparency #7/A:1-10 30 target a > save NhaA-pH75-plugged-top_compare.png supersample 3 transparentBackground > true > show #!23 models > hide sel > select clear > hide target c > hide #7/A:1-10 target a > hide ##name=""chain trace"" > lighting full > lighting shadows false > graphics silhouettes width 6 > graphics silhouettes width 8 > save NhaA-pH75-plugged-top_compare_res.png supersample 3 > transparentBackground true > hide #!23 models > graphics silhouettes width 2 > show #7/A target c > show #7/A:4-9 target a > save NhaA-pH75-plugged-top_compare.png supersample 3 transparentBackground > true > show #!23 models > hide #!23 models > hide #7 target c > hide ##name=""chain trace"" > hide #7/A:1-10 target a > show #!23 models > graphics silhouettes width 8 > transparency 0 target ap > transparency 100 target ap > save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3 > transparentBackground true > transparency 1 target p > save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3 > transparentBackground true > transparency 0 target ap > distance #7/A:252@OE1 #7/A:81@NH1 Distance between NhaA-nd-6F9-K_BTPpH75_plugged.pdb #7/A GLU 252 OE1 and ARG 81 NH1: 3.594Å > show #23.1 models > hide #23.1 models > ~distance #7/A:252@OE1 #7/A:81@NH1 > ~distance #7/A:256@NE2 #7/A:78@OE2 > ui mousemode right translate > view plug_top > transparency 100 target a > transparency 1 target p > save NhaA-pH75-plugged-top_compare_res_sil.png supersample 3 > transparentBackground true > view name plug_top_zoom > hide #!23 models > transparency 0 target ap > view cutaway > ~clip > hide #!7,9 atoms > show #!1 models > show #!3 models > show #!5 models > show #!11 models > show #!13 models > show #!15 models > show #!17 models > hide #!17 models > hide #!1 models > hide #!5 models > hide #!15 models > hide #!3,7,9,11,13 atoms > show /A:163,164 target a > hide #!3,7,9,11,13 atoms > show /A:163,164&sidechain target a > hide ##name=""chain trace"" > color #!3,7,9,11,13 byhetero > hide #!11 models > hide #!9 models > hide #!7 models > hide #!13 models > size tick 0.4 Expected a keyword > size stickRadius 0.4 Changed 168624 bond radii > size stickRadius 0.5 Changed 168624 bond radii > graphics silhouettes 2 Expected true or false or a keyword > graphics silhouettes width 2 > lighting full > lighting shadows false > lighting full multiShadow 1024 shadows false > save NhaA-K-pH63-plugged_cutaway_res.png supersample 3 transparentBackground > true > show #!5 models > hide #!3 models > hide #!5 models > show #!7 models > save NhaA-K-pH75-plugged_cutaway_res.png supersample 3 transparentBackground > true > hide #!7 models > show #!11 models > save NhaA-K-pH85-state1-plugged_cutaway_res.png supersample 3 > transparentBackground true > hide #!11 models > show #!9 models > save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3 > transparentBackground true > size stickRadius 0.6 Changed 168624 bond radii > save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3 > transparentBackground true > size stickRadius 0.7 Changed 168624 bond radii > save NhaA-K-pH75-unplugged_cutaway_res.png supersample 3 > transparentBackground true > hide #!9 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > save NhaA-K-pH63-plugged_cutaway_res.png supersample 3 transparentBackground > true > show #!1 models > hide #!3 models > hide #!1 atoms > show /A:163,164&sidechain target a > hide ##name=""chain trace"" > color #!1 byhetero > save NhaA-K-pH55-plugged_cutaway_res.png supersample 3 transparentBackground > true > hide #!1 models > show #!7 models > save NhaA-K-pH75-plugged_cutaway_res.png supersample 3 transparentBackground > true > hide #!7 models > show #!11 models > save NhaA-K-pH85-state1-plugged_cutaway_res.png supersample 3 > transparentBackground true > hide #!11 models > show #!5 models > hide #!5 models > show #!13 models > color #13&core orange > color #13&dimer khaki > color #!13 byhetero > save NhaA-K-pH85-state1-unplugged_cutaway_res.png supersample 3 > transparentBackground true > hide #!13 models > show #!15 models > color #15&deep sky bluie;col #15&dimer light blue; Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #15&core deep sky blue > color #15&dimer light blue > hide #!15 atoms > show /A:163,164&sidechain target a > hide ##name=""chain trace"" > show /A:163,164&sidechain target a > hide ##name=""chain trace"" > color #!15 byhetero > select #15/A:164@CA 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > graphics selection color black > graphics selection color black width 6 > graphics selection color black width 8 > graphics selection color black width 10 > save NhaA-K-pH85-state2_cutaway_res.png supersample 3 transparentBackground > true > graphics selection color black width 20 > graphics selection color black width 2 > graphics selection color ;ime wid 2 Invalid ""color"" argument: Invalid color name or specifier > graphics selection color lime width 2 > select clear > size stickRadius 0.3 Changed 168624 bond radii > show #!17 models > hide #!15,17 atoms > show /A target c > color #17&core dodger blue > color #17&dimer light sky blue > cartoon style modeHelix tube radius 1.4 sides 24 > color #17 dodger blue > color #15 light blue > color #17 dodger blue > color #15 deep sky blue > color #17 dodger blue > color #15 light blue > color #17 dodger blue > color #15 light sky blue > color #17 dodger blue > color #15 light blue > view mono_back_ > view mono_back > view mono_back_ > save NhaA-pH85-Na-vs-K-superpose.png supersample 3 transparentBackground > true > transparency 0 target c > save NhaA-pH85-Na-vs-K-superpose.png supersample 3 transparentBackground > true > cartoon style modeHelix default width 1.0 thickness 0.3 > view core_inner_side2 > hide dimer target c > show /A:164,132 target a > color #!15,17 byhetero > hide #!17 models > show #!17 models > hide #!15 models > show #!33 models > hide #!17,33 atoms > color #17 dodger blue > color #33 light sky blue > color #17 dodger blue > color #33 light blue > show /A:164,132 target a > color #!17,33 byhetero > size stickRadius 0.3 Changed 168624 bond radii > size stickRadius 0.4 Changed 168624 bond radii > select #17,33/A:130-144,150-174 580 atoms, 582 bonds, 1 pseudobond, 80 residues, 3 models selected > graphics selection color black width 4 > graphics selection color black width 6 > graphics selection color black width 4 > transparency #17,33/A&~:130-144,150-174 30 target c > save NhaA-Na-pH85_vs_K-pH85_inside_TM4c-5.png supersample 3 > transparentBackground true > select clear > show /A target c > transparency 0 target c > view binding_site > size stickRadius 0.3 Changed 168624 bond radii > show #17&(binding_site_res&sidechain Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #17&(binding_site_res&sidechain) > show #17,33&(binding_site_res&sidechain) > show #!23 models > hide #!23 models > transparency 30 target c > save NhaA-Na-pH85_vs_K-pH85_binding-site.png supersample 3 > transparentBackground true > show #!23 models > show #23.1 models > ui mousemode right distance > distance #33/A:300@NZ #33/A:163@OD1 Distance already exists; modify distance properties with 'distance style' > show #23 target p > hide :NA,HOH > distance #17/A:164@OD1 #17/A:132@O Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ASP 164 OD1 and THR 132 O: 4.183Å > ui mousemode right rotate > color sel dodgerblue > select clear > hide #23.1 models > hide target ac > transparency #23 1 target p > graphics silhouettes width 6 > show #17,33&(binding_site_res&sidechain|:132) target a > transparency #17,33/A 0 target a > transparency #23 0 target p > graphics silhouettes width 6 > hide sel > select clear > save NhaA-Na-pH85_vs_K-pH85_binding-site_sil.png supersample 3 > transparentBackground true > show /A target c > show /A target cgra sil wid 2 Invalid ""target"" argument: Target option can only include letters a = atoms, b = bonds, p = pseudobonds, c = cartoons, r = cartoons, s = surfaces, m = models, got g > graphics silhouettes width 2 > hide #!23 models > transparency 0 target a > transparency 100 target a > save NhaA-Na-pH85_vs_K-pH85_binding-site2.png supersample 3 > transparentBackground true > view binding_site > save NhaA-Na-pH85_vs_K-pH85_binding-site2.png supersample 3 > transparentBackground true > transparency 0 target ac > view cutaway > hide #!17 models > hide #!33 models > show #!29 models > hide #!29 models > show #!29 models > show #!28 models > hide #!28 models > hide #!29 models > show #!26 models > show #!26.1 models > select add #26.2 2921 atoms, 2979 bonds, 380 residues, 1 model selected > coulombic sel Coulombic values for NhaA-nd-6F9-K_BTPpH75_plugged_split 2_A SES surface #26.2.1: minimum, -15.57, mean -0.06, maximum 14.74 To also show corresponding color key, enter the above coulombic command and add key true > hide target c > select clear > lighting soft multiShadow 1024 > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > save NhaA-K-pH75-plugged_cutaway_surf.png supersample 3 > transparentBackground true > hide #!26 models > show #!27 models > show #!28 models > show #!29 models > show #27,28,29 target s Cell requested for row 27 is out of bounds for table with 54 rows! Resizing table model. > select add #27.2 2978 atoms, 3036 bonds, 380 residues, 2 models selected > select add #28.2 5900 atoms, 6016 bonds, 760 residues, 5 models selected > show #!29.2 models > select add #29.2 8819 atoms, 8993 bonds, 1140 residues, 8 models selected > coulombic sel Coulombic values for NhaA-nd-6F9-K-BTPpH85_state1-plugged_split 2_A SES surface #27.2.1: minimum, -16.15, mean -0.11, maximum 16.64 Coulombic values for NhaA-nd-6F9-K-MESpH55_plugged_split 2_A SES surface #29.2.1: minimum, -15.70, mean -0.04, maximum 13.35 Coulombic values for NhaA-nd-6F9-K-BTPpH63_plugged_split 2_A SES surface #28.2.1: minimum, -17.21, mean 0.03, maximum 15.32 To also show corresponding color key, enter the above coulombic command and add key true > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > select clear > hide #!28 models > hide #!29 models > save NhaA-K-pH85-state1-plugged_cutaway_surf.png supersample 3 > transparentBackground true > show #!28 models > hide #!27 models > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > save NhaA-K-pH63-plugged_cutaway_surf.png supersample 3 > transparentBackground true > show #!29 models > hide #!28 models > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3 > transparentBackground true > hide #!29 models > show #!28 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!28 models > show #!28 models > hide #!29 models > show #!29 models > hide #!28 models > view cutaway > show #!28 models > hide #!28 models > save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3 > transparentBackground true > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3 > transparentBackground true > clip front 0.4 position #17:NA > color ##name=""cap front"" black target s > transparency 0 target s > select #29.1.1.1 1 model selected > color sel medium purple > select clear > select #29.1.1.1 1 model selected > color sel medium purple > transparency sel 1 > select clear > save NhaA-K-pH55-plugged_cutaway.png supersample 3 transparentBackground > true > hide #!29 models > show #!28 models > select #28.2.1.1 1 model selected > color sel black > select #28.1.1.1 1 model selected > color sel medium purple > transparency sel 1 > select clear > save NhaA-K-pH63-plugged_cutaway.png supersample 3 transparentBackground > true > show #!27 models > hide #!28 models > select #27.2.1.1 1 model selected > select #27.2.1.1 1 model selected > color sel black > select #27.1.1.1 1 model selected > color sel medium purple > transparency sel 1 > select clear > save NhaA-K-pH85-state1-plugged_cutaway.png supersample 3 > transparentBackground true > show #!26 models > hide #!27 models > select #26.2.1.1 1 model selected > select up 2828 atoms, 378 residues, 3 models selected > select down 1 model selected > color sel black > select #26.1.1.1 1 model selected > color sel medium purple > transparency sel 1 > select clear > save NhaA-K-pH75-plugged_cutaway.png supersample 3 transparentBackground > true > hide #!26 models > show #!29 models > size #29 atomRadius default Changed 2982 atom radii > hide #!29.1.1 models > show #29.1.1 models > close #29.1.1 > select add #29.1 63 atoms, 65 bonds, 7 residues, 1 model selected > show sel surfaces > select clear > select #29.2.1.1 1 model selected > select up 2828 atoms, 378 residues, 3 models selected > select down 1 model selected > color sel black > select #29.1.1.1 1 model selected > color sel medium purple > transparency sel 1 > select clear > save NhaA-K-pH55-plugged_cutaway.png supersample 3 transparentBackground > true > transparency 30 target s > color ##name=""cap front"" white transparency 100 target s > save NhaA-K-pH55-plugged_cutaway_surf.png supersample 3 > transparentBackground true > view mono_back_ > hide #!29 models > show #!17 models > show #!17 cartoons > lighting simple > show #!14 models > hide #!14 models > show #!13 models > hide #!13 models > show #44 models > show #44#!17 cartoons > show #45 models > hide #44 models > show #45#!17 cartoons > show #46 models > show #45-46#!17 cartoons > show #!1 models > show #45-46#!1,17 cartoons > hide /B,C target c > hide #45 models > hide #46 models > show #!48 models > hide #!48 models > show #47 models > show /A target c > hide #47 models > show #47 models > hide #47 models > show #44 models > show #45 models > hide #44 models > show #46 models > show #47 models > hide #47 models > show #44 models > hide #44 models > show #43 models > show #44 models > show #47 models > hide #43 models > hide #44 models > hide #45 models > hide #46 models > hide #47 models > show #!1,17 atoms > hide #!1,17 cartoons > ui mousemode right distance > distance #17/A:162@N #1/A:162@N Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A ILE 162 N and NhaA- nd-6F9-K_MESpH55.pdb #1/A ILE 162 N: 1.777Å > show #!23 models > show #23.1 models > distance #17/A:159@N #1/A:159@N Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A LEU 159 N and NhaA- nd-6F9-K_MESpH55.pdb #1/A LEU 159 N: 1.621Å > hide #!23 models > hide #!1 models > hide #!17 atoms > coulombic #!17 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_A SES surface #17.1: minimum, -15.88, mean 0.07, maximum 15.24 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_B SES surface #17.2: minimum, -20.11, mean -1.82, maximum 11.17 Coulombic values for NhaA-nd-6F9-Na_BTPpH85.pdb_C SES surface #17.3: minimum, -14.41, mean -2.05, maximum 16.84 To also show corresponding color key, enter the above coulombic command and add key true > hide #!17 surfaces > show #!17 cartoons > show /A:ASP,GLU,LYS,ARG,HIS target a > distance #17/A:225@CE1 #17/A:65@OD1 Distance between NhaA-nd-6F9-Na_BTPpH85.pdb #17/A HIS 225 CE1 and ASP 65 OD1: 3.136Å > show #!23 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 540.120.3~37 Software: System Software Overview: System Version: macOS 12.7.5 (21H1222) Kernel Version: Darwin 21.6.0 Time since boot: 11 days 16:09 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: DELL U3821DW: Resolution: 6400 x 2666 UI Looks like: 3200 x 1333 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H5YZZ63 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Television: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect assigned normal Window Toolkit all ChimeraX