id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17325 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.4-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020184bac0 (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, 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chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, 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2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs"" Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size 400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Log from Thu Mar 27 15:32:10 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size 400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size 400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32 Log from Tue Mar 18 21:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/wujingyi/Desktop/RfxATPase_figure/figure_5/Rfxatp_state1_hollow.cxs Log from Mon Aug 12 10:58:14 2024 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 > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2hollow.pdb"" > hide #1 models > show #1 models > select add #1 4431 atoms, 3493 bonds, 4431 residues, 1 model selected > show sel surfaces > set bgColor white > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/state_1_Fo.pdb"" Chain information for state_1_Fo.pdb #2 --- Chain | Description H L O P | No description available I | No description available J K M N | No description available Q | No description available T Z | No description available U X | No description available V Y | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide sel atoms [Repeated 2 time(s)] > select add #2 15578 atoms, 14854 bonds, 2 pseudobonds, 5912 residues, 7 models selected > hide sel atoms > show sel cartoons > select subtract #1 11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 6 models selected > show sel surfaces > hide sel surfaces > select subtract #2.13 10824 atoms, 11031 bonds, 2 pseudobonds, 1443 residues, 18 models selected > select add #2.13 11147 atoms, 11031 bonds, 2 pseudobonds, 1481 residues, 17 models selected > hide #2.13 models > show #2.13 models > select add #2 11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 18 models selected > select subtract #2 16 models selected > select add #2.13 323 atoms, 38 residues, 1 model selected > select add #2.16 629 atoms, 74 residues, 2 models selected > select subtract #2.16 323 atoms, 38 residues, 3 models selected > select add #2.14 629 atoms, 74 residues, 2 models selected > hide sel cartoons > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo.pdb"" Chain information for RfxATP_state_1_Fo.pdb #3 --- Chain | Description H L O P | No description available I | No description available J K M N | No description available Q | No description available T Z | No description available U X | No description available V Y | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide sel cartoons > hide sel atoms > select add #3 11776 atoms, 11365 bonds, 2 pseudobonds, 1555 residues, 5 models selected > select add #2 22294 atoms, 22726 bonds, 4 pseudobonds, 2962 residues, 6 models selected > hide sel atoms > show sel cartoons > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > close #2 > show sel surfaces > hide sel surfaces > select subtract #3 16 models selected > select add #3.13 323 atoms, 38 residues, 1 model selected > select add #3.15 646 atoms, 76 residues, 2 models selected > hide sel cartoons > select add #3.14 952 atoms, 112 residues, 3 models selected > select add #3.16 1258 atoms, 148 residues, 4 models selected > hide sel cartoons > select add #3.2 1808 atoms, 224 residues, 5 models selected > select add #3.3 2331 atoms, 297 residues, 6 models selected > select add #3.4 2873 atoms, 372 residues, 7 models selected > select add #3.5 3415 atoms, 447 residues, 8 models selected > select add #3.6 3965 atoms, 523 residues, 9 models selected > select add #3.7 4507 atoms, 598 residues, 10 models selected > select add #3.8 5049 atoms, 673 residues, 11 models selected > select add #3.9 5599 atoms, 749 residues, 12 models selected > select add #3.10 6149 atoms, 825 residues, 13 models selected > select add #3.11 6683 atoms, 899 residues, 14 models selected > hide sel cartoons > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_inlet_hollow.pdb"" > select add #2 13913 atoms, 5473 bonds, 8129 residues, 16 models selected > show sel surfaces > hide sel surfaces > select subtract #3.2 13363 atoms, 5473 bonds, 8053 residues, 16 models selected > show sel surfaces > hide sel surfaces > select add #3 18377 atoms, 16838 bonds, 2 pseudobonds, 8711 residues, 16 models selected > select subtract #3 7230 atoms, 5473 bonds, 7230 residues, 17 models selected > show sel surfaces > select subtract #2 4 models selected > select add #2 7230 atoms, 5473 bonds, 7230 residues, 1 model selected > hide sel surfaces > hide sel atoms > select subtract #2 4 models selected > select add #2 7230 atoms, 5473 bonds, 7230 residues, 1 model selected > show sel atoms > select subtract #2 4 models selected > select add #2.1 1460 atoms, 1460 residues, 1 model selected > select add #2.2 5673 atoms, 5673 residues, 2 models selected > select add #2.3 7208 atoms, 7208 residues, 3 models selected > select add #2.4 7230 atoms, 7230 residues, 4 models selected > select subtract #2.4 7208 atoms, 7208 residues, 5 models selected > show sel cartoons > show sel surfaces > select add #2.4 7230 atoms, 7230 residues, 4 models selected > show sel surfaces [Repeated 1 time(s)] > hide sel surfaces > show sel surfaces > select subtract #2.4 7208 atoms, 7208 residues, 5 models selected > show sel surfaces > select add #2 7230 atoms, 5473 bonds, 7230 residues, 4 models selected > select subtract #2.4 7208 atoms, 5454 bonds, 7208 residues, 5 models selected > select add #2.4 7230 atoms, 5454 bonds, 7230 residues, 4 models selected > hide sel surfaces > select subtract #2.4 7208 atoms, 5454 bonds, 7208 residues, 5 models selected > show sel surfaces > select add #2 7230 atoms, 5473 bonds, 7230 residues, 4 models selected > show sel surfaces > hide sel surfaces > select subtract #2.4 7208 atoms, 5454 bonds, 7208 residues, 5 models selected > show sel surfaces > color #2.1 #87ceeb90 > select add #2 7230 atoms, 5473 bonds, 7230 residues, 4 models selected > hide sel atoms > color #2.1 #87ceeb82 > color #2.1 #87ceeb80 > color #2.2 #87ceeb80 > color #2.3 #87ceeb82 > color #2.3 #87ceeb80 > select subtract #2.4 7208 atoms, 5454 bonds, 7208 residues, 5 models selected > select subtract #2.3 5673 atoms, 4370 bonds, 5673 residues, 4 models selected > select subtract #2.2 1460 atoms, 1278 bonds, 1460 residues, 3 models selected > select subtract #2.1 1 model selected > hide #!3 models > show #!3 models > hide #!1 models > select add #3.2 550 atoms, 76 residues, 1 model selected > select add #3.3 1073 atoms, 149 residues, 2 models selected > select add #3.4 1615 atoms, 224 residues, 3 models selected > select add #3.5 2157 atoms, 299 residues, 4 models selected > show sel cartoons > hide sel cartoons > select subtract #3.2 1607 atoms, 223 residues, 5 models selected > select subtract #3.3 1084 atoms, 150 residues, 4 models selected > select subtract #3.4 542 atoms, 75 residues, 3 models selected > select subtract #3.5 1 model selected > select add #3.6 550 atoms, 76 residues, 1 model selected > select add #3.7 1092 atoms, 151 residues, 2 models selected > select add #3.8 1634 atoms, 226 residues, 3 models selected > select add #3.9 2184 atoms, 302 residues, 4 models selected > select add #3.10 2734 atoms, 378 residues, 5 models selected > select add #3.11 3268 atoms, 452 residues, 6 models selected > select add #3.12 5500 atoms, 743 residues, 7 models selected > select subtract #3.12 3268 atoms, 452 residues, 8 models selected > show sel cartoons > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_outlet_hollow2.pdb"" > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_intlet_hollow.pdb"" > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_outlet_hollow.pdb"" > select add #1 7699 atoms, 3493 bonds, 4883 residues, 8 models selected > select add #3 15578 atoms, 14858 bonds, 2 pseudobonds, 5912 residues, 13 models selected > select subtract #3 4431 atoms, 3493 bonds, 4431 residues, 21 models selected > close #1 > select add #6 5690 atoms, 4616 bonds, 5690 residues, 1 model selected > select add #5 12781 atoms, 9914 bonds, 12781 residues, 2 models selected > select add #4 19169 atoms, 14970 bonds, 19169 residues, 3 models selected > show sel surfaces > select subtract #4 12781 atoms, 9914 bonds, 12781 residues, 13 models selected > select subtract #5 5690 atoms, 4616 bonds, 5690 residues, 8 models selected > select subtract #6 3 models selected > select add #5.4 860 atoms, 860 residues, 1 model selected > select add #5.3 4775 atoms, 4775 residues, 2 models selected > select add #5.2 7013 atoms, 7013 residues, 3 models selected > select subtract #5.2 4775 atoms, 4775 residues, 4 models selected > select add #5.1 4853 atoms, 4853 residues, 3 models selected > select subtract #5.1 4775 atoms, 4775 residues, 4 models selected > select subtract #5.3 860 atoms, 860 residues, 3 models selected > select subtract #5.4 1 model selected > select add #5.2 2238 atoms, 2238 residues, 1 model selected > select subtract #5.2 1 model selected > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > show sel cartoons > select subtract #3 16 models selected > select add #3.13 323 atoms, 38 residues, 1 model selected > select add #3.14 629 atoms, 74 residues, 2 models selected > select add #3.16 935 atoms, 110 residues, 3 models selected > select add #3.15 1258 atoms, 148 residues, 4 models selected > hide sel cartoons > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 11147 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > undo [Repeated 5 time(s)] > select add #3.16 306 atoms, 36 residues, 1 model selected > select add #3.15 629 atoms, 74 residues, 2 models selected > select add #3.14 935 atoms, 110 residues, 3 models selected > select add #3.13 1258 atoms, 148 residues, 4 models selected > hide sel cartoons > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected > select subtract #3 16 models selected > select add #2 7230 atoms, 5473 bonds, 7230 residues, 1 model selected > select add #6 12920 atoms, 10089 bonds, 12920 residues, 6 models selected > select add #5 20011 atoms, 15387 bonds, 20011 residues, 10 models selected > select add #4 26399 atoms, 20443 bonds, 26399 residues, 15 models selected > show sel surfaces > select subtract #2 19169 atoms, 14970 bonds, 19169 residues, 18 models selected > select subtract #4 12781 atoms, 9914 bonds, 12781 residues, 13 models selected > select subtract #5 5690 atoms, 4616 bonds, 5690 residues, 8 models selected > select subtract #6 3 models selected > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > cartoon style (#!3 & sel) modeHelix tube sides 20 > select subtract #3.1 11147 atoms, 11365 bonds, 1481 residues, 17 models selected > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 18 models selected > select subtract #3 16 models selected > select add #3.2 550 atoms, 76 residues, 1 model selected > select add #3.3 1073 atoms, 149 residues, 2 models selected > select add #3.4 1615 atoms, 224 residues, 3 models selected > select add #3.5 2157 atoms, 299 residues, 4 models selected > select add #3.6 2707 atoms, 375 residues, 5 models selected > select add #3.7 3249 atoms, 450 residues, 6 models selected > select add #3.8 3791 atoms, 525 residues, 7 models selected > select add #3.9 4341 atoms, 601 residues, 8 models selected > select add #3.10 4891 atoms, 677 residues, 9 models selected > select add #3.11 5425 atoms, 751 residues, 10 models selected > color (#!3 & sel) #f5ccdcff > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected > select subtract #3 16 models selected > select add #3.12 2232 atoms, 291 residues, 1 model selected > select add #3.14 2538 atoms, 327 residues, 2 models selected > color (#!3 & sel) forest green > select subtract #3.14 2232 atoms, 291 residues, 3 models selected > select add #3.17 4464 atoms, 582 residues, 2 models selected > color (#!3 & sel) forest green > select subtract #3.17 2232 atoms, 291 residues, 3 models selected > select add #3.10 2782 atoms, 367 residues, 2 models selected > select add #3.9 3332 atoms, 443 residues, 3 models selected > select add #3.8 3874 atoms, 518 residues, 4 models selected > select add #3.7 4416 atoms, 593 residues, 5 models selected > select add #3.6 4966 atoms, 669 residues, 6 models selected > select add #3.5 5508 atoms, 744 residues, 7 models selected > select add #3.4 6050 atoms, 819 residues, 8 models selected > select add #3.3 6573 atoms, 892 residues, 9 models selected > select add #3.2 7123 atoms, 968 residues, 10 models selected > hide sel cartoons > select add #3.11 7657 atoms, 1042 residues, 11 models selected > select subtract #3.12 5425 atoms, 751 residues, 12 models selected > hide sel cartoons > show sel atoms > hide sel atoms > select add #3.17 7657 atoms, 1042 residues, 11 models selected > show sel atoms > hide sel atoms > show sel cartoons > hide sel cartoons > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 13 models selected > select subtract #3 16 models selected > select add #3.14 306 atoms, 36 residues, 1 model selected > select add #3.12 2538 atoms, 327 residues, 2 models selected > show sel cartoons > select subtract #3.14 2232 atoms, 291 residues, 3 models selected > select add #3.17 4464 atoms, 582 residues, 2 models selected > show sel cartoons > select add #3.14 4770 atoms, 618 residues, 3 models selected > select subtract #3.12 2538 atoms, 327 residues, 4 models selected > select subtract #3.17 306 atoms, 36 residues, 3 models selected > hide sel cartoons > color #3.14 #917297ff > select subtract #3.14 1 model selected > lighting soft > select add #3.2 550 atoms, 76 residues, 1 model selected > select add #3.3 1073 atoms, 149 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/H #3/L #3/O #3/P Alignment identifier is 1 > sequence chain #3/I Alignment identifier is 3/I > sequence chain #3/J #3/K #3/M #3/N Alignment identifier is 2 > sequence chain #3/Q Alignment identifier is 3/Q > select #3/Q:3-39,41-74 508 atoms, 515 bonds, 71 residues, 1 model selected > select #3/Q:59 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/Q:59 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color (#!3 & sel) byhetero > select #3/J-K,M-N:59 36 atoms, 32 bonds, 4 residues, 1 model selected > select #3/J-K,M-N:59 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 36 atom styles > color (#!3 & sel) byhetero > select #3/H,L,O-P:59 36 atoms, 32 bonds, 4 residues, 1 model selected > select #3/H,L,O-P:59 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 36 atom styles > color (#!3 & sel) byhetero > select #3/H,L,O-P:3-39,41-74 2032 atoms, 2060 bonds, 284 residues, 1 model selected > ui mousemode right select > select clear Drag select of 6 residues > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/T #3/Z Alignment identifier is 3 > select #3/T,Z:259 22 atoms, 20 bonds, 2 residues, 1 model selected > select #3/T,Z:259 22 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > color (#!3 & sel) byhetero > select clear Drag select of 9 atoms, 8 bonds > select clear [Repeated 1 time(s)] > select add #3.11 534 atoms, 74 residues, 1 model selected > select add #3.10 1084 atoms, 150 residues, 2 models selected > select subtract #3.11 550 atoms, 76 residues, 3 models selected > select subtract #3.10 1 model selected > select #3/I:59 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/I:59 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color (#!3 & sel) byhetero > select clear > open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95, shown at level 0.101, step 2, values float32 Drag select of rfxa2_intlet_hollow.pdb_E SES surface, 208 of 3672 triangles, rfxa2_intlet_hollow.pdb_F SES surface, 464 of 25208 triangles, 8 atoms, 8 bonds, 1 J276_003_volume_map_sharp.mrc > volume #1 step 1 > volume #1 level 0.2498 > select add #3 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 7 models selected > hide #!3 models > hide #3.1 models > hide #3.2 models > show #3.1 models > hide #!2 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > select clear [Repeated 1 time(s)] > close #1 > open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95, shown at level 0.101, step 2, values float32 > volume zlip #1 Expected a density maps specifier or a keyword > volume #1 step 1 > volume #1 level 0.224 > volume zlip #1 Expected a density maps specifier or a keyword > volume zflip #1 Expected a density maps specifier or a keyword > volume flip #1 Opened J276_003_volume_map_sharp.mrc z flip as #7, grid size 400,400,400, pixel 0.95, shown at step 1, values float32 > save /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc models #7 > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase > 结构/RFXATPase_state1_2.98A-1.pdb"" Chain information for RFXATPase_state1_2.98A-1.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H L O P | No description available I | No description available J K M N | No description available Q | No description available R | No description available S | No description available T Z | No description available U X | No description available V | No description available W | No description available Y | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select clear > hide #!8 atoms > show #!8 cartoons > select add #7 2 models selected Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 15 residues > ui mousemode right ""translate selected models"" > view matrix models > #7,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591,#8,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591 > view matrix models > #7,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779,#8,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779 > view matrix models > #7,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748,#8,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748 > ui mousemode right select Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 9 residues > select subtract #7 69 atoms, 9 residues, 1 model selected > select add #7 69 atoms, 9 residues, 3 models selected > select subtract #7 69 atoms, 9 residues, 1 model selected > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 3 residues Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 24 residues > select #8/X:110 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,-1.6308,0,1,0,1.9901,0,0,1,-10.325 > view matrix models #8,1,0,0,17.812,0,1,0,-0.57249,0,0,1,-3.5122 > view matrix models #8,1,0,0,8.9735,0,1,0,15.372,0,0,1,-18.231 > view matrix models #8,1,0,0,6.1384,0,1,0,40.464,0,0,1,-18.769 > view matrix models #8,1,0,0,0.28461,0,1,0,11.462,0,0,1,-11.994 > ui mousemode right select > select clear > volume #7 level 0.1787 Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 18 residues > select clear > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.90579,0.37073,-0.20519,328.38,-0.30373,-0.90572,-0.29566,478.69,-0.29545,-0.20548,0.933,94.403 > view matrix models > #8,-0.96264,0.27066,0.0076537,318.46,-0.26006,-0.91632,-0.3045,474.07,-0.075404,-0.29512,0.95248,66.029 > view matrix models > #8,-0.92958,-0.23864,0.28095,356.73,0.29128,-0.94264,0.16308,288.68,0.22591,0.23343,0.94577,-88.104 > view matrix models > #8,-0.84595,0.16919,0.50571,223.41,-0.021766,-0.9585,0.28426,328.28,0.53282,0.22946,0.81452,-121 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.84595,0.16919,0.50571,235.2,-0.021766,-0.9585,0.28426,367.87,0.53282,0.22946,0.81452,-65.315 > view matrix models > #8,-0.84595,0.16919,0.50571,220.58,-0.021766,-0.9585,0.28426,321.34,0.53282,0.22946,0.81452,-116.96 > view matrix models > #8,-0.84595,0.16919,0.50571,221.54,-0.021766,-0.9585,0.28426,322.24,0.53282,0.22946,0.81452,-114.19 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.83579,0.078648,0.54339,229.55,-0.07592,-0.99673,0.027491,386.99,0.54378,-0.018278,0.83903,-74.584 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.83579,0.078648,0.54339,222.57,-0.07592,-0.99673,0.027491,390.28,0.54378,-0.018278,0.83903,-87.165 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.91118,0.13459,0.38941,254.79,-0.039499,-0.96932,0.2426,338.58,0.41011,0.20567,0.88854,-112.87 > view matrix models > #8,-0.97717,-0.025638,0.21089,330.07,0.044447,-0.99539,0.084934,356.72,0.20775,0.092368,0.97381,-69.326 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.97717,-0.025638,0.21089,338.54,0.044447,-0.99539,0.084934,351.74,0.20775,0.092368,0.97381,-56.344 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.87329,0.37091,0.31591,-103.7,-0.46999,0.81218,0.34565,63.53,-0.12837,-0.45033,0.88359,124.89 > view matrix models > #8,0.87251,0.34682,0.34414,-104.27,-0.46902,0.79188,0.39108,58.745,-0.13689,-0.50263,0.85359,141.79 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.87251,0.34682,0.34414,-88.442,-0.46902,0.79188,0.39108,76.727,-0.13689,-0.50263,0.85359,134.61 > select add #7 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected > view matrix models > #7,1,0,0,-6.297,0,1,0,-4.732,0,0,1,-10.051,#8,0.87251,0.34682,0.34414,-93.356,-0.46902,0.79188,0.39108,70.651,-0.13689,-0.50263,0.85359,131.13 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.99677,-0.0017702,0.080268,-20.213,-0.0060842,0.99522,0.097502,-20.723,-0.080056,-0.097676,0.99199,25.283,#8,0.85954,0.30395,0.41086,-95.792,-0.48544,0.73697,0.47034,68.595,-0.15983,-0.60372,0.78101,164.94 > select subtract #8 2 models selected > view matrix models > #7,0.95476,-0.047178,0.29362,-43.084,-0.0629,0.93296,0.35444,-45.638,-0.29066,-0.35687,0.88778,134.06 > view matrix models > #7,-0.88421,-0.21366,0.41537,319.19,0.41454,-0.76875,0.48701,159.82,0.21526,0.60281,0.7683,-122.46 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.88421,-0.21366,0.41537,329.35,0.41454,-0.76875,0.48701,172.07,0.21526,0.60281,0.7683,-126.96 > view matrix models > #7,-0.88421,-0.21366,0.41537,332.67,0.41454,-0.76875,0.48701,178.44,0.21526,0.60281,0.7683,-131.73 > view matrix models > #7,-0.88421,-0.21366,0.41537,331.46,0.41454,-0.76875,0.48701,179.89,0.21526,0.60281,0.7683,-135.36 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.94832,0.25093,0.19421,-67.519,-0.30926,0.86791,0.38872,27.724,-0.071014,-0.42869,0.90066,90.153 > view matrix models > #7,0.70521,0.58704,0.39757,-122.03,-0.69527,0.68242,0.22562,167.18,-0.13886,-0.43553,0.8894,106.57 > view matrix models > #7,0.82451,0.45778,0.33259,-108.48,-0.56304,0.72221,0.40175,101.62,-0.056283,-0.51851,0.85322,113.1 > view matrix models > #7,0.82328,0.52176,0.22356,-100.14,-0.5672,0.77161,0.28794,114.17,-0.022268,-0.36385,0.93119,62.872 > view matrix models > #7,0.67235,0.54008,0.50622,-126.97,-0.70093,0.68439,0.20079,172.5,-0.23801,-0.48982,0.83871,145.28 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.67235,0.54008,0.50622,-119.87,-0.70093,0.68439,0.20079,159.37,-0.23801,-0.48982,0.83871,140.99 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.69879,0.54006,0.46907,-118.06,-0.69186,0.67684,0.25141,149.67,-0.18171,-0.50022,0.84662,130.67 > view matrix models > #7,0.83451,0.45787,0.30652,-98.483,-0.50917,0.85342,0.11141,107.12,-0.21058,-0.24905,0.94532,70.441 > view matrix models > #7,0.89321,0.41571,0.17135,-76.748,-0.44856,0.85022,0.27554,65.671,-0.031139,-0.32297,0.9459,49.832 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.85265,0.28815,0.43585,-93.839,-0.38349,0.91169,0.14749,65.269,-0.35486,-0.2929,0.88785,117.1 > ui tool show ""Fit in Map"" > fitmap #8 inMap #7 Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms average map value = 0.0361, steps = 248 shifted from previous position = 3.32 rotated from previous position = 3.59 degrees atoms outside contour = 36794, contour level = 0.17874 Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to RfxATP_state1_withoutADP_F1.mrc (#7) coordinates: Matrix rotation and translation 0.97702481 0.20658623 -0.05238958 -29.62036884 -0.18232674 0.93747643 0.29647078 -1.24036171 0.11036078 -0.28010728 0.95360391 47.42560830 Axis -0.80722577 -0.22785516 -0.54448928 Axis point 0.00000000 159.66635676 39.10884363 Rotation angle (degrees) 20.92438479 Shift along axis -1.62978743 > volume #7 level 0.3325 > volume #7 level 0.191 > surface dust #7 size 9.5 > volume #7 level 0.08035 > surface dust #7 size 9.5 [Repeated 1 time(s)] > volume #7 level 0.0503 > volume #7 level 0.103 > ui mousemode right select > select clear > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!8 models > surface dust #7 size 9.5 > show #!8 models > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 60 residues > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.81858,0.56012,0.12724,-82.604,-0.57128,0.81694,0.079034,132.39,-0.059679,-0.13738,0.98872,13.357,#8,0.7117,0.65856,0.24451,-101.51,-0.69838,0.62571,0.3475,152.04,0.075857,-0.41807,0.90524,62.186 > select subtract #7 471 atoms, 60 residues, 1 model selected > view matrix models > #8,-0.66704,-0.73627,0.11385,442.68,0.72058,-0.6764,-0.15248,219.63,0.18927,-0.019677,0.98173,-47.612 > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected > select add #7 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #7,0.81858,0.56012,0.12724,-107.08,-0.57128,0.81694,0.079034,119.88,-0.059679,-0.13738,0.98872,13.446,#8,-0.66704,-0.73627,0.11385,418.2,0.72058,-0.6764,-0.15248,207.12,0.18927,-0.019677,0.98173,-47.523 > select subtract #8 2 models selected > select subtract #7 Nothing selected > select add #8 41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected > view matrix models > #8,-0.66704,-0.73627,0.11385,415.23,0.72058,-0.6764,-0.15248,205.72,0.18927,-0.019677,0.98173,-48.196 > view matrix models > #8,-0.66704,-0.73627,0.11385,414.92,0.72058,-0.6764,-0.15248,206.56,0.18927,-0.019677,0.98173,-49.48 > view matrix models > #8,-0.66704,-0.73627,0.11385,413.85,0.72058,-0.6764,-0.15248,208.31,0.18927,-0.019677,0.98173,-47.84 > select subtract #8 Nothing selected > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.82946,0.54181,0.1358,-107.14,-0.55482,0.8273,0.088006,113.07,-0.064669,-0.14834,0.98682,16.887 > view matrix models > #7,0.82794,0.53632,0.16394,-110.95,-0.54873,0.83508,0.03928,119.35,-0.11584,-0.12248,0.98569,21.764 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.82794,0.53632,0.16394,-116.9,-0.54873,0.83508,0.03928,129.66,-0.11584,-0.12248,0.98569,21.897 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.80067,0.55879,0.21605,-125.69,-0.57153,0.82057,-0.0042587,144.83,-0.17966,-0.12007,0.97637,35.272 > view matrix models > #7,0.81894,0.56477,0.1019,-109.35,-0.54936,0.82283,-0.14542,166.11,-0.16597,0.063107,0.98411,-4.5857 > select subtract #7 Nothing selected > hide #!7 models > show #!7 models > fitmap #8 inMap #7 Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms average map value = 0.04304, steps = 80 shifted from previous position = 1.27 rotated from previous position = 1.72 degrees atoms outside contour = 33294, contour level = 0.103 Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to RfxATP_state1_withoutADP_F1.mrc (#7) coordinates: Matrix rotation and translation -0.97766050 -0.21015754 0.00371096 411.17643737 0.21004182 -0.97748108 -0.02032708 335.92463186 0.00789929 -0.01909353 0.99978651 8.97038534 Axis 0.00293548 -0.00996693 0.99994602 Axis point 187.72593879 189.84909480 0.00000000 Rotation angle (degrees) 167.87114146 Shift along axis 6.82876360 > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/Rfx ATPase ADP map/Rfx ATPase overall > map/J68_10.48w_2.89A_volumeZ_map.mrc.mrc"" Opened J68_10.48w_2.89A_volumeZ_map.mrc.mrc as #9, grid size 400,400,400, pixel 0.93, shown at level 0.0643, step 2, values float32 > select add #9 2 models selected > view matrix models > #9,0.94781,0.29555,0.11964,-65.963,-0.30155,0.9528,0.035199,59.073,-0.10359,-0.069439,0.99219,33.644 > view matrix models > #9,-0.16235,-0.98146,-0.10184,417.29,0.97581,-0.14439,-0.16413,56.511,0.14638,-0.12602,0.98117,-0.95683 > view matrix models > #9,-0.64648,-0.75883,0.079063,434.97,0.74348,-0.64985,-0.15787,192.08,0.17118,-0.04328,0.98429,-21.402 > hide #!7 models > view matrix models > #9,-0.63471,-0.72188,0.27572,390.81,0.71277,-0.68474,-0.15195,203.21,0.29849,0.10008,0.94915,-65.43 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.63471,-0.72188,0.27572,444.16,0.71277,-0.68474,-0.15195,299.14,0.29849,0.10008,0.94915,-102.44 > view matrix models > #9,-0.63471,-0.72188,0.27572,377.16,0.71277,-0.68474,-0.15195,204.9,0.29849,0.10008,0.94915,-87.29 > view matrix models > #9,-0.63471,-0.72188,0.27572,380.26,0.71277,-0.68474,-0.15195,209.91,0.29849,0.10008,0.94915,-89.722 > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.81475,-0.54434,0.19968,395.03,0.53788,-0.83818,-0.09021,259.98,0.21648,0.033908,0.9757,-66.876 > view matrix models > #9,-0.81553,-0.55997,0.14609,407.63,0.53884,-0.82683,-0.16124,270.41,0.21109,-0.052776,0.97604,-49.973 > view matrix models > #9,-0.72178,-0.67644,0.14653,411.36,0.64266,-0.7336,-0.22095,244.41,0.25695,-0.065305,0.96421,-54.174 > view matrix models > #9,-0.70922,-0.70009,0.082935,424.72,0.68767,-0.71291,-0.1374,217.21,0.15532,-0.040416,0.98704,-43.731 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.70922,-0.70009,0.082935,420.42,0.68767,-0.71291,-0.1374,222.59,0.15532,-0.040416,0.98704,-41.757 > show #!7 models > select subtract #9 Nothing selected > select add #7 2 models selected > view matrix models > #7,0.81894,0.56477,0.1019,-109.07,-0.54936,0.82283,-0.14542,166.67,-0.16597,0.063107,0.98411,-8.6208 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.82136,0.57001,0.021207,-95.736,-0.56458,0.81772,-0.11217,164.45,-0.081282,0.080162,0.99346,-29.777 > view matrix models > #7,-0.8497,-0.52724,0.0058055,439.44,0.52217,-0.84296,-0.12945,285.87,0.073144,-0.10696,0.99157,-22.184 > select subtract #7 Nothing selected > hide #!9 models > select add #7 2 models selected > view matrix models > #7,-0.83572,-0.53982,0.10088,421.78,0.53709,-0.84174,-0.054778,269.08,0.11449,0.0084053,0.99339,-52.947 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.83572,-0.53982,0.10088,417.08,0.53709,-0.84174,-0.054778,262.64,0.11449,0.0084053,0.99339,-42.059 > select subtract #7 Nothing selected [deleted to fit within ticket limits] Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_A SES surface #1.2: minimum, -18.27, mean -1.83, maximum 13.91 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_B SES surface #1.3: minimum, -15.47, mean -1.37, maximum 13.82 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_C SES surface #1.4: minimum, -16.31, mean -1.63, maximum 13.40 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_D SES surface #1.5: minimum, -28.87, mean -2.68, maximum 10.52 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_E SES surface #1.6: minimum, -20.09, mean -2.56, maximum 8.70 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_F SES surface #1.7: minimum, -18.01, mean -2.95, maximum 8.98 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_G SES surface #1.8: minimum, -16.97, mean 1.81, maximum 17.95 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_H SES surface #1.9: minimum, -10.11, mean -0.93, maximum 7.53 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_I SES surface #1.10: minimum, -10.05, mean -0.85, maximum 6.44 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_J SES surface #1.11: minimum, -12.46, mean -0.37, maximum 8.45 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_K SES surface #1.12: minimum, -11.92, mean -0.41, maximum 9.98 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_L SES surface #1.13: minimum, -10.16, mean -0.92, maximum 7.70 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_M SES surface #1.14: minimum, -9.92, mean -0.18, maximum 9.75 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_N SES surface #1.15: minimum, -10.12, mean -0.53, maximum 8.00 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_O SES surface #1.16: minimum, -10.15, mean -0.67, maximum 9.21 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_P SES surface #1.17: minimum, -11.20, mean -1.02, maximum 7.64 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Q SES surface #1.18: minimum, -10.56, mean -0.41, maximum 7.82 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_R SES surface #1.19: minimum, -19.83, mean -2.00, maximum 12.65 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_S SES surface #1.20: minimum, -13.38, mean -0.26, maximum 7.63 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_U SES surface #1.22: minimum, -7.30, mean -1.52, maximum 9.63 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_V SES surface #1.23: minimum, -9.18, mean -1.53, maximum 10.50 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_W SES surface #1.24: minimum, -13.86, mean -0.26, maximum 7.70 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_X SES surface #1.25: minimum, -8.05, mean -1.46, maximum 9.60 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Y SES surface #1.26: minimum, -8.08, mean -1.63, maximum 9.55 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76 To also show corresponding color key, enter the above coulombic command and add key true > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected > select subtract #1.21 36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected > hide sel surfaces > hide sel cartoons > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 27 models selected > select subtract #1 26 models selected > select add #1.21 1588 atoms, 265 residues, 1 model selected > hide sel cartoons > show sel surfaces > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting flat > lighting full > select clear > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:249 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:249 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:245 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:245 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:234 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/T:234 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/T:290 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select subtract #1.21 1 model selected > select add #1.27 1542 atoms, 278 residues, 1 model selected > show sel surfaces Alignment identifier is 1/Z > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:265-266 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/Z:265-270 44 atoms, 44 bonds, 6 residues, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268-269 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > color #1.21 #65b8bcff > select add #1.21 1597 atoms, 8 bonds, 266 residues, 2 models selected > coulombic sel Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62 Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76 To also show corresponding color key, enter the above coulombic command and add key true > select subtract #1.21 9 atoms, 8 bonds, 1 residue, 3 models selected > select add #1.25 751 atoms, 8 bonds, 150 residues, 2 models selected > select subtract #1.25 9 atoms, 8 bonds, 1 residue, 3 models selected > select subtract #1.27 1 model selected > select add #1.27 1542 atoms, 278 residues, 1 model selected > show sel surfaces > select clear > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel surfaces > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting shadows false > graphics silhouettes false > lighting flat > lighting full > lighting shadows false > lighting soft > view > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > save /Users/wujingyi/Desktop/figure/figure4/state1_a1电势.png width 1660 > height 1174 supersample 3 transparentBackground true > select add #1.21 1588 atoms, 265 residues, 1 model selected > hide sel surfaces > hide sel atoms > select clear > select add #1.27 1542 atoms, 278 residues, 1 model selected > show sel surfaces > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel surfaces > select subtract #1.27 1 model selected > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel surfaces > show sel cartoons > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!1 atoms > hide #!1 cartoons > show #!1 surfaces > undo > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel surfaces > select subtract #1.27 1 model selected > select add #1.1 3 pseudobonds, 1 model selected > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected > select subtract #1.27 36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected > hide sel surfaces > select clear Drag select of 5 atoms, 12 residues, 5 bonds > hide sel atoms > select clear > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel surfaces > hide sel cartoons > show sel surfaces > select #1/Z:234@CB 1 atom, 1 residue, 1 model selected > select clear > save /Users/wujingyi/Desktop/figure/figure4/state1_a2电势.png width 1660 > height 1174 supersample 3 transparentBackground true > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel surfaces > select subtract #1.27 1 model selected > select add #1.9 543 atoms, 75 residues, 1 model selected > select add #1.10 1059 atoms, 147 residues, 2 models selected > select add #1.11 1594 atoms, 221 residues, 3 models selected > select add #1.12 2129 atoms, 295 residues, 4 models selected > select add #1.14 2664 atoms, 369 residues, 5 models selected > select add #1.13 3207 atoms, 444 residues, 6 models selected > select add #1.15 3742 atoms, 518 residues, 7 models selected > select add #1.16 4285 atoms, 593 residues, 8 models selected > select add #1.17 4828 atoms, 668 residues, 9 models selected > select add #1.18 5355 atoms, 741 residues, 10 models selected > show sel surfaces > select clear > view > save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势.png width 1660 > height 1174 supersample 3 transparentBackground true > save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势图.cxs > select add #1.27 1542 atoms, 278 residues, 1 model selected > select subtract #1.27 1 model selected > select add #1.27 1542 atoms, 278 residues, 1 model selected > show sel surfaces > select add #1.26 2294 atoms, 429 residues, 2 models selected > select subtract #1.27 752 atoms, 151 residues, 3 models selected > select subtract #1.26 1 model selected > select add #1.20 365 atoms, 74 residues, 1 model selected > select add #1.19 1445 atoms, 212 residues, 2 models selected > select subtract #1.20 1080 atoms, 138 residues, 3 models selected > select subtract #1.19 1 model selected > select add #1.19 1080 atoms, 138 residues, 1 model selected > select subtract #1.19 1 model selected > select add #1.18 527 atoms, 73 residues, 1 model selected > select add #1.17 1070 atoms, 148 residues, 2 models selected > select add #1.16 1613 atoms, 223 residues, 3 models selected > select add #1.15 2148 atoms, 297 residues, 4 models selected > select add #1.14 2683 atoms, 371 residues, 5 models selected > select add #1.13 3226 atoms, 446 residues, 6 models selected > select add #1.12 3761 atoms, 520 residues, 7 models selected > select add #1.11 4296 atoms, 594 residues, 8 models selected > select add #1.10 4812 atoms, 666 residues, 9 models selected > select add #1.9 5355 atoms, 741 residues, 10 models selected > hide sel surfaces > select #1/Z:245 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:245 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:274@CB 1 atom, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:268 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/Z:274@CB 1 atom, 1 residue, 1 model selected > select #1/Z:276@O 1 atom, 1 residue, 1 model selected > select #1/Z:263@O 1 atom, 1 residue, 1 model selected > select subtract #1.27 1 model selected > select add #1.21 1588 atoms, 265 residues, 1 model selected > show sel surfaces > select clear > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!8 models > hide #!8 models > show #!1 models > show #!11 models > hide #!11 models > hide #!1 models > show #!1 models > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected > hide sel surfaces > show sel cartoons > select subtract #1 26 models selected > select add #1.21 1588 atoms, 265 residues, 1 model selected > select add #1.27 3130 atoms, 543 residues, 2 models selected > color (#!1 & sel) forest green > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 4 models selected > select subtract #1 26 models selected > select add #1 37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected > select subtract #1.21 36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected > select subtract #1.27 34862 atoms, 35344 bonds, 4829 residues, 26 models selected > hide sel cartoons > select clear > show #!11 models > select add #11.21 1588 atoms, 265 residues, 1 model selected > select add #11.27 3130 atoms, 543 residues, 2 models selected > show sel cartoons > select clear > ui tool show Matchmaker > matchmaker #11/Z to #1/T pairing ss Parameters --- Chain pairing | ss 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 J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1) with J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain Z (#11), sequence alignment score = 1208.4 RMSD between 157 pruned atom pairs is 1.357 angstroms; (across all 265 pairs: 3.245) > select add #1.27 1542 atoms, 278 residues, 1 model selected > hide sel cartoons > select add #11.21 3130 atoms, 543 residues, 3 models selected > hide sel cartoons > ui mousemode right select Drag select of 30 atoms, 5 residues, 25 bonds > hide sel atoms > hide sel cartoons > cartoon style (#!11 & sel) modeHelix tube sides 20 > select clear > select add #11.27 1542 atoms, 278 residues, 1 model selected > color (#!11 & sel) light gray > select clear > select add #11.21 1588 atoms, 265 residues, 1 model selected > select subtract #11.21 1 model selected > select add #11.27 1542 atoms, 278 residues, 1 model selected Alignment identifier is 11/Z > select add #1.21 3130 atoms, 543 residues, 3 models selected Alignment identifier is 1/T Destroying pre-existing alignment with identifier 11/Z Alignment identifier is 11/Z > select clear > select #11/Z:30 5 atoms, 4 bonds, 1 residue, 1 model selected > select #11/Z:30 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select #1/T:30 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/T:30 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select subtract #1.21 1 model selected Cell requested for row 0 is out of bounds for table with 37 rows! Resizing table model. > hide #!1 models > hide #!11 models > show #!8 models > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase > 结构/RfxATP_state_1_Fo-4-coot-2.pdb"" Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #10 --- Chain | Description H L O P | No description available I | No description available J K M N | No description available Q | No description available T Z | No description available U X | No description available V Y | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase > 结构/RfxATP_state_1_Fo-4-coot-2.pdb"" Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #12 --- Chain | Description H L O P | No description available I | No description available J K M N | No description available Q | No description available T Z | No description available U X | No description available V Y | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!8 models > select add #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > show sel surfaces > hide sel surfaces > select add #12 22294 atoms, 22730 bonds, 4 pseudobonds, 2962 residues, 20 models selected > show sel surfaces > hide sel surfaces > select subtract #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 34 models selected > select add #10.2 11697 atoms, 11365 bonds, 2 pseudobonds, 1557 residues, 19 models selected > select add #10.3 12220 atoms, 11365 bonds, 2 pseudobonds, 1630 residues, 20 models selected > select add #10.4 12762 atoms, 11365 bonds, 2 pseudobonds, 1705 residues, 21 models selected > select add #10.5 13304 atoms, 11365 bonds, 2 pseudobonds, 1780 residues, 22 models selected > select add #10.6 13854 atoms, 11365 bonds, 2 pseudobonds, 1856 residues, 23 models selected > select add #10.7 14396 atoms, 11365 bonds, 2 pseudobonds, 1931 residues, 24 models selected > select add #10.8 14938 atoms, 11365 bonds, 2 pseudobonds, 2006 residues, 25 models selected > select add #10.9 15488 atoms, 11365 bonds, 2 pseudobonds, 2082 residues, 26 models selected > select add #10.10 16038 atoms, 11365 bonds, 2 pseudobonds, 2158 residues, 27 models selected > select add #10.11 16572 atoms, 11365 bonds, 2 pseudobonds, 2232 residues, 28 models selected > select subtract #12 5425 atoms, 751 residues, 27 models selected > select add #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected > select subtract #10 16 models selected > select add #10.12 2232 atoms, 291 residues, 1 model selected > select add #10.17 4464 atoms, 582 residues, 2 models selected > color (#!10 & sel) forest green > hide sel atoms > show sel cartoons > select add #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected > select subtract #10 16 models selected > select add #12.12 2232 atoms, 291 residues, 1 model selected > select add #12.17 4464 atoms, 582 residues, 2 models selected > color (#!12 & sel) light gray > hide sel atoms > show sel cartoons > select subtract #12.17 2232 atoms, 291 residues, 3 models selected > select subtract #12.12 1 model selected > select add #12 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > select subtract #12.17 8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected > select subtract #12.12 6683 atoms, 6791 bonds, 899 residues, 16 models selected > hide sel cartoons > hide sel atoms > select add #12 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected > select subtract #12 16 models selected > select add #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > select subtract #10.12 8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected > select subtract #10.17 6683 atoms, 6791 bonds, 899 residues, 16 models selected > hide sel atoms > select add #10 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected > select subtract #10 16 models selected > select add #10.12 2232 atoms, 291 residues, 1 model selected > select add #10.17 4464 atoms, 582 residues, 2 models selected > show sel cartoons > select clear > select add #10.17 2232 atoms, 291 residues, 1 model selected > select add #10.12 4464 atoms, 582 residues, 2 models selected > show sel atoms > hide sel atoms > show sel cartoons > show sel surfaces > hide sel surfaces > select clear > show #!10,12 cartoons > select add #10.17 2232 atoms, 291 residues, 1 model selected > select clear > undo > select add #12.17 2232 atoms, 291 residues, 1 model selected > select subtract #12.17 1 model selected > select add #12.12 2232 atoms, 291 residues, 1 model selected > hide sel cartoons > select subtract #12.12 1 model selected > select add #10.17 2232 atoms, 291 residues, 1 model selected > select subtract #10.17 1 model selected > select add #10.17 2232 atoms, 291 residues, 1 model selected > select subtract #10.17 1 model selected > select add #10.17 2232 atoms, 291 residues, 1 model selected > hide sel cartoons > select subtract #10.17 1 model selected > ui tool show Matchmaker > matchmaker #12/Z to #10/T pairing ss Parameters --- Chain pairing | ss 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 RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score = 1380.4 RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs: 2.932) > matchmaker #12/Z to #10/T pairing ss Parameters --- Chain pairing | ss 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 RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score = 1380.4 RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs: 2.932) > select add #10.12 2232 atoms, 291 residues, 1 model selected > select add #12.17 4464 atoms, 582 residues, 3 models selected Alignment identifier is 1 > select #10/T:30 #12/Z:30 20 atoms, 20 bonds, 2 residues, 2 models selected > select #10/T:30 #12/Z:30 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [30] RMSD: 0.804 > show sel atoms > select #10/T:130 #12/Z:130 16 atoms, 14 bonds, 2 residues, 2 models selected > select #10/T:130 #12/Z:130 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [130] RMSD: 0.879 > show sel atoms > select #10/T:140 #12/Z:140 12 atoms, 10 bonds, 2 residues, 2 models selected > select #10/T:140 #12/Z:140 12 atoms, 10 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [140] RMSD: 3.423 > show sel atoms > select #10/T:187 #12/Z:187 14 atoms, 12 bonds, 2 residues, 2 models selected > select #10/T:187 #12/Z:187 14 atoms, 12 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [163] RMSD: 2.893 > show sel atoms > select #10/T:263 #12/Z:263 16 atoms, 14 bonds, 2 residues, 2 models selected > select #10/T:263 #12/Z:263 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [239] RMSD: 0.744 > select #10/T:263,268 #12/Z:263,268 34 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region chains T,Z [239] + 1 other block RMSD: 0.813 > show sel atoms > select #10/T:259 #12/Z:259 22 atoms, 20 bonds, 2 residues, 2 models selected > select #10/T:259 #12/Z:259 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [235] RMSD: 0.890 > show sel atoms > select #10/T:252 #12/Z:252 22 atoms, 20 bonds, 2 residues, 2 models selected > select #10/T:252 #12/Z:252 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [228] RMSD: 0.342 > show sel atoms > select #10/T:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314 > #12/Z:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314 2874 atoms, 2928 bonds, 368 residues, 2 models selected > select #10/T:248 #12/Z:248 12 atoms, 10 bonds, 2 residues, 2 models selected > select #10/T:248-249 #12/Z:248-249 30 atoms, 28 bonds, 4 residues, 2 models selected 1 [ID: 1] region chains T,Z [224-225] RMSD: 0.828 > show sel atoms > select #10/T:245 #12/Z:245 18 atoms, 16 bonds, 2 residues, 2 models selected > select #10/T:245 #12/Z:245 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [221] RMSD: 1.184 > show sel atoms > select #10/T:228 #12/Z:228 18 atoms, 16 bonds, 2 residues, 2 models selected > select #10/T:228 #12/Z:228 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [204] RMSD: 2.971 > show sel atoms > select clear > style #10,12 stick Changed 22294 atom styles > select clear > cartoon style #10,12 modeHelix tube sides 20 > select clear > select add #12.17 2232 atoms, 291 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light yellow > color sel lemon chiffon > color sel light goldenrod yellow > color sel old lace > color sel light yellow > color sel ivory > color sel light yellow > color sel lemon chiffon > select clear > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660 > height 1174 supersample 3 transparentBackground true > select add #12.17 2232 atoms, 291 residues, 1 model selected > select clear > select add #12 11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected > hide sel cartoons > show #!1 models > hide #!1 models > select add #10.12 13379 atoms, 11365 bonds, 2 pseudobonds, 1772 residues, 19 models selected > hide sel cartoons > select clear > color #10,12 byhetero > select clear > ui mousemode right select > select clear Drag select of 2 atoms, 1 bonds Drag select of 1 atoms, 1 bonds > ui tool show ""Color Actions"" > color sel lemon chiffon > select clear > select #12/Z:245@O 1 atom, 1 residue, 1 model selected > select add #12/Z:245@N 2 atoms, 1 bond, 1 residue, 2 models selected > color sel lemon chiffon > select clear > select add #12/Z:249@N 1 atom, 1 bond, 1 residue, 1 model selected > select subtract #12/Z:249@N 1 model selected > select add #12/Z:249@N 1 atom, 1 residue, 1 model selected > select add #12/Z:249@O 2 atoms, 1 bond, 1 residue, 2 models selected > color sel lemon chiffon > select clear > select add #10/T:248@O 1 atom, 1 residue, 1 model selected > select add #12/Z:248@O 2 atoms, 2 residues, 3 models selected > color sel lemon chiffon > select clear > select #12/Z:252@O 1 atom, 1 residue, 1 model selected > select subtract #12/Z:252@O Nothing selected > select add #12/Z:252@N 1 atom, 1 residue, 1 model selected > select add #12/Z:252@O 2 atoms, 1 residue, 1 model selected > color sel lemon chiffon > select clear > select #12/Z:259@O 1 atom, 1 residue, 1 model selected > select add #12/Z:259@N 2 atoms, 1 bond, 1 residue, 2 models selected > color sel lemon chiffon > select clear > select #12/Z:263@O 1 atom, 1 residue, 1 model selected > select add #12/Z:263@N 2 atoms, 1 bond, 1 residue, 2 models selected > color sel lemon chiffon > select clear > select #12/Z:130@O 1 atom, 1 residue, 1 model selected > select add #10/T:130@O 2 atoms, 1 bond, 2 residues, 2 models selected > select subtract #10/T:130@O 1 atom, 1 bond, 1 residue, 2 models selected > select add #12/Z:130@N 2 atoms, 1 bond, 1 residue, 1 model selected > select subtract #12/Z:130@N 1 atom, 1 bond, 1 residue, 1 model selected Drag select of 1 atoms > color sel lemon chiffon > select clear Drag select of 1 atoms, 1 bonds Drag select of 1 atoms > color sel lemon chiffon > select clear > select add #12/Z:268@O 1 atom, 1 residue, 1 model selected > select add #12/Z:268@N 2 atoms, 1 bond, 1 residue, 1 model selected > color sel lemon chiffon > select clear > select add #10.12 2232 atoms, 291 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lemon chiffon > select subtract #10.12 1 model selected > select add #12.17 2232 atoms, 291 residues, 1 model selected > color (#!12 & sel) forest green > select clear > select add #12.17 2232 atoms, 291 residues, 1 model selected > select add #10.12 4464 atoms, 582 residues, 3 models selected > show sel cartoons > select clear > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660 > height 1174 supersample 3 transparentBackground true > select add #10.12 2232 atoms, 291 residues, 1 model selected > select add #12.17 4464 atoms, 582 residues, 3 models selected > hide sel cartoons > select clear > ui mousemode right select > select #10/T:290 #12/Z:290 18 atoms, 16 bonds, 2 residues, 2 models selected > select #10/T:290 #12/Z:290 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [266] RMSD: 1.278 > show sel atoms > select clear > ui mousemode right select Drag select of 6 atoms, 4 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 3 atoms, 2 bonds > color (#!10 & sel) byhetero > select clear Drag select of 2 atoms, 1 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 1 atoms > color (#!10 & sel) byhetero > select clear Drag select of 5 atoms, 4 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 8 atoms, 7 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 1 atoms > color (#!10 & sel) byhetero > select clear Drag select of 3 atoms, 2 bonds > select subtract #10/T:140@C 2 atoms, 1 bond, 1 residue, 3 models selected > color (#!12 & sel) byhetero > select clear Drag select of 3 atoms, 2 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 7 atoms, 7 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 1 atoms > color sel byhetero > select clear > select #10/T:248@OG 1 atom, 1 residue, 1 model selected > select add #12/Z:248@OG 2 atoms, 2 residues, 3 models selected > color (#!10,12 & sel) byhetero > select clear Drag select of 6 atoms, 5 bonds > color (#!10,12 & sel) byhetero > select clear Drag select of 1 atoms > color (#!10,12 & sel) byhetero > select clear > select add #12/Z:187@OG1 1 atom, 1 residue, 1 model selected Drag select of 34 atoms, 32 bonds > color (#!10,12 & sel) byhetero > select clear > select #12/Z:30@N 1 atom, 1 residue, 1 model selected Drag select of 1 atoms > select clear > select #12/Z:30@N 1 atom, 1 residue, 1 model selected > color (#!12 & sel) forest green > select clear Drag select of 1 atoms > select add #10/T:30@N 2 atoms, 1 residue, 2 models selected > ui tool show ""Color Actions"" > color sel lemon chiffon > select clear > select #12/Z:30@O 1 atom, 1 residue, 1 model selected > color sel forest green > select clear Drag select of 1 atoms, 2 bonds > color sel lemon chiffon > select clear Drag select of 1 atoms > color sel forest green > select clear > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png"" width > 1660 height 1174 supersample 3 transparentBackground true > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png"" width > 1660 height 1591 supersample 3 transparentBackground true > select add #10.12 2232 atoms, 291 residues, 1 model selected > select add #12.17 4464 atoms, 582 residues, 3 models selected > show sel cartoons > ui mousemode right select > select clear > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660 > height 1591 supersample 3 transparentBackground true > save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .cxs"" > open > /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb #13 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H J K L M N O P | No description available I Q | No description available R | No description available S W | No description available T | No description available U X | No description available V | No description available Y | No description available Z | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!10,12-13 atoms > show #!10,12-13 cartoons Cell requested for row 11 is out of bounds for table with 47 rows! Resizing table model. > hide #!12 models > hide #!10 models > select add #13 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected > show sel surfaces > hide sel surfaces > select subtract #13 26 models selected > select add #13.2 3805 atoms, 498 residues, 1 model selected > select add #13.3 7598 atoms, 994 residues, 2 models selected > select add #13.4 11420 atoms, 1494 residues, 3 models selected > color (#!13 & sel) #0099ccff > select subtract #13.2 7615 atoms, 996 residues, 4 models selected > select subtract #13.3 3822 atoms, 500 residues, 3 models selected > select subtract #13.4 1 model selected > select add #13.5 3597 atoms, 469 residues, 1 model selected > select add #13.6 7202 atoms, 939 residues, 2 models selected > select add #13.7 10788 atoms, 1407 residues, 3 models selected > color (#!13 & sel) #e9d49bff > select subtract #13.5 7191 atoms, 938 residues, 4 models selected > select subtract #13.6 3586 atoms, 468 residues, 3 models selected > select subtract #13.7 1 model selected > select add #13.8 2282 atoms, 289 residues, 1 model selected > color (#!13 & sel) #002befff > color (#!13 & sel) #2befc8ff > select subtract #13.8 1 model selected > select add #13.9 535 atoms, 74 residues, 1 model selected > select add #13.10 1062 atoms, 147 residues, 2 models selected > select add #13.11 1597 atoms, 221 residues, 3 models selected > select add #13.12 2132 atoms, 295 residues, 4 models selected > select add #13.13 2667 atoms, 369 residues, 5 models selected > select add #13.14 3202 atoms, 443 residues, 6 models selected > select add #13.15 3737 atoms, 517 residues, 7 models selected > select add #13.16 4272 atoms, 591 residues, 8 models selected > select add #13.17 4807 atoms, 665 residues, 9 models selected > select add #13.18 5334 atoms, 738 residues, 10 models selected > color (#!13 & sel) #f5ccdcff > select add #13 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected > select subtract #13 26 models selected > select add #13.21 1588 atoms, 265 residues, 1 model selected > select add #13.27 3130 atoms, 543 residues, 2 models selected > color (#!13 & sel) forest green > select clear > select add #13.22 747 atoms, 150 residues, 1 model selected > select add #13.26 1959 atoms, 301 residues, 2 models selected > select subtract #13.26 747 atoms, 150 residues, 3 models selected > select add #13.25 1812 atoms, 300 residues, 2 models selected > color (#!13 & sel) #c5c5ecff > select clear > select add #13.23 764 atoms, 152 residues, 1 model selected > select add #13.26 1976 atoms, 303 residues, 2 models selected > color (#!13 & sel) #9e7bbaff > select clear > select add #13.20 365 atoms, 74 residues, 1 model selected > select subtract #13.20 1 model selected > select add #13 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected > select subtract #13.2 34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected > select add #13.2 38578 atoms, 35235 bonds, 3 pseudobonds, 5349 residues, 27 models selected > select subtract #13.9 38043 atoms, 34692 bonds, 3 pseudobonds, 5275 residues, 28 models selected > select subtract #13.10 37516 atoms, 34157 bonds, 3 pseudobonds, 5202 residues, 27 models selected > select subtract #13.12 36981 atoms, 33614 bonds, 3 pseudobonds, 5128 residues, 26 models selected > select subtract #13.11 36446 atoms, 33071 bonds, 3 pseudobonds, 5054 residues, 25 models selected > select subtract #13.13 35911 atoms, 32528 bonds, 3 pseudobonds, 4980 residues, 24 models selected > select subtract #13.14 35376 atoms, 31985 bonds, 3 pseudobonds, 4906 residues, 23 models selected > select subtract #13.15 34841 atoms, 31442 bonds, 3 pseudobonds, 4832 residues, 22 models selected > select subtract #13.16 34306 atoms, 30899 bonds, 3 pseudobonds, 4758 residues, 21 models selected > select subtract #13.17 33771 atoms, 30356 bonds, 3 pseudobonds, 4684 residues, 20 models selected > select subtract #13.18 33244 atoms, 29821 bonds, 3 pseudobonds, 4611 residues, 19 models selected > select subtract #13.21 31656 atoms, 28218 bonds, 1 pseudobond, 4346 residues, 18 models selected > select subtract #13.27 30114 atoms, 26668 bonds, 4068 residues, 16 models selected > hide sel cartoons > select clear > select add #13.21 1588 atoms, 265 residues, 1 model selected > select add #13.27 3130 atoms, 543 residues, 2 models selected > color (#!13 & sel) dark gray > select clear > select add #13.9 535 atoms, 74 residues, 1 model selected > select add #13.10 1062 atoms, 147 residues, 2 models selected > select add #13.11 1597 atoms, 221 residues, 3 models selected > select add #13.12 2132 atoms, 295 residues, 4 models selected > select add #13.13 2667 atoms, 369 residues, 5 models selected > select add #13.14 3202 atoms, 443 residues, 6 models selected > select add #13.15 3737 atoms, 517 residues, 7 models selected > select add #13.16 4272 atoms, 591 residues, 8 models selected > select add #13.17 4807 atoms, 665 residues, 9 models selected > select add #13.18 5334 atoms, 738 residues, 10 models selected > hide sel cartoons > select add #13 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected > select subtract #13 26 models selected > select add #13.21 1588 atoms, 265 residues, 1 model selected > hide sel cartoons > show #!4 models > hide #!4 models > show #!5 models > show #!6 models > cartoon style (#!13 & sel) modeHelix tube sides 20 > select clear > select add #13 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected > select subtract #13 26 models selected > select add #13.21 1588 atoms, 265 residues, 1 model selected > select add #13.27 3130 atoms, 543 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light slate gray > color sel lavender > color sel light steel blue > select clear > color light steel blue > undo > select #13/Z:241 5 atoms, 4 bonds, 1 residue, 1 model selected > color #13.27 #b0bed1ff > color #13.27 #b8c6daff > undo > select subtract #13.27 1 model selected > select add #13.27 1542 atoms, 278 residues, 1 model selected > color (#!13 & sel) #b8c6daff > color (#!13 & sel) #b4c2d5ff > color (#!13 & sel) #b0bed1ff > color (#!13 & sel) #b0bdd0ff > color (#!13 & sel) #b0bed0ff > color (#!13 & sel) #adbbcdff > color (#!13 & sel) #abb9cbff > color (#!13 & sel) #aab7c9ff > color (#!13 & sel) #abb8caff > color (#!13 & sel) #adbaccff > color (#!13 & sel) #adbacdff > color (#!13 & sel) #afbdd0ff > color (#!13 & sel) #afbdd5ff > color (#!13 & sel) #afbdd9ff > color (#!13 & sel) #afbddbff > color (#!13 & sel) #afbde0ff > color (#!13 & sel) #afbddfff > color (#!13 & sel) #afbdddff > color (#!13 & sel) #afbddbff > color (#!13 & sel) #afbdd9ff > color (#!13 & sel) #afbdd5ff > color (#!13 & sel) #afbdd3ff > color (#!13 & sel) #afbdd2ff > color (#!13 & sel) #a9bdd2ff > color (#!13 & sel) #a3bdd2ff > color (#!13 & sel) #a5bdd2ff > color (#!13 & sel) #abbdd2ff > color (#!13 & sel) #afbdd2ff > color (#!13 & sel) #aebdd2ff > color (#!13 & sel) #abbdd2ff > color (#!13 & sel) #abb9d2ff > color (#!13 & sel) #abb6d2ff > color (#!13 & sel) #abb5d2ff > color (#!13 & sel) #abb7d2ff > color (#!13 & sel) #abb9d2ff > color (#!13 & sel) #abbad2ff > color (#!13 & sel) #abbbd2ff > color (#!13 & sel) #abbdd2ff > select subtract #13.27 1 model selected > select add #13.27 1542 atoms, 278 residues, 1 model selected > color (#!13 & sel) #abbdd2ff > color (#!13 & sel) #abbdd5ff > color (#!13 & sel) #abbdd8ff > color (#!13 & sel) #abbdddff > color (#!13 & sel) #abbde3ff > color (#!13 & sel) #abbde9ff > color (#!13 & sel) #abbdeeff > color (#!13 & sel) #abbdecff > color (#!13 & sel) #abbdebff > color (#!13 & sel) #abbde1ff > color (#!13 & sel) #abbdd4ff > color (#!13 & sel) #abbdd3ff > color (#!13 & sel) #abbdd2ff > color (#!13 & sel) #abbdd7ff > select subtract #13.27 1 model selected > select clear > select #13/Z:259 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style (#!13 & sel) stick Changed 11 atom styles > select clear > select add #13.10 527 atoms, 73 residues, 1 model selected > select add #13.11 1062 atoms, 147 residues, 2 models selected > select add #13.12 1597 atoms, 221 residues, 3 models selected > select add #13.13 2132 atoms, 295 residues, 4 models selected > select add #13.14 2667 atoms, 369 residues, 5 models selected > select add #13.15 3202 atoms, 443 residues, 6 models selected > select add #13.16 3737 atoms, 517 residues, 7 models selected > select add #13.17 4272 atoms, 591 residues, 8 models selected > select add #13.18 4799 atoms, 664 residues, 9 models selected Alignment identifier is 2 Alignment identifier is 3 > select #13/I,Q:59 18 atoms, 16 bonds, 2 residues, 1 model selected > select #13/I,Q:59-60 28 atoms, 26 bonds, 4 residues, 1 model selected > select #13/I,Q:59 18 atoms, 16 bonds, 2 residues, 1 model selected > select #13/I,Q:59 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > show sel cartoons > hide sel cartoons > style (#!13 & sel) stick Changed 18 atom styles > select clear > select #13/P,O,N,L-M,K,J:59 63 atoms, 56 bonds, 7 residues, 1 model selected > select #13/P,O,N,L-M,K,J:59 63 atoms, 56 bonds, 7 residues, 1 model selected > show sel atoms > style (#!13 & sel) stick Changed 63 atom styles > select clear > select #10/T:290 #12/Z:290 18 atoms, 16 bonds, 2 residues, 2 models selected > select #10/T:290 #12/Z:290 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region chains T,Z [266] RMSD: 1.278 > show #!5-6,13 atoms > hide #!5-6,13 atoms > undo Drag select of 4 atoms, 5 bonds > select clear > select add #13.9 535 atoms, 74 residues, 1 model selected > select subtract #13.9 1 model selected > select add #13.10 527 atoms, 73 residues, 1 model selected > select subtract #13.10 1 model selected > select add #13.9 535 atoms, 74 residues, 1 model selected Alignment identifier is 13/H > select #13/H:59 9 atoms, 8 bonds, 1 residue, 1 model selected > select #13/H:59 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style (#!13 & sel) stick Changed 9 atom styles > select clear > open > /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb #14 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H J K L M N O P | No description available I Q | No description available R | No description available S W | No description available T | No description available U X | No description available V | No description available Y | No description available Z | No description available 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!5-6,13-14 atoms > select add #14 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected > show sel surfaces > hide sel surfaces > select subtract #14.2 34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected > select subtract #14.3 30980 atoms, 31384 bonds, 3 pseudobonds, 4355 residues, 27 models selected > select subtract #14.4 27158 atoms, 27504 bonds, 3 pseudobonds, 3855 residues, 26 models selected > select subtract #14.5 23561 atoms, 23844 bonds, 3 pseudobonds, 3386 residues, 25 models selected > select subtract #14.6 19956 atoms, 20176 bonds, 3 pseudobonds, 2916 residues, 24 models selected > select subtract #14.7 16370 atoms, 16527 bonds, 3 pseudobonds, 2448 residues, 23 models selected > select subtract #14.8 14088 atoms, 14217 bonds, 3 pseudobonds, 2159 residues, 22 models selected > select subtract #14.27 12546 atoms, 12667 bonds, 2 pseudobonds, 1881 residues, 21 models selected > select subtract #14.26 11334 atoms, 11445 bonds, 2 pseudobonds, 1730 residues, 20 models selected > select subtract #14.25 10269 atoms, 10378 bonds, 2 pseudobonds, 1580 residues, 19 models selected > select subtract #14.24 9904 atoms, 10014 bonds, 2 pseudobonds, 1506 residues, 18 models selected > select subtract #14.23 9140 atoms, 9251 bonds, 2 pseudobonds, 1354 residues, 17 models selected > select subtract #14.22 8393 atoms, 8505 bonds, 2 pseudobonds, 1204 residues, 16 models selected > select subtract #14.21 6805 atoms, 6902 bonds, 939 residues, 14 models selected > select subtract #14.20 6440 atoms, 6538 bonds, 865 residues, 13 models selected > select subtract #14.19 5548 atoms, 5636 bonds, 748 residues, 12 models selected > show sel atoms > hide sel atoms > show sel cartoons > color (#!14 & sel) #f5ccdcff Cell requested for row 13 is out of bounds for table with 41 rows! Resizing table model. > select add #14 38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected > select subtract #14 26 models selected > hide #!13 models > hide #!6 models > hide #!5 models Drag select of 738 residues Alignment identifier is 1 Alignment identifier is 4 > show #!13 models > show #!5 models > show #!6 models > select #14/P,O,N,L-M,K,J,H:76 64 atoms, 56 bonds, 8 residues, 1 model selected > select #14/P,O,N,L-M,K,J,H 4280 atoms, 4344 bonds, 592 residues, 1 model selected > hide sel cartoons > select #14/P,O,N,L-M,K,J,H:59 72 atoms, 64 bonds, 8 residues, 1 model selected > select #14/P,O,N,L-M,K,J,H:59 72 atoms, 64 bonds, 8 residues, 1 model selected > show sel atoms > show sel cartoons > select #14/I,Q:75 22 atoms, 20 bonds, 2 residues, 1 model selected > select #14/I,Q 1054 atoms, 1070 bonds, 146 residues, 1 model selected > hide sel cartoons > select #14/I,Q:59 18 atoms, 16 bonds, 2 residues, 1 model selected > select #14/I,Q:59 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > show sel cartoons > select clear > style #5-6,13-14 ball Changed 89937 atom styles > style #5-6,13-14 stick Changed 89937 atom styles > select clear ===== 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 Metal - 88 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple 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: Mac15,6 Model Number: MRX63CH/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4 (23E214) Kernel Version: Darwin 23.4.0 Time since boot: 46天3小时39分钟 Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Redmi 27 NU: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Resolution: 3024 x 1964 UI Looks like: 1512 x 982 @ 120.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX