id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16194 Crash rendering QToolButton icon: QPainter::begin: Paint device returned engine == 0, type: 2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.9.dev202407040137 (2024-07-04 01:37:03 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 0x00007ff84f230dc0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 323 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1030 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1193 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, 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, PIL._imagingmath (total: 123) {""app_name"":""ChimeraX"",""timestamp"":""2024-10-25 11:02:57.00 -0700"",""app_version"":""1.9.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""BB6558FA-C129-4462-A63C-6BC403563569""} { ""uptime"" : 410000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,1"", ""coalitionID"" : 15246, ""osVersion"" : { ""train"" : ""macOS 14.6.1"", ""build"" : ""23G93"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-10-25 11:02:37.1712 -0700"", ""codeSigningMonitor"" : 0, ""incident"" : ""BB6558FA-C129-4462-A63C-6BC403563569"", ""pid"" : 4347, ""cpuType"" : ""X86-64"", 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Bytes before following region: 4351971304\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10365d000-103661000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":4347}, ""vmregioninfo"" : ""0x18 is not in any region. 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University of California. All rights reserved. > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v0.cxs"" Log from Mon Oct 14 18:43:18 2024 Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9.dev202407040137 (2024-07-04) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/Alphafold_prediction/PumNav14_with_template_hNav14_9fa5e/PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb"" Chain information for PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #1 --- Chain | Description A | No description available > color bfactor #1 palette alphafold 14707 atoms, 1843 residues, atom bfactor range 20.8 to 95.3 > open 8T6L 8t6l title: Cryo-EM structure of rat cardiac sodium channel NaV1.5 with batrachotoxin analog BTX-B [more info...] Chain information for 8t6l #2 --- Chain | Description | UniProt A | Sodium channel protein type 5 subunit alpha,Green fluorescent protein | SCN5A_RAT 1-1931, GFP_AEQVI 1946-2182 Non-standard residues in 8t6l #2 --- 9Z9 — (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) LBN — 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine ((2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Y01 — cholesterol hemisuccinate YIJ — (1R)-1-[(5aR,7aR,9R,11aS,11bS,12R,13aR)-9,12-dihydroxy-2,11a-dimethyl-1,2,3,4,7a,8,9,10,11,11a,12,13-dodecahydro-7H-9,11b-epoxy-13a,5a-prop[1]enophenanthro[2,1-f][1,4]oxazepin-14-yl]ethyl benzoate 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui mousemode right select > select add #2 10980 atoms, 11288 bonds, 4 pseudobonds, 1279 residues, 3 models selected Drag select of 85 atoms, 151 residues, 82 bonds > select add #2 10980 atoms, 11288 bonds, 4 pseudobonds, 1279 residues, 3 models selected Drag select of 102 atoms, 107 residues, 93 bonds > select add #2 10980 atoms, 11288 bonds, 4 pseudobonds, 1279 residues, 3 models selected > ui mousemode right select > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-43.553,0,1,0,-34.438,0,0,1,-57.686 > view matrix models #2,1,0,0,-88.86,0,1,0,-73.528,0,0,1,-120.38 > view matrix models #2,1,0,0,-65.567,0,1,0,-64.765,0,0,1,-104.5 > select subtract #2 Nothing selected > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 8t6l, chain A (#2), sequence alignment score = 5749.2 RMSD between 1090 pruned atom pairs is 0.896 angstroms; (across all 1236 pairs: 3.532) > hide #1 models > ui mousemode right select Drag select of 3 bonds Drag select of 25 atoms, 18 residues, 26 bonds > select #2/A:3012@C4 1 atom, 1 residue, 1 model selected > select #2/A:3012@C32 1 atom, 1 residue, 1 model selected > select clear Drag select of 4 atoms, 3 bonds Drag select of 4 atoms, 4 bonds > select #2/A:3012@C4 1 atom, 1 residue, 1 model selected Drag select of 4 atoms, 3 bonds > hide #!2 target m [Repeated 1 time(s)] > show #!2 target m > hide sel target a Drag select of 4 atoms, 4 bonds > select #2/A:3012@C32 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C28 1 atom, 1 bond, 1 residue, 1 model selected > select clear > select #2/A:3012@C32 1 atom, 1 residue, 1 model selected > select #2/A:3012@C28 1 atom, 1 residue, 1 model selected > select #2/A:3012@C32 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C28 2 atoms, 1 residue, 1 model selected > select clear > select #2/A:3012@C30 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C12 1 atom, 15 bonds, 1 residue, 1 model selected > hide sel target ab > undo > surface hidePatches sel > undo > hide sel target ab > select #2/A:3012@C30 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C29 2 atoms, 1 residue, 1 model selected > select add #2/A:3012@C32 3 atoms, 1 residue, 1 model selected Drag select of 7 atoms, 1 residues Drag select of 5 atoms > select clear > select #2/A:3012@C26 1 atom, 1 residue, 1 model selected > select add #2/A:3012@O6 2 atoms, 1 residue, 1 model selected > select #2/A:3012@C28 1 atom, 1 residue, 1 model selected Drag select of 6 atoms > hide sel target a > select #2/A:3012@C30 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C32 2 atoms, 1 residue, 1 model selected > select add #2/A:3012@C29 3 atoms, 1 residue, 1 model selected > select add #2/A:3012@O5 4 atoms, 1 residue, 1 model selected > select add #2/A:3012@C3 5 atoms, 1 residue, 1 model selected > select add #2/A:3012@O3 6 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:3012@P1 7 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:3012@C2 8 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/A:3012@O2 9 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:3012@O8 10 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/A:3012@C6 11 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/A:3012@C15 12 atoms, 7 bonds, 1 residue, 1 model selected > hide sel target ab Drag select of 4 atoms, 4 residues, 1 pseudobonds > select #2/A:3012@O4 1 atom, 1 residue, 1 model selected > select add #2/A:3012@C9 2 atoms, 1 residue, 1 model selected > select add #2/A:3012@N1 3 atoms, 1 residue, 1 model selected > select add #2/A:3012@C18 4 atoms, 1 residue, 1 model selected > hide sel target a > select #2/A:3012@O7 1 atom, 1 residue, 1 model selected > select add #2/A:3012@O1 2 atoms, 1 residue, 1 model selected > select add #2/A:3012@C1 3 atoms, 1 residue, 1 model selected > hide > undo Drag select of 207 atoms, 43 residues, 204 bonds > hide sel target a Drag select of 11 atoms, 51 residues, 5 bonds > hide sel target a > show #1 models > hide #1 models Drag select of 143 atoms, 86 residues, 140 bonds > hide sel target a Drag select of 23 atoms, 26 residues, 24 bonds Drag select of 25 atoms, 33 residues, 24 bonds > hide sel target a Drag select of 41 atoms, 23 residues, 39 bonds > hide sel target a > select #2/A:136@SD 1 atom, 1 residue, 1 model selected > hide sel target a Drag select of 40 atoms, 43 residues, 40 bonds > hide sel target a Drag select of 2 atoms > hide sel target a > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v1.pdb"" models #2 > displayedOnly true Drag select of 2 atoms, 10 residues, 2 bonds Drag select of 57 atoms, 56 residues, 60 bonds > select clear Drag select of 41 atoms, 38 residues, 41 bonds Drag select of 76 atoms, 85 residues, 78 bonds Drag select of 110 atoms, 125 residues, 111 bonds > hide sel target a Drag select of 4 atoms, 2 residues, 2 bonds > hide sel target a Drag select of 4 atoms, 7 residues, 3 bonds Drag select of 29 atoms, 44 residues, 26 bonds > hide sel target a Drag select of 6 atoms, 3 residues, 5 bonds > hide sel target a Drag select of 38 atoms, 7 residues, 37 bonds > hide sel target a Drag select of 3 atoms, 8 residues, 4 bonds > hide sel target a Drag select of 30 atoms, 11 residues, 34 bonds > hide sel target a Drag select of 1 atoms > hide sel target a Drag select of 3 atoms > hide sel target a Drag select of 14 atoms, 2 residues, 13 bonds > hide sel target a Drag select of 57 atoms, 55 residues, 58 bonds > hide sel target a Drag select of 5 atoms, 15 residues, 4 bonds > hide sel target a Drag select of 8 atoms, 4 residues, 8 bonds > hide sel target a Drag select of 19 atoms, 28 residues, 18 bonds > hide sel target a > select #2/A:3010@O8 1 atom, 1 residue, 1 model selected > hide sel target a Drag select of 12 atoms, 13 residues, 12 bonds > hide sel target a Drag select of 17 atoms, 7 residues, 16 bonds > hide sel target a Drag select of 35 atoms, 11 residues, 38 bonds > hide sel target a Drag select of 31 atoms, 34 bonds > hide sel target a Drag select of 66 atoms, 10 residues, 70 bonds > hide sel target a Drag select of 12 atoms, 8 residues, 10 bonds > hide sel target a Drag select of 4 atoms, 2 residues, 2 bonds > select add #2/A:3011@C22 21 atoms, 4 bonds, 3 residues, 1 model selected > select subtract #2/A:3011@C20 20 atoms, 3 bonds, 3 residues, 1 model selected > select add #2/A:3011@C20 21 atoms, 3 bonds, 3 residues, 1 model selected > select add #2/A:3011@C36 22 atoms, 4 bonds, 3 residues, 1 model selected > hide sel target ab > select clear > select #2/A:3011@C37 1 atom, 1 residue, 1 model selected > select add #2/A:3011@C8 2 atoms, 1 residue, 1 model selected > select add #2/A:3011@C14 3 atoms, 1 residue, 1 model selected > select add #2/A:3011@C17 4 atoms, 1 residue, 1 model selected > hide sel target a Drag select of 35 atoms, 12 residues, 38 bonds > hide sel target a Drag select of 31 atoms, 5 residues, 34 bonds > hide sel target a Drag select of 15 atoms, 1 residues, 13 bonds > hide sel target a Drag select of 14 atoms, 2 residues, 14 bonds > hide sel target a Drag select of 10 atoms, 2 residues, 9 bonds > hide sel target a Drag select of 17 atoms, 5 residues, 16 bonds > hide sel target a Drag select of 33 atoms, 8 residues, 38 bonds > hide sel target a > select #2/A:3023@CAD 1 atom, 1 residue, 1 model selected > select add #2/A:3023@CAE 2 atoms, 1 residue, 1 model selected > hide sel target a Drag select of 130 atoms, 65 residues, 141 bonds > hide sel target a Drag select of 5 atoms, 9 residues, 4 bonds > hide sel target a Drag select of 5 atoms, 8 residues, 4 bonds > hide sel target a Drag select of 4 atoms, 6 residues, 3 bonds > hide sel target a Drag select of 12 atoms, 8 residues, 13 bonds > hide sel target a Drag select of 5 atoms, 7 residues, 4 bonds > hide sel target a > hide sel target b > select #2/A:899@SG 1 atom, 1 residue, 1 model selected > select add #2/A:899@CB 2 atoms, 1 residue, 1 model selected > hide sel target a > select add #2/A:1420@CD1 1 atom, 8 bonds, 1 residue, 1 model selected > select add #2/A:1420@CZ 2 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:1420@CE2 3 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:1420@CD2 4 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:1420@CG 5 atoms, 8 bonds, 1 residue, 1 model selected > hide sel target ab > select #2/A:1420@CE1 1 atom, 1 residue, 1 model selected > select add #2/A:1420@CB 2 atoms, 1 residue, 1 model selected > hide sel target a > select add #2/A:1464@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1464@CG 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1464@CD2 3 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:1464@CD1 4 atoms, 4 bonds, 1 residue, 1 model selected > hide sel target a > select add #2/A:1347@CH2 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1347@CZ3 2 atoms, 1 bond, 1 residue, 1 model selected > select add #2/A:1347@CE3 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1347@CD2 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:1347@CE2 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/A:1347@CZ2 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:1347@NE1 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/A:1347@CD1 8 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:1347@CG 9 atoms, 9 bonds, 1 residue, 1 model selected > select subtract #2/A:1347@CD2 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/A:1347@CD2 9 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/A:1347@CB 10 atoms, 11 bonds, 1 residue, 1 model selected > hide sel target a > select clear > select add #2/A:1712@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1712@OG 2 atoms, 2 bonds, 1 residue, 1 model selected > hide sel target a > select #2/A:1762@CZ 1 atom, 1 residue, 1 model selected > select add #2/A:1762@CD1 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1762@CG 3 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:1762@CE2 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/A:1762@CD2 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:1762@CB 6 atoms, 7 bonds, 1 residue, 1 model selected > hide sel target a > select #2/A:3101@O 1 atom, 1 residue, 1 model selected > hide sel target a > select add #2/A:1765@CG1 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1765@CG2 2 atoms, 2 bonds, 1 residue, 1 model selected > hide sel target ab > select #2/A:1765@CB 1 atom, 1 residue, 1 model selected > hide sel target a > select add #2/A:1768@CE 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1768@CG 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1768@SD 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1768@CB 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a > select add #2/A:395@CE 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:395@SD 2 atoms, 1 bond, 1 residue, 1 model selected > select add #2/A:395@CG 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:395@CB 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a > select add #2/A:398@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:398@CG1 2 atoms, 1 bond, 1 residue, 1 model selected > select add #2/A:398@CD1 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:398@CG2 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a > select add #2/A:1707@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:1707@CG 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1707@CZ 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:1707@CE1 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/A:1707@CD1 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:1707@CD2 6 atoms, 6 bonds, 1 residue, 1 model selected > select subtract #2/A:1707@CG 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:1707@CG 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel target a > select #2/A:1707@CE2 1 atom, 1 residue, 1 model selected > hide sel target a > select #2/A:372@OE1 1 atom, 1 residue, 1 model selected > select add #2/A:372@CD 2 atoms, 1 bond, 1 residue, 1 model selected > select add #2/A:372@NE2 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:372@CG 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:372@CB 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel target a > select #2/A:854@CZ 1 atom, 1 residue, 1 model selected > select add #2/A:854@CE2 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:854@CD2 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:854@CG 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/A:854@CD1 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:854@CE1 6 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/A:854@CB 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel target a Drag select of 7 atoms, 5 residues, 8 bonds > hide sel target a > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v2.pdb"" models #2 > displayedOnly true > select #2/A:1762@CE1 1 atom, 1 residue, 1 model selected > hide sel target a Drag select of 11 atoms, 24 residues, 8 bonds > hide sel target a > select clear Drag select of 3 residues, 1 bonds > select add #2/A:403@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:403@CG 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:403@CD1 3 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:403@CE1 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:403@CZ 5 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:403@CE2 6 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:403@CD2 7 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a Drag select of 6 atoms, 2 residues, 5 bonds > hide sel target a Drag select of 5 atoms, 8 residues, 1 pseudobonds, 4 bonds > hide (#!2 & sel) target a > show #1 models > hide #1 models > select add #2/A:399@CB 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/A:399@CG 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #2/A:399@CD2 3 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:399@CE2 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:399@CZ 5 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:399@CE1 6 atoms, 3 bonds, 1 residue, 1 model selected > select add #2/A:399@CD1 7 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a > select #2/A:1666@CD2 1 atom, 1 residue, 1 model selected > select add #2/A:1666@CD1 2 atoms, 1 residue, 1 model selected > select add #2/A:1666@CG 3 atoms, 1 residue, 1 model selected > select add #2/A:1666@CB 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel target a > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" models #2 > displayedOnly true > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" Summary of feedback from opening /Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 17 GLN A 32 1 16 Start residue of secondary structure not found: HELIX 2 2 GLN A 56 GLN A 60 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 66 GLY A 70 1 5 Start residue of secondary structure not found: HELIX 4 4 ASN A 110 VAL A 114 1 5 Start residue of secondary structure not found: HELIX 5 5 HIS A 119 VAL A 130 1 12 69 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (281 ) Cannot find LINK/SSBOND residue CYS (327 ) Cannot find LINK/SSBOND residue CYS (909 ) Cannot find LINK/SSBOND residue CYS (1365 ) Cannot find LINK/SSBOND residue CYS (1730 ) 16 messages similar to the above omitted Chain information for 8T6L_rNav1.5_BTX-v3.pdb #3 --- Chain | Description A | No description available > hide #!2 models > show #!2 models > hide #!3 models > close #3 > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v2.pdb"" Summary of feedback from opening /Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v2.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 17 GLN A 32 1 16 Start residue of secondary structure not found: HELIX 2 2 GLN A 56 GLN A 60 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 66 GLY A 70 1 5 Start residue of secondary structure not found: HELIX 4 4 ASN A 110 VAL A 114 1 5 Start residue of secondary structure not found: HELIX 5 5 HIS A 119 VAL A 130 1 12 69 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (281 ) Cannot find LINK/SSBOND residue CYS (327 ) Cannot find LINK/SSBOND residue CYS (909 ) Cannot find LINK/SSBOND residue CYS (1365 ) Cannot find LINK/SSBOND residue CYS (1730 ) 16 messages similar to the above omitted Chain information for 8T6L_rNav1.5_BTX-v2.pdb #3 --- Chain | Description A | No description available > hide #!2 models > close #3 > close #1 > show #!2 models > ui mousemode right select > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" Chain information for 8T6L_rNav1.5_BTX-v3.pdb #1 --- Chain | Description A | No description available 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!2 models > show #!2 models > hide #!1 models > close #1 > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" displayedOnly > true > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" Summary of feedback from opening /Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 17 GLN A 32 1 16 Start residue of secondary structure not found: HELIX 2 2 GLN A 56 GLN A 60 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 66 GLY A 70 1 5 Start residue of secondary structure not found: HELIX 4 4 ASN A 110 VAL A 114 1 5 Start residue of secondary structure not found: HELIX 5 5 HIS A 119 VAL A 130 1 12 69 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (281 ) Cannot find LINK/SSBOND residue CYS (327 ) Cannot find LINK/SSBOND residue CYS (909 ) Cannot find LINK/SSBOND residue CYS (1365 ) Cannot find LINK/SSBOND residue CYS (1730 ) 16 messages similar to the above omitted Chain information for 8T6L_rNav1.5_BTX-v3.pdb #1 --- Chain | Description A | No description available > select add #1 181 atoms, 175 bonds, 18 pseudobonds, 25 residues, 4 models selected > select subtract #1 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #2 10980 atoms, 11288 bonds, 4 pseudobonds, 1279 residues, 3 models selected > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > close #1 > select add #2 10980 atoms, 11288 bonds, 4 pseudobonds, 1279 residues, 3 models selected > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" selectedOnly true > select subtract #2 Nothing selected > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v3.pdb"" Chain information for 8T6L_rNav1.5_BTX-v3.pdb #1 --- Chain | Description A | No description available 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!2 models > show #!2 models > hide #!1 models > close #1 > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/8T6L_rNav1.5_BTX-v0.cxs"" ——— End of log from Mon Oct 14 18:43:18 2024 ——— opened ChimeraX session > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/Alphafold_prediction/PumNav14_with_template_hNav14_9fa5e/PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb"" Chain information for PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #1 --- Chain | Description A | No description available > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 8t6l, chain A (#2), sequence alignment score = 5749.2 RMSD between 1090 pruned atom pairs is 0.896 angstroms; (across all 1236 pairs: 3.532) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 8t6l, chain A (#2), sequence alignment score = 5749.2 RMSD between 1090 pruned atom pairs is 0.896 angstroms; (across all 1236 pairs: 3.532) > select add #1 14707 atoms, 15051 bonds, 1843 residues, 1 model selected > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select subtract #1 Nothing selected > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 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 > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 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 cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select add #1 14707 atoms, 15051 bonds, 1843 residues, 1 model selected > select subtract #1 Nothing selected > set bgColor white > set bgColor black > set bgColor white > color #2 #7a81ffff > color #2 #0433ffff > color #2 #005493ff > color #2 #011993ff > color #2 #005493ff > color #2 #009193ff > color #2 #005493ff > color #2 #0096ffff > color #2 #0433ffff > color #2 #011993ff > color #2 #531b93ff > color #2 #011993ff > color #2 #005493ff > color #2 #531b93ff > color #2 #9437ffff > color #2 #0433ffff > color #2 #005493ff > color #2 #0062aeff > color #2 #0061acff > color #2 #011993ff > color #2 #0433ffff > color #2 #0096ffff > color #2 #0433ffff > color #2 #032eefff > color #2 #531b93ff > color #2 #011993ff > color #2 #005493ff > color #2 #0096ffff > color #2 #00fdffff > color #2 #00fa92ff > color #2 #00fdffff > color #2 #0096ffff > color #2 #0433ffff > color #2 #7a81ffff > color #2 #4a4f9dff > color #2 #4f55a9ff > color #2 #3b3f7eff > color #2 #5257aeff > color #2 #575db9ff > color #2 #595fbdff > color #1 #008f00ff > color #1 #4f8f00ff > color #1 #929000ff > color #1 #9437ffff > color #1 #942193ff > color #1 #941751ff > color #1 #942193ff > color #1 #941751ff > color #1 #ff2f92ff > color #1 #9437ffff > color #1 #ff2f92ff > color #1 #941751ff > color #1 #d52176ff > color #1 #a5195bff > color #1 #be1d69ff > color #1 #ab1a5eff > ui mousemode right select > select #1/A:813 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:391 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:392 11 atoms, 11 bonds, 1 residue, 1 model selected > ui mousemode right select > ui mousemode right ""move label"" > ui mousemode right select > select clear > ui mousemode right label > label delete residues > ui mousemode right zone > ui mousemode right label > ui mousemode right ""move label"" > ui mousemode right label > label delete residues > ui mousemode right select > select clear > ui mousemode right ""move label"" > ui mousemode right rotate > ui mousemode right select > select clear > delete label Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > ui mousemode right label > label delete residues > ui mousemode right ""move label"" > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting simple > save /Users/fayal/Desktop/image2.png supersample 3 > save /Users/fayal/Desktop/image3.png supersample 3 > save ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/PumNav1.4-rNav1.5-BTX.cxs"" > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/Alphafold_prediction/PumNav14_with_template_hNav14_9fa5e/PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb"" Chain information for PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #3 --- Chain | Description A | No description available > hide #!2 models > hide #1 models > color bfactor #3 palette alphafold 14707 atoms, 1843 residues, atom bfactor range 20.8 to 95.3 > select add #3 14707 atoms, 15051 bonds, 1843 residues, 1 model selected > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/Alphafold_prediction/PumNav14_with_template_hNav14_9fa5e/PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb"" Chain information for PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb #4 --- Chain | Description A | No description available > color bfactor #4 palette alphafold 14707 atoms, 1843 residues, atom bfactor range 19.8 to 93.9 > hide #3 models > select subtract #3 Nothing selected > matchmaker #4 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#3) with PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb, chain A (#4), sequence alignment score = 9361.6 RMSD between 1105 pruned atom pairs is 0.989 angstroms; (across all 1843 pairs: 12.359) > select add #4 14707 atoms, 15051 bonds, 1843 residues, 1 model selected > show #3 models > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select subtract #4 Nothing selected > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > hide #4 models > show #3 models > show #4 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > close #4 > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > save /Users/fayal/Desktop/image2.png supersample 3 > show #!2 models > show #1 models > hide #3 models > hide #1 models > show #1 models > hide #!2 models > show #3 models > show #!2 models > hide #1 models > hide #!2 models > lighting full > lighting soft > lighting simple > save /Users/fayal/Desktop/image3.png supersample 3 > open ""/Users/fayal/Documents/taf/1-Fayal lab/4-Projects/Toxin > survival_autoresistance/BTX_birds/6agf.pdb"" 6agf.pdb title: Structure of the human voltage-gated sodium channel NAV1.4 In complex with Β1 [more info...] Chain information for 6agf.pdb #4 --- Chain | Description | UniProt A | sodium channel protein type 4 subunit α | SCN4A_HUMAN 1-1836 B | sodium channel subunit β-1 | SCN1B_HUMAN 1-218 Non-standard residues in 6agf.pdb #4 --- 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate 9Z9 — (3Β,14Β,17Β,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en BMA — β-D-mannopyranose NAG — 2-acetamido-2-deoxy-β-D-glucopyranose > hide #3 models > matchmaker #4 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#3) with 6agf.pdb, chain A (#4), sequence alignment score = 6509 RMSD between 1080 pruned atom pairs is 0.824 angstroms; (across all 1138 pairs: 1.259) > show #3 models > select add #4 10980 atoms, 11243 bonds, 3 pseudobonds, 1327 residues, 3 models selected > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select subtract #4 Nothing selected > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > ui mousemode right select > select #4/B:169 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:175 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:186 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/B:190 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/B:64 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:190 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/B:191 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:192 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/B:191 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #4/B:190 21 atoms, 18 bonds, 3 residues, 1 model selected > select add #4/B:189 28 atoms, 24 bonds, 4 residues, 1 model selected > select add #4/B:188 33 atoms, 28 bonds, 5 residues, 1 model selected > select add #4/B:186 38 atoms, 32 bonds, 6 residues, 1 model selected > select add #4/B:187 43 atoms, 36 bonds, 7 residues, 1 model selected > select subtract #4/B:187 38 atoms, 32 bonds, 6 residues, 1 model selected > select subtract #4/B:186 33 atoms, 28 bonds, 5 residues, 1 model selected > select add #4/B:186 38 atoms, 32 bonds, 6 residues, 1 model selected > cartoon hide sel > select add #4/B:187 43 atoms, 36 bonds, 7 residues, 1 model selected > select add #4/B:185 51 atoms, 43 bonds, 8 residues, 1 model selected > select add #4/B:184 60 atoms, 51 bonds, 9 residues, 1 model selected > select add #4/B:183 69 atoms, 59 bonds, 10 residues, 1 model selected > select add #4/B:182 81 atoms, 71 bonds, 11 residues, 1 model selected > select add #4/B:181 87 atoms, 76 bonds, 12 residues, 1 model selected > select add #4/B:180 99 atoms, 88 bonds, 13 residues, 1 model selected > select add #4/B:179 107 atoms, 95 bonds, 14 residues, 1 model selected > select add #4/B:178 115 atoms, 102 bonds, 15 residues, 1 model selected > select add #4/B:177 124 atoms, 110 bonds, 16 residues, 1 model selected > select add #4/B:176 129 atoms, 114 bonds, 17 residues, 1 model selected > select add #4/B:175 136 atoms, 120 bonds, 18 residues, 1 model selected > select add #4/B:174 144 atoms, 127 bonds, 19 residues, 1 model selected > select subtract #4/B:174 136 atoms, 120 bonds, 18 residues, 1 model selected > select add #4/B:174 144 atoms, 127 bonds, 19 residues, 1 model selected > select add #4/B:173 158 atoms, 142 bonds, 20 residues, 1 model selected > select add #4/B:171 165 atoms, 148 bonds, 21 residues, 1 model selected > select add #4/B:170 173 atoms, 155 bonds, 22 residues, 1 model selected > select add #4/B:169 180 atoms, 161 bonds, 23 residues, 1 model selected > cartoon hide sel > select #4/B:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/B:168 15 atoms, 13 bonds, 2 residues, 1 model selected > select add #4/B:167 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #4/B:166 31 atoms, 27 bonds, 4 residues, 1 model selected > select add #4/B:165 38 atoms, 33 bonds, 5 residues, 1 model selected > select add #4/B:164 50 atoms, 45 bonds, 6 residues, 1 model selected > select add #4/B:163 58 atoms, 52 bonds, 7 residues, 1 model selected > select add #4/B:162 66 atoms, 59 bonds, 8 residues, 1 model selected > select add #4/B:161 74 atoms, 66 bonds, 9 residues, 1 model selected > select add #4/B:160 83 atoms, 74 bonds, 10 residues, 1 model selected > select add #4/B:159 89 atoms, 79 bonds, 11 residues, 1 model selected > select add #4/B:158 96 atoms, 85 bonds, 12 residues, 1 model selected > select add #4/B:157 104 atoms, 92 bonds, 13 residues, 1 model selected > select add #4/B:156 110 atoms, 97 bonds, 14 residues, 1 model selected > select add #4/B:155 115 atoms, 101 bonds, 15 residues, 1 model selected > select add #4/B:154 123 atoms, 108 bonds, 16 residues, 1 model selected > cartoon hide sel Drag select of 28 atoms, 92 residues, 28 bonds > cartoon hide sel Drag select of 28 atoms, 2 residues, 28 bonds > cartoon hide sel Drag select of 28 atoms, 28 bonds > cartoon hide sel > hide sel target a > select #4/B:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/B:101 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #4/B:99 26 atoms, 23 bonds, 3 residues, 1 model selected > select add #4/B:100 34 atoms, 30 bonds, 4 residues, 1 model selected > select add #4/B:98 41 atoms, 36 bonds, 5 residues, 1 model selected > select add #4/B:97 45 atoms, 39 bonds, 6 residues, 1 model selected > select add #4/B:76 54 atoms, 47 bonds, 7 residues, 1 model selected > select add #4/B:75 62 atoms, 54 bonds, 8 residues, 1 model selected > select add #4/B:74 71 atoms, 62 bonds, 9 residues, 1 model selected > hide sel target a > cartoon hide sel > select #4/B:123 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #4/B:124 19 atoms, 18 bonds, 2 residues, 1 model selected > select add #4/B:125 30 atoms, 28 bonds, 3 residues, 1 model selected > select add #4/B:126 38 atoms, 35 bonds, 4 residues, 1 model selected > select add #4/B:127 46 atoms, 42 bonds, 5 residues, 1 model selected > select add #4/B:138 53 atoms, 48 bonds, 6 residues, 1 model selected > select add #4/B:137 59 atoms, 53 bonds, 7 residues, 1 model selected > select add #4/B:129 70 atoms, 64 bonds, 8 residues, 1 model selected > select add #4/B:130 79 atoms, 72 bonds, 9 residues, 1 model selected > select add #4/B:131 87 atoms, 79 bonds, 10 residues, 1 model selected > select add #4/B:132 99 atoms, 91 bonds, 11 residues, 1 model selected > select add #4/B:135 107 atoms, 98 bonds, 12 residues, 1 model selected > hide sel target a > cartoon hide sel > select #4/B:128 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/B:134 21 atoms, 21 bonds, 2 residues, 1 model selected > select add #4/B:136 28 atoms, 27 bonds, 3 residues, 1 model selected > select add #4/B:133 37 atoms, 35 bonds, 4 residues, 1 model selected > cartoon hide sel > select #4/B:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #4/B:23 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #4/B:22 23 atoms, 20 bonds, 3 residues, 1 model selected > select add #4/B:20 27 atoms, 23 bonds, 4 residues, 1 model selected > select add #4/B:21 33 atoms, 28 bonds, 5 residues, 1 model selected > cartoon hide sel > select #4/B:54 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/B:53 18 atoms, 17 bonds, 2 residues, 1 model selected > select add #4/B:52 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #4/B:51 32 atoms, 29 bonds, 4 residues, 1 model selected > select add #4/B:50 40 atoms, 36 bonds, 5 residues, 1 model selected > select add #4/B:49 47 atoms, 42 bonds, 6 residues, 1 model selected > select add #4/B:48 56 atoms, 50 bonds, 7 residues, 1 model selected > select add #4/B:47 62 atoms, 55 bonds, 8 residues, 1 model selected > select add #4/B:46 73 atoms, 65 bonds, 9 residues, 1 model selected > select add #4/B:44 82 atoms, 73 bonds, 10 residues, 1 model selected > select add #4/B:45 93 atoms, 83 bonds, 11 residues, 1 model selected > select add #4/B:43 99 atoms, 88 bonds, 12 residues, 1 model selected > cartoon hide sel > select #4/E:2@C4 1 atom, 1 residue, 1 model selected Drag select of 27 atoms, 28 bonds > hide sel target a > select #4/E:1@C8 1 atom, 1 residue, 1 model selected > hide sel target a > show #1 models > matchmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 6agf.pdb, chain A (#4), sequence alignment score = 6509 RMSD between 1080 pruned atom pairs is 0.824 angstroms; (across all 1138 pairs: 1.259) > hide #1 models > show #!2 models > show #1 models > hide #1 models > hide #!4 models > show #!4 models > hide #!2 models > select clear > ui mousemode right label > ui mousemode right ""move label"" > ui mousemode right select > select add #4/D:2@C6 1 atom, 1 bond, 1 residue, 1 model selected Drag select of 19 atoms, 20 bonds > hide sel target a Drag select of 9 atoms, 7 bonds > hide sel target a Drag select of 10 atoms, 12 bonds > hide sel target a Drag select of 10 atoms, 8 bonds > hide sel target a Drag select of 19 atoms, 19 bonds > hide sel target a > select #4/A:1909@N29 1 atom, 1 residue, 1 model selected > select add #4/A:1909@O25 2 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@O26 3 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@P23 4 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@C27 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@O22 6 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/A:1909@C21 7 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:1909@C20 8 atoms, 9 bonds, 1 residue, 1 model selected > hide sel target a > select #4/A:1909@C28 1 atom, 1 residue, 1 model selected > select add #4/A:1909@O24 2 atoms, 1 residue, 1 model selected > hide sel target a > select #4/A:1909@O30 1 atom, 1 residue, 1 model selected > select add #4/A:1909@O32 2 atoms, 1 residue, 1 model selected > select add #4/A:1909@C31 3 atoms, 1 residue, 1 model selected > select add #4/A:1909@C33 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #4/A:1909@C34 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1909@C35 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@C36 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #4/A:1909@C37 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/A:1909@C38 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:1909@C39 10 atoms, 9 bonds, 1 residue, 1 model selected > select add #4/A:1909@C40 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #4/A:1909@C41 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/A:1909@C42 13 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:1909@C43 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #4/A:1909@C44 15 atoms, 14 bonds, 1 residue, 1 model selected > select add #4/A:1426 23 atoms, 22 bonds, 2 residues, 1 model selected > select subtract #4/A:1426 15 atoms, 15 bonds, 1 residue, 1 model selected > select add #4/A:1909@C45 16 atoms, 15 bonds, 1 residue, 1 model selected > hide sel target a > select #4/A:1909@C19 1 atom, 1 residue, 1 model selected > select add #4/A:1909@C16 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #4/A:1909@O17 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #4/A:1909@C15 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1909@C14 5 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1909@C13 6 atoms, 6 bonds, 1 residue, 1 model selected > select add #4/A:1909@C12 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/A:1909@C11 8 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:1909@C10 9 atoms, 9 bonds, 1 residue, 1 model selected > select add #4/A:1909@C09 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #4/A:1909@C08 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/A:1909@C07 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:1909@C06 13 atoms, 13 bonds, 1 residue, 1 model selected > select add #4/A:1909@C05 14 atoms, 14 bonds, 1 residue, 1 model selected > select add #4/A:1909@C04 15 atoms, 14 bonds, 1 residue, 1 model selected > select subtract #4/A:1909@C04 14 atoms, 14 bonds, 1 residue, 1 model selected > select add #4/A:1909@C04 15 atoms, 14 bonds, 1 residue, 1 model selected > select add #4/A:1909@C03 16 atoms, 16 bonds, 1 residue, 1 model selected > select add #4/A:1909@C02 17 atoms, 17 bonds, 1 residue, 1 model selected > select add #4/A:1909@C01 18 atoms, 18 bonds, 1 residue, 1 model selected > hide sel target a > select #4/A:1909@O18 1 atom, 1 residue, 1 model selected > hide sel target a > select #4/A:1913@N29 1 atom, 1 residue, 1 model selected > select add #4/A:1913@C28 2 atoms, 1 bond, 1 residue, 1 model selected > select add #4/A:1913@C27 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #4/A:1913@O26 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #4/A:1913@P23 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1913@O24 6 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1913@O25 7 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1913@O22 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/A:1913@C21 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:1913@C20 10 atoms, 9 bonds, 1 residue, 1 model selected > select add #4/A:1913@C19 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #4/A:1913@O18 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/A:1913@C16 13 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:1913@O17 14 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:1913@C15 15 atoms, 14 bonds, 1 residue, 1 model selected > select add #4/A:1913@C14 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #4/A:1913@C13 17 atoms, 16 bonds, 1 residue, 1 model selected > select add #4/A:1913@C12 18 atoms, 17 bonds, 1 residue, 1 model selected > select add #4/A:1913@C11 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #4/A:1913@C10 20 atoms, 19 bonds, 1 residue, 1 model selected > select add #4/A:1913@C09 21 atoms, 20 bonds, 1 residue, 1 model selected > select add #4/A:1913@C08 22 atoms, 21 bonds, 1 residue, 1 model selected > select add #4/A:1913@C07 23 atoms, 22 bonds, 1 residue, 1 model selected > select add #4/A:1913@C06 24 atoms, 23 bonds, 1 residue, 1 model selected > select add #4/A:1913@C05 25 atoms, 24 bonds, 1 residue, 1 model selected > select add #4/A:1913@C04 26 atoms, 25 bonds, 1 residue, 1 model selected > select add #4/A:1913@C03 27 atoms, 26 bonds, 1 residue, 1 model selected > select add #4/A:1913@O30 28 atoms, 27 bonds, 1 residue, 1 model selected > select add #4/A:1913@C31 29 atoms, 28 bonds, 1 residue, 1 model selected > select add #4/A:1913@O32 30 atoms, 28 bonds, 1 residue, 1 model selected > select add #4/A:1913@C33 31 atoms, 30 bonds, 1 residue, 1 model selected > select add #4/A:1913@C34 32 atoms, 31 bonds, 1 residue, 1 model selected > select add #4/A:1913@C35 33 atoms, 32 bonds, 1 residue, 1 model selected > select add #4/A:1913@C36 34 atoms, 33 bonds, 1 residue, 1 model selected > select add #4/A:1913@C37 35 atoms, 34 bonds, 1 residue, 1 model selected > select add #4/A:1913@C38 36 atoms, 34 bonds, 1 residue, 1 model selected > select add #4/A:1913@C39 37 atoms, 36 bonds, 1 residue, 1 model selected > select add #4/A:1913@C40 38 atoms, 37 bonds, 1 residue, 1 model selected > select add #4/A:1913@C41 39 atoms, 38 bonds, 1 residue, 1 model selected > select add #4/A:1913@C42 40 atoms, 39 bonds, 1 residue, 1 model selected > select add #4/A:1913@C43 41 atoms, 40 bonds, 1 residue, 1 model selected > select add #4/A:1913@C44 42 atoms, 41 bonds, 1 residue, 1 model selected > select add #4/A:1913@C45 43 atoms, 42 bonds, 1 residue, 1 model selected > hide sel target a > select add #4/A:1908@N29 44 atoms, 42 bonds, 2 residues, 1 model selected > select add #4/A:1908@C28 45 atoms, 43 bonds, 2 residues, 1 model selected > select add #4/A:1908@C27 46 atoms, 44 bonds, 2 residues, 1 model selected > select add #4/A:1908@O26 47 atoms, 45 bonds, 2 residues, 1 model selected > select add #4/A:1908@P23 48 atoms, 46 bonds, 2 residues, 1 model selected > select add #4/A:1908@O25 49 atoms, 47 bonds, 2 residues, 1 model selected > select add #4/A:1908@O24 50 atoms, 48 bonds, 2 residues, 1 model selected > select add #4/A:1908@O22 51 atoms, 49 bonds, 2 residues, 1 model selected > select add #4/A:1908@C21 52 atoms, 50 bonds, 2 residues, 1 model selected > select add #4/A:1908@C20 53 atoms, 51 bonds, 2 residues, 1 model selected > select add #4/A:1908@O30 54 atoms, 52 bonds, 2 residues, 1 model selected > select add #4/A:1908@C31 55 atoms, 53 bonds, 2 residues, 1 model selected > select add #4/A:1908@O32 56 atoms, 54 bonds, 2 residues, 1 model selected > select add #4/A:1908@C19 57 atoms, 55 bonds, 2 residues, 1 model selected > select add #4/A:1908@O18 58 atoms, 56 bonds, 2 residues, 1 model selected > select add #4/A:1908@C16 59 atoms, 57 bonds, 2 residues, 1 model selected > select add #4/A:1908@O17 60 atoms, 58 bonds, 2 residues, 1 model selected > select add #4/A:1908@C33 61 atoms, 59 bonds, 2 residues, 1 model selected > select add #4/A:1908@C34 62 atoms, 60 bonds, 2 residues, 1 model selected > select add #4/A:1908@C15 63 atoms, 61 bonds, 2 residues, 1 model selected > select add #4/A:1908@C14 64 atoms, 62 bonds, 2 residues, 1 model selected > select add #4/A:1908@C35 65 atoms, 63 bonds, 2 residues, 1 model selected > select add #4/A:1908@C36 66 atoms, 64 bonds, 2 residues, 1 model selected > select add #4/A:1908@C13 67 atoms, 65 bonds, 2 residues, 1 model selected > select add #4/A:1908@C12 68 atoms, 66 bonds, 2 residues, 1 model selected > select add #4/A:1908@C37 69 atoms, 67 bonds, 2 residues, 1 model selected > select add #4/A:1908@C38 70 atoms, 68 bonds, 2 residues, 1 model selected > select add #4/A:1908@C39 71 atoms, 69 bonds, 2 residues, 1 model selected > select add #4/A:1908@C40 72 atoms, 70 bonds, 2 residues, 1 model selected > select add #4/A:1908@C41 73 atoms, 71 bonds, 2 residues, 1 model selected > select add #4/A:1908@C43 74 atoms, 73 bonds, 2 residues, 1 model selected > select add #4/A:1908@C44 75 atoms, 74 bonds, 2 residues, 1 model selected > select add #4/A:1908@C11 76 atoms, 75 bonds, 2 residues, 1 model selected > select add #4/A:1908@C10 77 atoms, 76 bonds, 2 residues, 1 model selected > select add #4/A:1908@C09 78 atoms, 77 bonds, 2 residues, 1 model selected > select add #4/A:1908@C08 79 atoms, 78 bonds, 2 residues, 1 model selected > select add #4/A:1908@C07 80 atoms, 79 bonds, 2 residues, 1 model selected > select add #4/A:1908@C06 81 atoms, 80 bonds, 2 residues, 1 model selected > select add #4/A:1908@C05 82 atoms, 81 bonds, 2 residues, 1 model selected > select add #4/A:1908@C04 83 atoms, 82 bonds, 2 residues, 1 model selected > hide sel target a > select #4/A:1908@C42 1 atom, 1 residue, 1 model selected > hide sel target a > select add #4/A:1912@N29 2 atoms, 2 residues, 1 model selected > select add #4/A:1912@C28 3 atoms, 1 bond, 2 residues, 1 model selected > select add #4/A:1912@C27 4 atoms, 2 bonds, 2 residues, 1 model selected > select add #4/A:1912@O26 5 atoms, 3 bonds, 2 residues, 1 model selected > select add #4/A:1912@P23 6 atoms, 4 bonds, 2 residues, 1 model selected > select add #4/A:1912@O24 7 atoms, 5 bonds, 2 residues, 1 model selected > select add #4/A:1912@O25 8 atoms, 6 bonds, 2 residues, 1 model selected > select add #4/A:1912@O22 9 atoms, 7 bonds, 2 residues, 1 model selected > select add #4/A:1912@C21 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #4/A:1912@C20 11 atoms, 9 bonds, 2 residues, 1 model selected > select add #4/A:1912@O30 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #4/A:1912@C31 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #4/A:1912@O32 14 atoms, 12 bonds, 2 residues, 1 model selected > select subtract #4/A:1912@O32 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #4/A:1912@O32 14 atoms, 11 bonds, 2 residues, 1 model selected > select add #4/A:1912@C33 15 atoms, 13 bonds, 2 residues, 1 model selected > select add #4/A:1912@C34 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #4/A:1912@C35 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #4/A:1912@C36 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #4/A:1912@C37 19 atoms, 17 bonds, 2 residues, 1 model selected > select add #4/A:1912@C38 20 atoms, 18 bonds, 2 residues, 1 model selected > select add #4/A:1912@C39 21 atoms, 19 bonds, 2 residues, 1 model selected > select add #4/A:1912@C19 22 atoms, 20 bonds, 2 residues, 1 model selected > select add #4/A:1912@O18 23 atoms, 21 bonds, 2 residues, 1 model selected > select add #4/A:1912@C16 24 atoms, 22 bonds, 2 residues, 1 model selected > select subtract #4/A:1912@C16 23 atoms, 21 bonds, 2 residues, 1 model selected > select add #4/A:1912@C16 24 atoms, 21 bonds, 2 residues, 1 model selected > select add #4/A:1912@O17 25 atoms, 22 bonds, 2 residues, 1 model selected > select add #4/A:1912@C15 26 atoms, 24 bonds, 2 residues, 1 model selected > select add #4/A:1912@C14 27 atoms, 25 bonds, 2 residues, 1 model selected > select add #4/A:1912@C13 28 atoms, 26 bonds, 2 residues, 1 model selected > select add #4/A:1912@C12 29 atoms, 27 bonds, 2 residues, 1 model selected > select add #4/A:1912@C11 30 atoms, 28 bonds, 2 residues, 1 model selected > select add #4/A:1912@C10 31 atoms, 29 bonds, 2 residues, 1 model selected > select add #4/A:1912@C09 32 atoms, 30 bonds, 2 residues, 1 model selected > select add #4/A:1912@C08 33 atoms, 31 bonds, 2 residues, 1 model selected > select add #4/A:1912@C07 34 atoms, 32 bonds, 2 residues, 1 model selected > select add #4/A:1912@C06 35 atoms, 33 bonds, 2 residues, 1 model selected > select add #4/A:1912@C05 36 atoms, 34 bonds, 2 residues, 1 model selected > select add #4/A:1912@C04 37 atoms, 35 bonds, 2 residues, 1 model selected > hide sel target a > select add #4/A:1910@C45 38 atoms, 35 bonds, 3 residues, 1 model selected > select add #4/A:1910@C44 39 atoms, 36 bonds, 3 residues, 1 model selected > select add #4/A:1910@C43 40 atoms, 37 bonds, 3 residues, 1 model selected > select add #4/A:1910@C42 41 atoms, 38 bonds, 3 residues, 1 model selected > select add #4/A:1910@C41 42 atoms, 39 bonds, 3 residues, 1 model selected > select add #4/A:1910@C40 43 atoms, 40 bonds, 3 residues, 1 model selected > select add #4/A:1910@C39 44 atoms, 41 bonds, 3 residues, 1 model selected > select add #4/A:1910@C38 45 atoms, 42 bonds, 3 residues, 1 model selected > select add #4/A:1910@C37 46 atoms, 43 bonds, 3 residues, 1 model selected > select add #4/A:1910@C36 47 atoms, 44 bonds, 3 residues, 1 model selected > select add #4/A:1910@C35 48 atoms, 45 bonds, 3 residues, 1 model selected > select add #4/A:1910@C34 49 atoms, 46 bonds, 3 residues, 1 model selected > select add #4/A:1910@C33 50 atoms, 47 bonds, 3 residues, 1 model selected > select add #4/A:1910@C31 51 atoms, 48 bonds, 3 residues, 1 model selected > select add #4/A:1910@O32 52 atoms, 49 bonds, 3 residues, 1 model selected > select add #4/A:1910@O30 53 atoms, 50 bonds, 3 residues, 1 model selected > select add #4/A:1910@C20 54 atoms, 51 bonds, 3 residues, 1 model selected > select add #4/A:1910@C19 55 atoms, 52 bonds, 3 residues, 1 model selected > select add #4/A:1910@O18 56 atoms, 53 bonds, 3 residues, 1 model selected > select add #4/A:1910@C16 57 atoms, 54 bonds, 3 residues, 1 model selected > select add #4/A:1910@O17 58 atoms, 55 bonds, 3 residues, 1 model selected > select add #4/A:1910@C21 59 atoms, 56 bonds, 3 residues, 1 model selected > select add #4/A:1910@O22 60 atoms, 57 bonds, 3 residues, 1 model selected > select add #4/A:1910@P23 61 atoms, 58 bonds, 3 residues, 1 model selected > select add #4/A:1910@O24 62 atoms, 59 bonds, 3 residues, 1 model selected > select add #4/A:1910@O25 63 atoms, 60 bonds, 3 residues, 1 model selected > select add #4/A:1910@O26 64 atoms, 61 bonds, 3 residues, 1 model selected > select add #4/A:1910@C27 65 atoms, 62 bonds, 3 residues, 1 model selected > select add #4/A:1910@C28 66 atoms, 63 bonds, 3 residues, 1 model selected > select add #4/A:1910@N29 67 atoms, 64 bonds, 3 residues, 1 model selected > hide sel target a > select add #4/A:1914@C26 68 atoms, 64 bonds, 4 residues, 1 model selected > select add #4/A:1914@O25 69 atoms, 65 bonds, 4 residues, 1 model selected > select add #4/A:1914@C24 70 atoms, 66 bonds, 4 residues, 1 model selected > select add #4/A:1914@C23 71 atoms, 67 bonds, 4 residues, 1 model selected > select add #4/A:1914@C48 72 atoms, 68 bonds, 4 residues, 1 model selected > select add #4/A:1914@C22 73 atoms, 69 bonds, 4 residues, 1 model selected > select add #4/A:1914@O20 74 atoms, 70 bonds, 4 residues, 1 model selected > hide sel target a > select add #4/A:1914@C21 75 atoms, 70 bonds, 4 residues, 1 model selected > select add #4/A:1914@O49 76 atoms, 70 bonds, 4 residues, 1 model selected > select add #4/A:1914@C50 77 atoms, 71 bonds, 4 residues, 1 model selected > select add #4/A:1914@C17 78 atoms, 71 bonds, 4 residues, 1 model selected > select add #4/A:1914@C18 79 atoms, 72 bonds, 4 residues, 1 model selected > select add #4/A:1914@C19 80 atoms, 73 bonds, 4 residues, 1 model selected > select add #4/A:1914@C16 81 atoms, 74 bonds, 4 residues, 1 model selected > select add #4/A:1914@C13 82 atoms, 75 bonds, 4 residues, 1 model selected > select add #4/A:1914@C11 83 atoms, 76 bonds, 4 residues, 1 model selected > select add #4/A:1914@C08 84 atoms, 78 bonds, 4 residues, 1 model selected > select add #4/A:1914@C14 85 atoms, 79 bonds, 4 residues, 1 model selected > select add #4/A:1914@C15 86 atoms, 80 bonds, 4 residues, 1 model selected > select add #4/A:1914@C07 87 atoms, 81 bonds, 4 residues, 1 model selected > select add #4/A:1914@C09 88 atoms, 83 bonds, 4 residues, 1 model selected > select add #4/A:1914@C12 89 atoms, 84 bonds, 4 residues, 1 model selected > select add #4/A:1914@C10 90 atoms, 85 bonds, 4 residues, 1 model selected > select add #4/A:1914@C02 91 atoms, 86 bonds, 4 residues, 1 model selected > select add #4/A:1914@C06 92 atoms, 87 bonds, 4 residues, 1 model selected > select add #4/A:1914@C03 93 atoms, 89 bonds, 4 residues, 1 model selected > select add #4/A:1914@C01 94 atoms, 90 bonds, 4 residues, 1 model selected > select add #4/A:1914@C05 95 atoms, 91 bonds, 4 residues, 1 model selected > select add #4/A:1914@C04 96 atoms, 92 bonds, 4 residues, 1 model selected > select add #4/A:1914@C74 97 atoms, 94 bonds, 4 residues, 1 model selected > select add #4/A:1914@C75 98 atoms, 94 bonds, 4 residues, 1 model selected > select subtract #4/A:1914@C74 97 atoms, 93 bonds, 4 residues, 1 model selected > select add #4/A:1914@C74 98 atoms, 93 bonds, 4 residues, 1 model selected > select add #4/A:1914@O72 99 atoms, 95 bonds, 4 residues, 1 model selected > select add #4/A:1914@C73 100 atoms, 96 bonds, 4 residues, 1 model selected > hide sel target a > select add #4/A:1914@O80 101 atoms, 97 bonds, 4 residues, 1 model selected > select add #4/A:1914@C79 102 atoms, 98 bonds, 4 residues, 1 model selected > select add #4/A:1914@C78 103 atoms, 99 bonds, 4 residues, 1 model selected > select add #4/A:1914@C81 104 atoms, 100 bonds, 4 residues, 1 model selected > select add #4/A:1914@C77 105 atoms, 101 bonds, 4 residues, 1 model selected > select add #4/A:1914@C76 106 atoms, 102 bonds, 4 residues, 1 model selected > hide sel target a > select #4/A:1911@N29 1 atom, 1 residue, 1 model selected > select add #4/A:1911@C28 2 atoms, 1 bond, 1 residue, 1 model selected > select add #4/A:1911@C27 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #4/A:1911@O24 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #4/A:1911@P23 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:1911@O25 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1911@O22 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #4/A:1911@C21 8 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:1911@C20 9 atoms, 9 bonds, 1 residue, 1 model selected > select add #4/A:1911@O30 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #4/A:1911@C19 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #4/A:1911@C34 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:1911@C33 13 atoms, 13 bonds, 1 residue, 1 model selected > select add #4/A:1911@O18 14 atoms, 15 bonds, 1 residue, 1 model selected > select add #4/A:1911@C16 15 atoms, 15 bonds, 1 residue, 1 model selected > select add #4/A:1911@O17 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #4/A:1911@C36 17 atoms, 18 bonds, 1 residue, 1 model selected > select add #4/A:1911@C37 18 atoms, 19 bonds, 1 residue, 1 model selected > select add #4/A:1911@C38 19 atoms, 20 bonds, 1 residue, 1 model selected > select add #4/A:1911@C39 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #4/A:1911@C15 21 atoms, 22 bonds, 1 residue, 1 model selected > select add #4/A:1911@C14 22 atoms, 23 bonds, 1 residue, 1 model selected > select add #4/A:1911@C13 23 atoms, 24 bonds, 1 residue, 1 model selected > select add #4/A:1911@C12 24 atoms, 25 bonds, 1 residue, 1 model selected > select add #4/A:1911@C11 25 atoms, 25 bonds, 1 residue, 1 model selected > hide sel target a > select add #4/A:1911@C31 26 atoms, 26 bonds, 1 residue, 1 model selected > select add #4/A:1911@O32 27 atoms, 27 bonds, 1 residue, 1 model selected > select add #4/A:1911@O26 28 atoms, 27 bonds, 1 residue, 1 model selected > select add #4/A:1911@C35 29 atoms, 27 bonds, 1 residue, 1 model selected > hide sel target a > show #1 models > select add #4 10980 atoms, 11243 bonds, 3 pseudobonds, 1327 residues, 3 models selected > select subtract #4 Nothing selected > select clear > ui mousemode right label > ui mousemode right ""move label"" > ui mousemode right select > hide #!4 models > show #!4 models > hide #!4 models > hide #1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > show #1 models > matchmaker #4 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 6agf.pdb, chain A (#4), sequence alignment score = 6509 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #1/A, 6agf.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 1080 pruned atom pairs is 0.824 angstroms; (across all 1138 pairs: 1.259) > ui tool show ""Render/Select by Attribute"" > key blue-white-red :0.06 :2.50 :4.96 showTool true > ui mousemode right ""color key"" > ui mousemode right select > color byattribute r:seq_rmsd #1#!4 target sabc palette > 0.06,blue:2.5,white:4.96246,red 25687 atoms, 3170 residues, atom seq_rmsd range 0.0659 to 11.5 > hide #1 models > hide #!4 models > show #!4 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #!4 models > hide #1 models > show #1 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #1 models > show #!4 models > show #1 models > hide #!4 models > show #!4 models > hide #1 models > show #1 models > hide #!4 models > show #!4 models > hide #1 models > close #5 > show #1 models > hide #1 models > hide #!4 models > show #!4 models > show #1 models > matchmaker #4 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 6agf.pdb, chain A (#4), sequence alignment score = 6509 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #1/A, 6agf.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 1080 pruned atom pairs is 0.824 angstroms; (across all 1138 pairs: 1.259) > ui tool show ""Render/Select by Attribute"" > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > hide #1 models > show #1 models > matchmaker #2 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb, chain A (#1) with 8t6l, chain A (#2), sequence alignment score = 5749.2 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: PumNav14_with_template_hNav14_9fa5e_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #1/A, 8t6l #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 1090 pruned atom pairs is 0.896 angstroms; (across all 1236 pairs: 3.532) > ui tool show ""Render/Select by Attribute"" > key blue-white-red :0.05 :2.00 :5.00 showTool true > ui mousemode right ""color key"" > key blue-white-red :0.05 :2.00 :5.0 > key blue-white-red :0.05 :2.0 :5.0 > ui mousemode right select > key blue-white-red :0.1 :2.0 :5.0 showTool true > ui mousemode right ""color key"" > ui mousemode right select > color byattribute r:seq_rmsd #1#!2 target sabc palette > 0.1,blue:2,white:5,red 25687 atoms, 3122 residues, atom seq_rmsd range 0.0361 to 36.9 > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #!2 models > show #!2 models > hide #1 models > hide #!2 models > show #!2 models > hide #!2 models > show #3 models > close #3 > show #!2 models > show #!4 models > hide #!4 models > show #1 models > hide #1 models > show #1 models > hide #!2 models > hide #6 models > show #6 models > hide #1 models > show #1 models > show #!2 models > hide #1 models > color #2 #fa4821ff > color #2 #e8b791ff > color #2 #ecbcb1ff > color #2 #eaa8a0ff > color #2 #e89b8fff > color #2 #ebb9aeff > color #2 #e9aa9bff > color #2 #e6998aff > color #2 #e9a89cff > color #2 #e8a798ff > color #2 #e79a8bff > color #2 #e8ad95ff > color #2 #e89e8fff > color #2 #e9a89aff > color #2 #eab4a9ff > color #2 #e9a599ff > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > close #6 > show #1 models > hide #!2 models > show #!2 models > hide #!2 models QPainter::begin: Paint device returned engine == 0, type: 2 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9.dev202407040137 (2024-07-04) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.0, Qt 6.7.1 Qt runtime version: 6.7.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 17 days, 22 hours, 38 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501U-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 2 Displays: DELL P3223QE: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: C3M9WN3 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort 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: 2.13 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.3 ChimeraX-AtomicLibrary: 14.1.1 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: 2.13 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: 1.9.dev202407040137 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-DeepMutationalScan: 1.0 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-Foldseek: 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: 1.3 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: 2.1.4 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-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 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: 3.1.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.12.1 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: 1.16.6 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: 1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.4 ChimeraX-uniprot: 2.3.1 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: 1.8.2 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: 2.10.1 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: 6.7.0 PyQt6-Qt6: 6.7.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.2 PyQt6-WebEngineSubwheel-Qt6: 6.7.2 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: 2.32.3 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: 2.2.2 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 can't reproduce Greg Couch Eric Pettersen all ChimeraX