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Opened 12 months ago
Closed 12 months ago
#16194 closed defect (can't reproduce)
Crash rendering QToolButton icon: QPainter::begin: Paint device returned engine == 0, type: 2
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Greg Couch, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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)
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{
"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",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-14 18:43:38.6735 -0700",
"procStartAbsTime" : 168368296469559,
"procExitAbsTime" : 412089773645295,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"09960507-331A-58B2-8E71-A3D72B1C8B67","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F61753C3-C3EF-C2A7-AE02-99293A3B58AC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 11,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "CB8257D3-99A9-4A9B-BF07-1479BECEA407",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. 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. 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",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202407040137 (2024-07-04)
© 2016-2024 Regents of the 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
Change History (2)
comment:1 by , 12 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash rendering QToolButton icon: QPainter::begin: Paint device returned engine == 0, type: 2 |
comment:2 by , 12 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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I suspect this is related to the Mac external display issues as high up in the stack trace is