![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17325 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.4-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020184bac0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 124)
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{
"uptime" : 2500000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 1825,
"osVersion" : {
"train" : "macOS 14.4",
"build" : "23E214",
"releaseType" : "User"
},
"captureTime" : "2025-04-08 21:08:04.3390 +0800",
"codeSigningMonitor" : 1,
"incident" : "BB84EA3C-6556-44AF-8C71-E2C8648A2D21",
"pid" : 76887,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-01 21:18:08.3253 +0800",
"procStartAbsTime" : 53401234958656,
"procExitAbsTime" : 62004766438961,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"49F00EFF-C531-5FD5-8F10-11418D9C2A6A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8BF29B20-E336-8E38-8810-E698BC388B76",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 20154,
"sleepWakeUUID" : "7C640D44-C103-4CE4-AFA1-C3D4218CEAC2",
"sip" : "enabled",
"vmRegionInfo" : "0x3ba636d2c2c8 is not in any region. Bytes after previous region: 65104034054857 Bytes before following region: 39968045874488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00003ba636d2c2c8","rawCodes":[1,65585070392008],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003ba636d2c2c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":76887},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs"
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Log from Thu Mar 27 15:32:10 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32
Log from Tue Mar 18 21:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/wujingyi/Desktop/RfxATPase_figure/figure_5/Rfxatp_state1_hollow.cxs
Log from Mon Aug 12 10:58:14 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2hollow.pdb"
> hide #1 models
> show #1 models
> select add #1
4431 atoms, 3493 bonds, 4431 residues, 1 model selected
> show sel surfaces
> set bgColor white
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/state_1_Fo.pdb"
Chain information for state_1_Fo.pdb #2
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel atoms
[Repeated 2 time(s)]
> select add #2
15578 atoms, 14854 bonds, 2 pseudobonds, 5912 residues, 7 models selected
> hide sel atoms
> show sel cartoons
> select subtract #1
11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 6 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #2.13
10824 atoms, 11031 bonds, 2 pseudobonds, 1443 residues, 18 models selected
> select add #2.13
11147 atoms, 11031 bonds, 2 pseudobonds, 1481 residues, 17 models selected
> hide #2.13 models
> show #2.13 models
> select add #2
11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 18 models selected
> select subtract #2
16 models selected
> select add #2.13
323 atoms, 38 residues, 1 model selected
> select add #2.16
629 atoms, 74 residues, 2 models selected
> select subtract #2.16
323 atoms, 38 residues, 3 models selected
> select add #2.14
629 atoms, 74 residues, 2 models selected
> hide sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo.pdb"
Chain information for RfxATP_state_1_Fo.pdb #3
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel cartoons
> hide sel atoms
> select add #3
11776 atoms, 11365 bonds, 2 pseudobonds, 1555 residues, 5 models selected
> select add #2
22294 atoms, 22726 bonds, 4 pseudobonds, 2962 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> show sel surfaces
> hide sel surfaces
> select subtract #3
16 models selected
> select add #3.13
323 atoms, 38 residues, 1 model selected
> select add #3.15
646 atoms, 76 residues, 2 models selected
> hide sel cartoons
> select add #3.14
952 atoms, 112 residues, 3 models selected
> select add #3.16
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select add #3.2
1808 atoms, 224 residues, 5 models selected
> select add #3.3
2331 atoms, 297 residues, 6 models selected
> select add #3.4
2873 atoms, 372 residues, 7 models selected
> select add #3.5
3415 atoms, 447 residues, 8 models selected
> select add #3.6
3965 atoms, 523 residues, 9 models selected
> select add #3.7
4507 atoms, 598 residues, 10 models selected
> select add #3.8
5049 atoms, 673 residues, 11 models selected
> select add #3.9
5599 atoms, 749 residues, 12 models selected
> select add #3.10
6149 atoms, 825 residues, 13 models selected
> select add #3.11
6683 atoms, 899 residues, 14 models selected
> hide sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_inlet_hollow.pdb"
> select add #2
13913 atoms, 5473 bonds, 8129 residues, 16 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #3.2
13363 atoms, 5473 bonds, 8053 residues, 16 models selected
> show sel surfaces
> hide sel surfaces
> select add #3
18377 atoms, 16838 bonds, 2 pseudobonds, 8711 residues, 16 models selected
> select subtract #3
7230 atoms, 5473 bonds, 7230 residues, 17 models selected
> show sel surfaces
> select subtract #2
4 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> select subtract #2
4 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> show sel atoms
> select subtract #2
4 models selected
> select add #2.1
1460 atoms, 1460 residues, 1 model selected
> select add #2.2
5673 atoms, 5673 residues, 2 models selected
> select add #2.3
7208 atoms, 7208 residues, 3 models selected
> select add #2.4
7230 atoms, 7230 residues, 4 models selected
> select subtract #2.4
7208 atoms, 7208 residues, 5 models selected
> show sel cartoons
> show sel surfaces
> select add #2.4
7230 atoms, 7230 residues, 4 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> select subtract #2.4
7208 atoms, 7208 residues, 5 models selected
> show sel surfaces
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> select add #2.4
7230 atoms, 5454 bonds, 7230 residues, 4 models selected
> hide sel surfaces
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> show sel surfaces
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> show sel surfaces
> color #2.1 #87ceeb90
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 4 models selected
> hide sel atoms
> color #2.1 #87ceeb82
> color #2.1 #87ceeb80
> color #2.2 #87ceeb80
> color #2.3 #87ceeb82
> color #2.3 #87ceeb80
> select subtract #2.4
7208 atoms, 5454 bonds, 7208 residues, 5 models selected
> select subtract #2.3
5673 atoms, 4370 bonds, 5673 residues, 4 models selected
> select subtract #2.2
1460 atoms, 1278 bonds, 1460 residues, 3 models selected
> select subtract #2.1
1 model selected
> hide #!3 models
> show #!3 models
> hide #!1 models
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> select add #3.4
1615 atoms, 224 residues, 3 models selected
> select add #3.5
2157 atoms, 299 residues, 4 models selected
> show sel cartoons
> hide sel cartoons
> select subtract #3.2
1607 atoms, 223 residues, 5 models selected
> select subtract #3.3
1084 atoms, 150 residues, 4 models selected
> select subtract #3.4
542 atoms, 75 residues, 3 models selected
> select subtract #3.5
1 model selected
> select add #3.6
550 atoms, 76 residues, 1 model selected
> select add #3.7
1092 atoms, 151 residues, 2 models selected
> select add #3.8
1634 atoms, 226 residues, 3 models selected
> select add #3.9
2184 atoms, 302 residues, 4 models selected
> select add #3.10
2734 atoms, 378 residues, 5 models selected
> select add #3.11
3268 atoms, 452 residues, 6 models selected
> select add #3.12
5500 atoms, 743 residues, 7 models selected
> select subtract #3.12
3268 atoms, 452 residues, 8 models selected
> show sel cartoons
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_outlet_hollow2.pdb"
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_intlet_hollow.pdb"
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_outlet_hollow.pdb"
> select add #1
7699 atoms, 3493 bonds, 4883 residues, 8 models selected
> select add #3
15578 atoms, 14858 bonds, 2 pseudobonds, 5912 residues, 13 models selected
> select subtract #3
4431 atoms, 3493 bonds, 4431 residues, 21 models selected
> close #1
> select add #6
5690 atoms, 4616 bonds, 5690 residues, 1 model selected
> select add #5
12781 atoms, 9914 bonds, 12781 residues, 2 models selected
> select add #4
19169 atoms, 14970 bonds, 19169 residues, 3 models selected
> show sel surfaces
> select subtract #4
12781 atoms, 9914 bonds, 12781 residues, 13 models selected
> select subtract #5
5690 atoms, 4616 bonds, 5690 residues, 8 models selected
> select subtract #6
3 models selected
> select add #5.4
860 atoms, 860 residues, 1 model selected
> select add #5.3
4775 atoms, 4775 residues, 2 models selected
> select add #5.2
7013 atoms, 7013 residues, 3 models selected
> select subtract #5.2
4775 atoms, 4775 residues, 4 models selected
> select add #5.1
4853 atoms, 4853 residues, 3 models selected
> select subtract #5.1
4775 atoms, 4775 residues, 4 models selected
> select subtract #5.3
860 atoms, 860 residues, 3 models selected
> select subtract #5.4
1 model selected
> select add #5.2
2238 atoms, 2238 residues, 1 model selected
> select subtract #5.2
1 model selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel cartoons
> select subtract #3
16 models selected
> select add #3.13
323 atoms, 38 residues, 1 model selected
> select add #3.14
629 atoms, 74 residues, 2 models selected
> select add #3.16
935 atoms, 110 residues, 3 models selected
> select add #3.15
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11147 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
[Repeated 5 time(s)]
> select add #3.16
306 atoms, 36 residues, 1 model selected
> select add #3.15
629 atoms, 74 residues, 2 models selected
> select add #3.14
935 atoms, 110 residues, 3 models selected
> select add #3.13
1258 atoms, 148 residues, 4 models selected
> hide sel cartoons
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected
> select subtract #3
16 models selected
> select add #2
7230 atoms, 5473 bonds, 7230 residues, 1 model selected
> select add #6
12920 atoms, 10089 bonds, 12920 residues, 6 models selected
> select add #5
20011 atoms, 15387 bonds, 20011 residues, 10 models selected
> select add #4
26399 atoms, 20443 bonds, 26399 residues, 15 models selected
> show sel surfaces
> select subtract #2
19169 atoms, 14970 bonds, 19169 residues, 18 models selected
> select subtract #4
12781 atoms, 9914 bonds, 12781 residues, 13 models selected
> select subtract #5
5690 atoms, 4616 bonds, 5690 residues, 8 models selected
> select subtract #6
3 models selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> cartoon style (#!3 & sel) modeHelix tube sides 20
> select subtract #3.1
11147 atoms, 11365 bonds, 1481 residues, 17 models selected
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 18 models selected
> select subtract #3
16 models selected
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> select add #3.4
1615 atoms, 224 residues, 3 models selected
> select add #3.5
2157 atoms, 299 residues, 4 models selected
> select add #3.6
2707 atoms, 375 residues, 5 models selected
> select add #3.7
3249 atoms, 450 residues, 6 models selected
> select add #3.8
3791 atoms, 525 residues, 7 models selected
> select add #3.9
4341 atoms, 601 residues, 8 models selected
> select add #3.10
4891 atoms, 677 residues, 9 models selected
> select add #3.11
5425 atoms, 751 residues, 10 models selected
> color (#!3 & sel) #f5ccdcff
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #3
16 models selected
> select add #3.12
2232 atoms, 291 residues, 1 model selected
> select add #3.14
2538 atoms, 327 residues, 2 models selected
> color (#!3 & sel) forest green
> select subtract #3.14
2232 atoms, 291 residues, 3 models selected
> select add #3.17
4464 atoms, 582 residues, 2 models selected
> color (#!3 & sel) forest green
> select subtract #3.17
2232 atoms, 291 residues, 3 models selected
> select add #3.10
2782 atoms, 367 residues, 2 models selected
> select add #3.9
3332 atoms, 443 residues, 3 models selected
> select add #3.8
3874 atoms, 518 residues, 4 models selected
> select add #3.7
4416 atoms, 593 residues, 5 models selected
> select add #3.6
4966 atoms, 669 residues, 6 models selected
> select add #3.5
5508 atoms, 744 residues, 7 models selected
> select add #3.4
6050 atoms, 819 residues, 8 models selected
> select add #3.3
6573 atoms, 892 residues, 9 models selected
> select add #3.2
7123 atoms, 968 residues, 10 models selected
> hide sel cartoons
> select add #3.11
7657 atoms, 1042 residues, 11 models selected
> select subtract #3.12
5425 atoms, 751 residues, 12 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select add #3.17
7657 atoms, 1042 residues, 11 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 13 models selected
> select subtract #3
16 models selected
> select add #3.14
306 atoms, 36 residues, 1 model selected
> select add #3.12
2538 atoms, 327 residues, 2 models selected
> show sel cartoons
> select subtract #3.14
2232 atoms, 291 residues, 3 models selected
> select add #3.17
4464 atoms, 582 residues, 2 models selected
> show sel cartoons
> select add #3.14
4770 atoms, 618 residues, 3 models selected
> select subtract #3.12
2538 atoms, 327 residues, 4 models selected
> select subtract #3.17
306 atoms, 36 residues, 3 models selected
> hide sel cartoons
> color #3.14 #917297ff
> select subtract #3.14
1 model selected
> lighting soft
> select add #3.2
550 atoms, 76 residues, 1 model selected
> select add #3.3
1073 atoms, 149 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/H #3/L #3/O #3/P
Alignment identifier is 1
> sequence chain #3/I
Alignment identifier is 3/I
> sequence chain #3/J #3/K #3/M #3/N
Alignment identifier is 2
> sequence chain #3/Q
Alignment identifier is 3/Q
> select #3/Q:3-39,41-74
508 atoms, 515 bonds, 71 residues, 1 model selected
> select #3/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/Q:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!3 & sel) byhetero
> select #3/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/J-K,M-N:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> color (#!3 & sel) byhetero
> select #3/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/H,L,O-P:59
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> color (#!3 & sel) byhetero
> select #3/H,L,O-P:3-39,41-74
2032 atoms, 2060 bonds, 284 residues, 1 model selected
> ui mousemode right select
> select clear
Drag select of 6 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/T #3/Z
Alignment identifier is 3
> select #3/T,Z:259
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/T,Z:259
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color (#!3 & sel) byhetero
> select clear
Drag select of 9 atoms, 8 bonds
> select clear
[Repeated 1 time(s)]
> select add #3.11
534 atoms, 74 residues, 1 model selected
> select add #3.10
1084 atoms, 150 residues, 2 models selected
> select subtract #3.11
550 atoms, 76 residues, 3 models selected
> select subtract #3.10
1 model selected
> select #3/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/I:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color (#!3 & sel) byhetero
> select clear
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32
Drag select of rfxa2_intlet_hollow.pdb_E SES surface, 208 of 3672 triangles,
rfxa2_intlet_hollow.pdb_F SES surface, 464 of 25208 triangles, 8 atoms, 8
bonds, 1 J276_003_volume_map_sharp.mrc
> volume #1 step 1
> volume #1 level 0.2498
> select add #3
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 7 models selected
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> show #3.1 models
> hide #!2 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> select clear
[Repeated 1 time(s)]
> close #1
> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc
Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32
> volume zlip #1
Expected a density maps specifier or a keyword
> volume #1 step 1
> volume #1 level 0.224
> volume zlip #1
Expected a density maps specifier or a keyword
> volume zflip #1
Expected a density maps specifier or a keyword
> volume flip #1
Opened J276_003_volume_map_sharp.mrc z flip as #7, grid size 400,400,400,
pixel 0.95, shown at step 1, values float32
> save /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc models #7
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb"
Chain information for RFXATPase_state1_2.98A-1.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
R | No description available
S | No description available
T Z | No description available
U X | No description available
V | No description available
W | No description available
Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select clear
> hide #!8 atoms
> show #!8 cartoons
> select add #7
2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 15 residues
> ui mousemode right "translate selected models"
> view matrix models
> #7,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591,#8,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591
> view matrix models
> #7,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779,#8,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779
> view matrix models
> #7,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748,#8,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748
> ui mousemode right select
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 9 residues
> select subtract #7
69 atoms, 9 residues, 1 model selected
> select add #7
69 atoms, 9 residues, 3 models selected
> select subtract #7
69 atoms, 9 residues, 1 model selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 3 residues
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 24 residues
> select #8/X:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-1.6308,0,1,0,1.9901,0,0,1,-10.325
> view matrix models #8,1,0,0,17.812,0,1,0,-0.57249,0,0,1,-3.5122
> view matrix models #8,1,0,0,8.9735,0,1,0,15.372,0,0,1,-18.231
> view matrix models #8,1,0,0,6.1384,0,1,0,40.464,0,0,1,-18.769
> view matrix models #8,1,0,0,0.28461,0,1,0,11.462,0,0,1,-11.994
> ui mousemode right select
> select clear
> volume #7 level 0.1787
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 18 residues
> select clear
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.90579,0.37073,-0.20519,328.38,-0.30373,-0.90572,-0.29566,478.69,-0.29545,-0.20548,0.933,94.403
> view matrix models
> #8,-0.96264,0.27066,0.0076537,318.46,-0.26006,-0.91632,-0.3045,474.07,-0.075404,-0.29512,0.95248,66.029
> view matrix models
> #8,-0.92958,-0.23864,0.28095,356.73,0.29128,-0.94264,0.16308,288.68,0.22591,0.23343,0.94577,-88.104
> view matrix models
> #8,-0.84595,0.16919,0.50571,223.41,-0.021766,-0.9585,0.28426,328.28,0.53282,0.22946,0.81452,-121
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.84595,0.16919,0.50571,235.2,-0.021766,-0.9585,0.28426,367.87,0.53282,0.22946,0.81452,-65.315
> view matrix models
> #8,-0.84595,0.16919,0.50571,220.58,-0.021766,-0.9585,0.28426,321.34,0.53282,0.22946,0.81452,-116.96
> view matrix models
> #8,-0.84595,0.16919,0.50571,221.54,-0.021766,-0.9585,0.28426,322.24,0.53282,0.22946,0.81452,-114.19
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.83579,0.078648,0.54339,229.55,-0.07592,-0.99673,0.027491,386.99,0.54378,-0.018278,0.83903,-74.584
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.83579,0.078648,0.54339,222.57,-0.07592,-0.99673,0.027491,390.28,0.54378,-0.018278,0.83903,-87.165
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.91118,0.13459,0.38941,254.79,-0.039499,-0.96932,0.2426,338.58,0.41011,0.20567,0.88854,-112.87
> view matrix models
> #8,-0.97717,-0.025638,0.21089,330.07,0.044447,-0.99539,0.084934,356.72,0.20775,0.092368,0.97381,-69.326
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.97717,-0.025638,0.21089,338.54,0.044447,-0.99539,0.084934,351.74,0.20775,0.092368,0.97381,-56.344
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.87329,0.37091,0.31591,-103.7,-0.46999,0.81218,0.34565,63.53,-0.12837,-0.45033,0.88359,124.89
> view matrix models
> #8,0.87251,0.34682,0.34414,-104.27,-0.46902,0.79188,0.39108,58.745,-0.13689,-0.50263,0.85359,141.79
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87251,0.34682,0.34414,-88.442,-0.46902,0.79188,0.39108,76.727,-0.13689,-0.50263,0.85359,134.61
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected
> view matrix models
> #7,1,0,0,-6.297,0,1,0,-4.732,0,0,1,-10.051,#8,0.87251,0.34682,0.34414,-93.356,-0.46902,0.79188,0.39108,70.651,-0.13689,-0.50263,0.85359,131.13
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99677,-0.0017702,0.080268,-20.213,-0.0060842,0.99522,0.097502,-20.723,-0.080056,-0.097676,0.99199,25.283,#8,0.85954,0.30395,0.41086,-95.792,-0.48544,0.73697,0.47034,68.595,-0.15983,-0.60372,0.78101,164.94
> select subtract #8
2 models selected
> view matrix models
> #7,0.95476,-0.047178,0.29362,-43.084,-0.0629,0.93296,0.35444,-45.638,-0.29066,-0.35687,0.88778,134.06
> view matrix models
> #7,-0.88421,-0.21366,0.41537,319.19,0.41454,-0.76875,0.48701,159.82,0.21526,0.60281,0.7683,-122.46
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.88421,-0.21366,0.41537,329.35,0.41454,-0.76875,0.48701,172.07,0.21526,0.60281,0.7683,-126.96
> view matrix models
> #7,-0.88421,-0.21366,0.41537,332.67,0.41454,-0.76875,0.48701,178.44,0.21526,0.60281,0.7683,-131.73
> view matrix models
> #7,-0.88421,-0.21366,0.41537,331.46,0.41454,-0.76875,0.48701,179.89,0.21526,0.60281,0.7683,-135.36
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.94832,0.25093,0.19421,-67.519,-0.30926,0.86791,0.38872,27.724,-0.071014,-0.42869,0.90066,90.153
> view matrix models
> #7,0.70521,0.58704,0.39757,-122.03,-0.69527,0.68242,0.22562,167.18,-0.13886,-0.43553,0.8894,106.57
> view matrix models
> #7,0.82451,0.45778,0.33259,-108.48,-0.56304,0.72221,0.40175,101.62,-0.056283,-0.51851,0.85322,113.1
> view matrix models
> #7,0.82328,0.52176,0.22356,-100.14,-0.5672,0.77161,0.28794,114.17,-0.022268,-0.36385,0.93119,62.872
> view matrix models
> #7,0.67235,0.54008,0.50622,-126.97,-0.70093,0.68439,0.20079,172.5,-0.23801,-0.48982,0.83871,145.28
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.67235,0.54008,0.50622,-119.87,-0.70093,0.68439,0.20079,159.37,-0.23801,-0.48982,0.83871,140.99
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69879,0.54006,0.46907,-118.06,-0.69186,0.67684,0.25141,149.67,-0.18171,-0.50022,0.84662,130.67
> view matrix models
> #7,0.83451,0.45787,0.30652,-98.483,-0.50917,0.85342,0.11141,107.12,-0.21058,-0.24905,0.94532,70.441
> view matrix models
> #7,0.89321,0.41571,0.17135,-76.748,-0.44856,0.85022,0.27554,65.671,-0.031139,-0.32297,0.9459,49.832
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.85265,0.28815,0.43585,-93.839,-0.38349,0.91169,0.14749,65.269,-0.35486,-0.2929,0.88785,117.1
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms
average map value = 0.0361, steps = 248
shifted from previous position = 3.32
rotated from previous position = 3.59 degrees
atoms outside contour = 36794, contour level = 0.17874
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:
Matrix rotation and translation
0.97702481 0.20658623 -0.05238958 -29.62036884
-0.18232674 0.93747643 0.29647078 -1.24036171
0.11036078 -0.28010728 0.95360391 47.42560830
Axis -0.80722577 -0.22785516 -0.54448928
Axis point 0.00000000 159.66635676 39.10884363
Rotation angle (degrees) 20.92438479
Shift along axis -1.62978743
> volume #7 level 0.3325
> volume #7 level 0.191
> surface dust #7 size 9.5
> volume #7 level 0.08035
> surface dust #7 size 9.5
[Repeated 1 time(s)]
> volume #7 level 0.0503
> volume #7 level 0.103
> ui mousemode right select
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> surface dust #7 size 9.5
> show #!8 models
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 60 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.81858,0.56012,0.12724,-82.604,-0.57128,0.81694,0.079034,132.39,-0.059679,-0.13738,0.98872,13.357,#8,0.7117,0.65856,0.24451,-101.51,-0.69838,0.62571,0.3475,152.04,0.075857,-0.41807,0.90524,62.186
> select subtract #7
471 atoms, 60 residues, 1 model selected
> view matrix models
> #8,-0.66704,-0.73627,0.11385,442.68,0.72058,-0.6764,-0.15248,219.63,0.18927,-0.019677,0.98173,-47.612
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> select add #7
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.81858,0.56012,0.12724,-107.08,-0.57128,0.81694,0.079034,119.88,-0.059679,-0.13738,0.98872,13.446,#8,-0.66704,-0.73627,0.11385,418.2,0.72058,-0.6764,-0.15248,207.12,0.18927,-0.019677,0.98173,-47.523
> select subtract #8
2 models selected
> select subtract #7
Nothing selected
> select add #8
41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected
> view matrix models
> #8,-0.66704,-0.73627,0.11385,415.23,0.72058,-0.6764,-0.15248,205.72,0.18927,-0.019677,0.98173,-48.196
> view matrix models
> #8,-0.66704,-0.73627,0.11385,414.92,0.72058,-0.6764,-0.15248,206.56,0.18927,-0.019677,0.98173,-49.48
> view matrix models
> #8,-0.66704,-0.73627,0.11385,413.85,0.72058,-0.6764,-0.15248,208.31,0.18927,-0.019677,0.98173,-47.84
> select subtract #8
Nothing selected
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.82946,0.54181,0.1358,-107.14,-0.55482,0.8273,0.088006,113.07,-0.064669,-0.14834,0.98682,16.887
> view matrix models
> #7,0.82794,0.53632,0.16394,-110.95,-0.54873,0.83508,0.03928,119.35,-0.11584,-0.12248,0.98569,21.764
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.82794,0.53632,0.16394,-116.9,-0.54873,0.83508,0.03928,129.66,-0.11584,-0.12248,0.98569,21.897
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.80067,0.55879,0.21605,-125.69,-0.57153,0.82057,-0.0042587,144.83,-0.17966,-0.12007,0.97637,35.272
> view matrix models
> #7,0.81894,0.56477,0.1019,-109.35,-0.54936,0.82283,-0.14542,166.11,-0.16597,0.063107,0.98411,-4.5857
> select subtract #7
Nothing selected
> hide #!7 models
> show #!7 models
> fitmap #8 inMap #7
Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms
average map value = 0.04304, steps = 80
shifted from previous position = 1.27
rotated from previous position = 1.72 degrees
atoms outside contour = 33294, contour level = 0.103
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:
Matrix rotation and translation
-0.97766050 -0.21015754 0.00371096 411.17643737
0.21004182 -0.97748108 -0.02032708 335.92463186
0.00789929 -0.01909353 0.99978651 8.97038534
Axis 0.00293548 -0.00996693 0.99994602
Axis point 187.72593879 189.84909480 0.00000000
Rotation angle (degrees) 167.87114146
Shift along axis 6.82876360
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/Rfx ATPase ADP map/Rfx ATPase overall
> map/J68_10.48w_2.89A_volumeZ_map.mrc.mrc"
Opened J68_10.48w_2.89A_volumeZ_map.mrc.mrc as #9, grid size 400,400,400,
pixel 0.93, shown at level 0.0643, step 2, values float32
> select add #9
2 models selected
> view matrix models
> #9,0.94781,0.29555,0.11964,-65.963,-0.30155,0.9528,0.035199,59.073,-0.10359,-0.069439,0.99219,33.644
> view matrix models
> #9,-0.16235,-0.98146,-0.10184,417.29,0.97581,-0.14439,-0.16413,56.511,0.14638,-0.12602,0.98117,-0.95683
> view matrix models
> #9,-0.64648,-0.75883,0.079063,434.97,0.74348,-0.64985,-0.15787,192.08,0.17118,-0.04328,0.98429,-21.402
> hide #!7 models
> view matrix models
> #9,-0.63471,-0.72188,0.27572,390.81,0.71277,-0.68474,-0.15195,203.21,0.29849,0.10008,0.94915,-65.43
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.63471,-0.72188,0.27572,444.16,0.71277,-0.68474,-0.15195,299.14,0.29849,0.10008,0.94915,-102.44
> view matrix models
> #9,-0.63471,-0.72188,0.27572,377.16,0.71277,-0.68474,-0.15195,204.9,0.29849,0.10008,0.94915,-87.29
> view matrix models
> #9,-0.63471,-0.72188,0.27572,380.26,0.71277,-0.68474,-0.15195,209.91,0.29849,0.10008,0.94915,-89.722
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.81475,-0.54434,0.19968,395.03,0.53788,-0.83818,-0.09021,259.98,0.21648,0.033908,0.9757,-66.876
> view matrix models
> #9,-0.81553,-0.55997,0.14609,407.63,0.53884,-0.82683,-0.16124,270.41,0.21109,-0.052776,0.97604,-49.973
> view matrix models
> #9,-0.72178,-0.67644,0.14653,411.36,0.64266,-0.7336,-0.22095,244.41,0.25695,-0.065305,0.96421,-54.174
> view matrix models
> #9,-0.70922,-0.70009,0.082935,424.72,0.68767,-0.71291,-0.1374,217.21,0.15532,-0.040416,0.98704,-43.731
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.70922,-0.70009,0.082935,420.42,0.68767,-0.71291,-0.1374,222.59,0.15532,-0.040416,0.98704,-41.757
> show #!7 models
> select subtract #9
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,0.81894,0.56477,0.1019,-109.07,-0.54936,0.82283,-0.14542,166.67,-0.16597,0.063107,0.98411,-8.6208
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.82136,0.57001,0.021207,-95.736,-0.56458,0.81772,-0.11217,164.45,-0.081282,0.080162,0.99346,-29.777
> view matrix models
> #7,-0.8497,-0.52724,0.0058055,439.44,0.52217,-0.84296,-0.12945,285.87,0.073144,-0.10696,0.99157,-22.184
> select subtract #7
Nothing selected
> hide #!9 models
> select add #7
2 models selected
> view matrix models
> #7,-0.83572,-0.53982,0.10088,421.78,0.53709,-0.84174,-0.054778,269.08,0.11449,0.0084053,0.99339,-52.947
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.83572,-0.53982,0.10088,417.08,0.53709,-0.84174,-0.054778,262.64,0.11449,0.0084053,0.99339,-42.059
> select subtract #7
Nothing selected
[deleted to fit within ticket limits]
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_A SES
surface #1.2: minimum, -18.27, mean -1.83, maximum 13.91
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_B SES
surface #1.3: minimum, -15.47, mean -1.37, maximum 13.82
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_C SES
surface #1.4: minimum, -16.31, mean -1.63, maximum 13.40
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_D SES
surface #1.5: minimum, -28.87, mean -2.68, maximum 10.52
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_E SES
surface #1.6: minimum, -20.09, mean -2.56, maximum 8.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_F SES
surface #1.7: minimum, -18.01, mean -2.95, maximum 8.98
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_G SES
surface #1.8: minimum, -16.97, mean 1.81, maximum 17.95
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_H SES
surface #1.9: minimum, -10.11, mean -0.93, maximum 7.53
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_I SES
surface #1.10: minimum, -10.05, mean -0.85, maximum 6.44
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_J SES
surface #1.11: minimum, -12.46, mean -0.37, maximum 8.45
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_K SES
surface #1.12: minimum, -11.92, mean -0.41, maximum 9.98
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_L SES
surface #1.13: minimum, -10.16, mean -0.92, maximum 7.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_M SES
surface #1.14: minimum, -9.92, mean -0.18, maximum 9.75
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_N SES
surface #1.15: minimum, -10.12, mean -0.53, maximum 8.00
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_O SES
surface #1.16: minimum, -10.15, mean -0.67, maximum 9.21
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_P SES
surface #1.17: minimum, -11.20, mean -1.02, maximum 7.64
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Q SES
surface #1.18: minimum, -10.56, mean -0.41, maximum 7.82
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_R SES
surface #1.19: minimum, -19.83, mean -2.00, maximum 12.65
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_S SES
surface #1.20: minimum, -13.38, mean -0.26, maximum 7.63
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_U SES
surface #1.22: minimum, -7.30, mean -1.52, maximum 9.63
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_V SES
surface #1.23: minimum, -9.18, mean -1.53, maximum 10.50
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_W SES
surface #1.24: minimum, -13.86, mean -0.26, maximum 7.70
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_X SES
surface #1.25: minimum, -8.05, mean -1.46, maximum 9.60
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Y SES
surface #1.26: minimum, -8.08, mean -1.63, maximum 9.55
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.21
36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected
> hide sel surfaces
> hide sel cartoons
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 27 models selected
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> select clear
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:249
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:249
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:290
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #1.21
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
Alignment identifier is 1/Z
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:265-266
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/Z:265-270
44 atoms, 44 bonds, 6 residues, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268-269
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> color #1.21 #65b8bcff
> select add #1.21
1597 atoms, 8 bonds, 266 residues, 2 models selected
> coulombic sel
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1.21
9 atoms, 8 bonds, 1 residue, 3 models selected
> select add #1.25
751 atoms, 8 bonds, 150 residues, 2 models selected
> select subtract #1.25
9 atoms, 8 bonds, 1 residue, 3 models selected
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> view
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_a1电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!1 atoms
> hide #!1 cartoons
> show #!1 surfaces
> undo
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.1
3 pseudobonds, 1 model selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.27
36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected
> hide sel surfaces
> select clear
Drag select of 5 atoms, 12 residues, 5 bonds
> hide sel atoms
> select clear
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> select #1/Z:234@CB
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/wujingyi/Desktop/figure/figure4/state1_a2电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel surfaces
> select subtract #1.27
1 model selected
> select add #1.9
543 atoms, 75 residues, 1 model selected
> select add #1.10
1059 atoms, 147 residues, 2 models selected
> select add #1.11
1594 atoms, 221 residues, 3 models selected
> select add #1.12
2129 atoms, 295 residues, 4 models selected
> select add #1.14
2664 atoms, 369 residues, 5 models selected
> select add #1.13
3207 atoms, 444 residues, 6 models selected
> select add #1.15
3742 atoms, 518 residues, 7 models selected
> select add #1.16
4285 atoms, 593 residues, 8 models selected
> select add #1.17
4828 atoms, 668 residues, 9 models selected
> select add #1.18
5355 atoms, 741 residues, 10 models selected
> show sel surfaces
> select clear
> view
> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势.png width 1660
> height 1174 supersample 3 transparentBackground true
> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势图.cxs
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> select subtract #1.27
1 model selected
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> show sel surfaces
> select add #1.26
2294 atoms, 429 residues, 2 models selected
> select subtract #1.27
752 atoms, 151 residues, 3 models selected
> select subtract #1.26
1 model selected
> select add #1.20
365 atoms, 74 residues, 1 model selected
> select add #1.19
1445 atoms, 212 residues, 2 models selected
> select subtract #1.20
1080 atoms, 138 residues, 3 models selected
> select subtract #1.19
1 model selected
> select add #1.19
1080 atoms, 138 residues, 1 model selected
> select subtract #1.19
1 model selected
> select add #1.18
527 atoms, 73 residues, 1 model selected
> select add #1.17
1070 atoms, 148 residues, 2 models selected
> select add #1.16
1613 atoms, 223 residues, 3 models selected
> select add #1.15
2148 atoms, 297 residues, 4 models selected
> select add #1.14
2683 atoms, 371 residues, 5 models selected
> select add #1.13
3226 atoms, 446 residues, 6 models selected
> select add #1.12
3761 atoms, 520 residues, 7 models selected
> select add #1.11
4296 atoms, 594 residues, 8 models selected
> select add #1.10
4812 atoms, 666 residues, 9 models selected
> select add #1.9
5355 atoms, 741 residues, 10 models selected
> hide sel surfaces
> select #1/Z:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/T:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:274@CB
1 atom, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/Z:274@CB
1 atom, 1 residue, 1 model selected
> select #1/Z:276@O
1 atom, 1 residue, 1 model selected
> select #1/Z:263@O
1 atom, 1 residue, 1 model selected
> select subtract #1.27
1 model selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> show sel surfaces
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!1 models
> show #!11 models
> hide #!11 models
> hide #!1 models
> show #!1 models
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select subtract #1
26 models selected
> select add #1.21
1588 atoms, 265 residues, 1 model selected
> select add #1.27
3130 atoms, 543 residues, 2 models selected
> color (#!1 & sel) forest green
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 4 models selected
> select subtract #1
26 models selected
> select add #1
37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected
> select subtract #1.21
36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected
> select subtract #1.27
34862 atoms, 35344 bonds, 4829 residues, 26 models selected
> hide sel cartoons
> select clear
> show #!11 models
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select add #11.27
3130 atoms, 543 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #11/Z to #1/T pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain Z (#11), sequence
alignment score = 1208.4
RMSD between 157 pruned atom pairs is 1.357 angstroms; (across all 265 pairs:
3.245)
> select add #1.27
1542 atoms, 278 residues, 1 model selected
> hide sel cartoons
> select add #11.21
3130 atoms, 543 residues, 3 models selected
> hide sel cartoons
> ui mousemode right select
Drag select of 30 atoms, 5 residues, 25 bonds
> hide sel atoms
> hide sel cartoons
> cartoon style (#!11 & sel) modeHelix tube sides 20
> select clear
> select add #11.27
1542 atoms, 278 residues, 1 model selected
> color (#!11 & sel) light gray
> select clear
> select add #11.21
1588 atoms, 265 residues, 1 model selected
> select subtract #11.21
1 model selected
> select add #11.27
1542 atoms, 278 residues, 1 model selected
Alignment identifier is 11/Z
> select add #1.21
3130 atoms, 543 residues, 3 models selected
Alignment identifier is 1/T
Destroying pre-existing alignment with identifier 11/Z
Alignment identifier is 11/Z
> select clear
> select #11/Z:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/Z:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select #1/T:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/T:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select subtract #1.21
1 model selected
Cell requested for row 0 is out of bounds for table with 37 rows! Resizing
table model.
> hide #!1 models
> hide #!11 models
> show #!8 models
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb"
Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #10
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb"
Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #12
---
Chain | Description
H L O P | No description available
I | No description available
J K M N | No description available
Q | No description available
T Z | No description available
U X | No description available
V Y | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!8 models
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select add #12
22294 atoms, 22730 bonds, 4 pseudobonds, 2962 residues, 20 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 34 models selected
> select add #10.2
11697 atoms, 11365 bonds, 2 pseudobonds, 1557 residues, 19 models selected
> select add #10.3
12220 atoms, 11365 bonds, 2 pseudobonds, 1630 residues, 20 models selected
> select add #10.4
12762 atoms, 11365 bonds, 2 pseudobonds, 1705 residues, 21 models selected
> select add #10.5
13304 atoms, 11365 bonds, 2 pseudobonds, 1780 residues, 22 models selected
> select add #10.6
13854 atoms, 11365 bonds, 2 pseudobonds, 1856 residues, 23 models selected
> select add #10.7
14396 atoms, 11365 bonds, 2 pseudobonds, 1931 residues, 24 models selected
> select add #10.8
14938 atoms, 11365 bonds, 2 pseudobonds, 2006 residues, 25 models selected
> select add #10.9
15488 atoms, 11365 bonds, 2 pseudobonds, 2082 residues, 26 models selected
> select add #10.10
16038 atoms, 11365 bonds, 2 pseudobonds, 2158 residues, 27 models selected
> select add #10.11
16572 atoms, 11365 bonds, 2 pseudobonds, 2232 residues, 28 models selected
> select subtract #12
5425 atoms, 751 residues, 27 models selected
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected
> select subtract #10
16 models selected
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #10.17
4464 atoms, 582 residues, 2 models selected
> color (#!10 & sel) forest green
> hide sel atoms
> show sel cartoons
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected
> select subtract #10
16 models selected
> select add #12.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 2 models selected
> color (#!12 & sel) light gray
> hide sel atoms
> show sel cartoons
> select subtract #12.17
2232 atoms, 291 residues, 3 models selected
> select subtract #12.12
1 model selected
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> select subtract #12.17
8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected
> select subtract #12.12
6683 atoms, 6791 bonds, 899 residues, 16 models selected
> hide sel cartoons
> hide sel atoms
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected
> select subtract #12
16 models selected
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> select subtract #10.12
8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected
> select subtract #10.17
6683 atoms, 6791 bonds, 899 residues, 16 models selected
> hide sel atoms
> select add #10
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected
> select subtract #10
16 models selected
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #10.17
4464 atoms, 582 residues, 2 models selected
> show sel cartoons
> select clear
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select add #10.12
4464 atoms, 582 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select clear
> show #!10,12 cartoons
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select clear
> undo
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select subtract #12.17
1 model selected
> select add #12.12
2232 atoms, 291 residues, 1 model selected
> hide sel cartoons
> select subtract #12.12
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select subtract #10.17
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> select subtract #10.17
1 model selected
> select add #10.17
2232 atoms, 291 residues, 1 model selected
> hide sel cartoons
> select subtract #10.17
1 model selected
> ui tool show Matchmaker
> matchmaker #12/Z to #10/T pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)
> matchmaker #12/Z to #10/T pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
Alignment identifier is 1
> select #10/T:30 #12/Z:30
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:30 #12/Z:30
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [30] RMSD: 0.804
> show sel atoms
> select #10/T:130 #12/Z:130
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/T:130 #12/Z:130
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [130] RMSD: 0.879
> show sel atoms
> select #10/T:140 #12/Z:140
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #10/T:140 #12/Z:140
12 atoms, 10 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [140] RMSD: 3.423
> show sel atoms
> select #10/T:187 #12/Z:187
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #10/T:187 #12/Z:187
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [163] RMSD: 2.893
> show sel atoms
> select #10/T:263 #12/Z:263
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/T:263 #12/Z:263
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [239] RMSD: 0.744
> select #10/T:263,268 #12/Z:263,268
34 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains T,Z [239] + 1 other block RMSD: 0.813
> show sel atoms
> select #10/T:259 #12/Z:259
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:259 #12/Z:259
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [235] RMSD: 0.890
> show sel atoms
> select #10/T:252 #12/Z:252
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #10/T:252 #12/Z:252
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [228] RMSD: 0.342
> show sel atoms
> select #10/T:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314
> #12/Z:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314
2874 atoms, 2928 bonds, 368 residues, 2 models selected
> select #10/T:248 #12/Z:248
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #10/T:248-249 #12/Z:248-249
30 atoms, 28 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains T,Z [224-225] RMSD: 0.828
> show sel atoms
> select #10/T:245 #12/Z:245
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:245 #12/Z:245
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [221] RMSD: 1.184
> show sel atoms
> select #10/T:228 #12/Z:228
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:228 #12/Z:228
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [204] RMSD: 2.971
> show sel atoms
> select clear
> style #10,12 stick
Changed 22294 atom styles
> select clear
> cartoon style #10,12 modeHelix tube sides 20
> select clear
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> color sel lemon chiffon
> color sel light goldenrod yellow
> color sel old lace
> color sel light yellow
> color sel ivory
> color sel light yellow
> color sel lemon chiffon
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1174 supersample 3 transparentBackground true
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select clear
> select add #12
11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> select add #10.12
13379 atoms, 11365 bonds, 2 pseudobonds, 1772 residues, 19 models selected
> hide sel cartoons
> select clear
> color #10,12 byhetero
> select clear
> ui mousemode right select
> select clear
Drag select of 2 atoms, 1 bonds
Drag select of 1 atoms, 1 bonds
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> select #12/Z:245@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:245@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select add #12/Z:249@N
1 atom, 1 bond, 1 residue, 1 model selected
> select subtract #12/Z:249@N
1 model selected
> select add #12/Z:249@N
1 atom, 1 residue, 1 model selected
> select add #12/Z:249@O
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select add #10/T:248@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:248@O
2 atoms, 2 residues, 3 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:252@O
1 atom, 1 residue, 1 model selected
> select subtract #12/Z:252@O
Nothing selected
> select add #12/Z:252@N
1 atom, 1 residue, 1 model selected
> select add #12/Z:252@O
2 atoms, 1 residue, 1 model selected
> color sel lemon chiffon
> select clear
> select #12/Z:259@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:259@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:263@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:263@N
2 atoms, 1 bond, 1 residue, 2 models selected
> color sel lemon chiffon
> select clear
> select #12/Z:130@O
1 atom, 1 residue, 1 model selected
> select add #10/T:130@O
2 atoms, 1 bond, 2 residues, 2 models selected
> select subtract #10/T:130@O
1 atom, 1 bond, 1 residue, 2 models selected
> select add #12/Z:130@N
2 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #12/Z:130@N
1 atom, 1 bond, 1 residue, 1 model selected
Drag select of 1 atoms
> color sel lemon chiffon
> select clear
Drag select of 1 atoms, 1 bonds
Drag select of 1 atoms
> color sel lemon chiffon
> select clear
> select add #12/Z:268@O
1 atom, 1 residue, 1 model selected
> select add #12/Z:268@N
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel lemon chiffon
> select clear
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> select subtract #10.12
1 model selected
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> color (#!12 & sel) forest green
> select clear
> select add #12.17
2232 atoms, 291 residues, 1 model selected
> select add #10.12
4464 atoms, 582 residues, 3 models selected
> show sel cartoons
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1174 supersample 3 transparentBackground true
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
> hide sel cartoons
> select clear
> ui mousemode right select
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [266] RMSD: 1.278
> show sel atoms
> select clear
> ui mousemode right select
Drag select of 6 atoms, 4 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> color (#!10 & sel) byhetero
> select clear
Drag select of 2 atoms, 1 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10 & sel) byhetero
> select clear
Drag select of 5 atoms, 4 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 8 atoms, 7 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> select subtract #10/T:140@C
2 atoms, 1 bond, 1 residue, 3 models selected
> color (#!12 & sel) byhetero
> select clear
Drag select of 3 atoms, 2 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 7 atoms, 7 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color sel byhetero
> select clear
> select #10/T:248@OG
1 atom, 1 residue, 1 model selected
> select add #12/Z:248@OG
2 atoms, 2 residues, 3 models selected
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 6 atoms, 5 bonds
> color (#!10,12 & sel) byhetero
> select clear
Drag select of 1 atoms
> color (#!10,12 & sel) byhetero
> select clear
> select add #12/Z:187@OG1
1 atom, 1 residue, 1 model selected
Drag select of 34 atoms, 32 bonds
> color (#!10,12 & sel) byhetero
> select clear
> select #12/Z:30@N
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms
> select clear
> select #12/Z:30@N
1 atom, 1 residue, 1 model selected
> color (#!12 & sel) forest green
> select clear
Drag select of 1 atoms
> select add #10/T:30@N
2 atoms, 1 residue, 2 models selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> select #12/Z:30@O
1 atom, 1 residue, 1 model selected
> color sel forest green
> select clear
Drag select of 1 atoms, 2 bonds
> color sel lemon chiffon
> select clear
Drag select of 1 atoms
> color sel forest green
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png" width
> 1660 height 1174 supersample 3 transparentBackground true
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png" width
> 1660 height 1591 supersample 3 transparentBackground true
> select add #10.12
2232 atoms, 291 residues, 1 model selected
> select add #12.17
4464 atoms, 582 residues, 3 models selected
> show sel cartoons
> ui mousemode right select
> select clear
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png" width 1660
> height 1591 supersample 3 transparentBackground true
> save "/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .cxs"
> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb
Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I Q | No description available
R | No description available
S W | No description available
T | No description available
U X | No description available
V | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!10,12-13 atoms
> show #!10,12-13 cartoons
Cell requested for row 11 is out of bounds for table with 47 rows! Resizing
table model.
> hide #!12 models
> hide #!10 models
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #13
26 models selected
> select add #13.2
3805 atoms, 498 residues, 1 model selected
> select add #13.3
7598 atoms, 994 residues, 2 models selected
> select add #13.4
11420 atoms, 1494 residues, 3 models selected
> color (#!13 & sel) #0099ccff
> select subtract #13.2
7615 atoms, 996 residues, 4 models selected
> select subtract #13.3
3822 atoms, 500 residues, 3 models selected
> select subtract #13.4
1 model selected
> select add #13.5
3597 atoms, 469 residues, 1 model selected
> select add #13.6
7202 atoms, 939 residues, 2 models selected
> select add #13.7
10788 atoms, 1407 residues, 3 models selected
> color (#!13 & sel) #e9d49bff
> select subtract #13.5
7191 atoms, 938 residues, 4 models selected
> select subtract #13.6
3586 atoms, 468 residues, 3 models selected
> select subtract #13.7
1 model selected
> select add #13.8
2282 atoms, 289 residues, 1 model selected
> color (#!13 & sel) #002befff
> color (#!13 & sel) #2befc8ff
> select subtract #13.8
1 model selected
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select add #13.10
1062 atoms, 147 residues, 2 models selected
> select add #13.11
1597 atoms, 221 residues, 3 models selected
> select add #13.12
2132 atoms, 295 residues, 4 models selected
> select add #13.13
2667 atoms, 369 residues, 5 models selected
> select add #13.14
3202 atoms, 443 residues, 6 models selected
> select add #13.15
3737 atoms, 517 residues, 7 models selected
> select add #13.16
4272 atoms, 591 residues, 8 models selected
> select add #13.17
4807 atoms, 665 residues, 9 models selected
> select add #13.18
5334 atoms, 738 residues, 10 models selected
> color (#!13 & sel) #f5ccdcff
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> color (#!13 & sel) forest green
> select clear
> select add #13.22
747 atoms, 150 residues, 1 model selected
> select add #13.26
1959 atoms, 301 residues, 2 models selected
> select subtract #13.26
747 atoms, 150 residues, 3 models selected
> select add #13.25
1812 atoms, 300 residues, 2 models selected
> color (#!13 & sel) #c5c5ecff
> select clear
> select add #13.23
764 atoms, 152 residues, 1 model selected
> select add #13.26
1976 atoms, 303 residues, 2 models selected
> color (#!13 & sel) #9e7bbaff
> select clear
> select add #13.20
365 atoms, 74 residues, 1 model selected
> select subtract #13.20
1 model selected
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> select subtract #13.2
34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected
> select add #13.2
38578 atoms, 35235 bonds, 3 pseudobonds, 5349 residues, 27 models selected
> select subtract #13.9
38043 atoms, 34692 bonds, 3 pseudobonds, 5275 residues, 28 models selected
> select subtract #13.10
37516 atoms, 34157 bonds, 3 pseudobonds, 5202 residues, 27 models selected
> select subtract #13.12
36981 atoms, 33614 bonds, 3 pseudobonds, 5128 residues, 26 models selected
> select subtract #13.11
36446 atoms, 33071 bonds, 3 pseudobonds, 5054 residues, 25 models selected
> select subtract #13.13
35911 atoms, 32528 bonds, 3 pseudobonds, 4980 residues, 24 models selected
> select subtract #13.14
35376 atoms, 31985 bonds, 3 pseudobonds, 4906 residues, 23 models selected
> select subtract #13.15
34841 atoms, 31442 bonds, 3 pseudobonds, 4832 residues, 22 models selected
> select subtract #13.16
34306 atoms, 30899 bonds, 3 pseudobonds, 4758 residues, 21 models selected
> select subtract #13.17
33771 atoms, 30356 bonds, 3 pseudobonds, 4684 residues, 20 models selected
> select subtract #13.18
33244 atoms, 29821 bonds, 3 pseudobonds, 4611 residues, 19 models selected
> select subtract #13.21
31656 atoms, 28218 bonds, 1 pseudobond, 4346 residues, 18 models selected
> select subtract #13.27
30114 atoms, 26668 bonds, 4068 residues, 16 models selected
> hide sel cartoons
> select clear
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> color (#!13 & sel) dark gray
> select clear
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select add #13.10
1062 atoms, 147 residues, 2 models selected
> select add #13.11
1597 atoms, 221 residues, 3 models selected
> select add #13.12
2132 atoms, 295 residues, 4 models selected
> select add #13.13
2667 atoms, 369 residues, 5 models selected
> select add #13.14
3202 atoms, 443 residues, 6 models selected
> select add #13.15
3737 atoms, 517 residues, 7 models selected
> select add #13.16
4272 atoms, 591 residues, 8 models selected
> select add #13.17
4807 atoms, 665 residues, 9 models selected
> select add #13.18
5334 atoms, 738 residues, 10 models selected
> hide sel cartoons
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> cartoon style (#!13 & sel) modeHelix tube sides 20
> select clear
> select add #13
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> select subtract #13
26 models selected
> select add #13.21
1588 atoms, 265 residues, 1 model selected
> select add #13.27
3130 atoms, 543 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel lavender
> color sel light steel blue
> select clear
> color light steel blue
> undo
> select #13/Z:241
5 atoms, 4 bonds, 1 residue, 1 model selected
> color #13.27 #b0bed1ff
> color #13.27 #b8c6daff
> undo
> select subtract #13.27
1 model selected
> select add #13.27
1542 atoms, 278 residues, 1 model selected
> color (#!13 & sel) #b8c6daff
> color (#!13 & sel) #b4c2d5ff
> color (#!13 & sel) #b0bed1ff
> color (#!13 & sel) #b0bdd0ff
> color (#!13 & sel) #b0bed0ff
> color (#!13 & sel) #adbbcdff
> color (#!13 & sel) #abb9cbff
> color (#!13 & sel) #aab7c9ff
> color (#!13 & sel) #abb8caff
> color (#!13 & sel) #adbaccff
> color (#!13 & sel) #adbacdff
> color (#!13 & sel) #afbdd0ff
> color (#!13 & sel) #afbdd5ff
> color (#!13 & sel) #afbdd9ff
> color (#!13 & sel) #afbddbff
> color (#!13 & sel) #afbde0ff
> color (#!13 & sel) #afbddfff
> color (#!13 & sel) #afbdddff
> color (#!13 & sel) #afbddbff
> color (#!13 & sel) #afbdd9ff
> color (#!13 & sel) #afbdd5ff
> color (#!13 & sel) #afbdd3ff
> color (#!13 & sel) #afbdd2ff
> color (#!13 & sel) #a9bdd2ff
> color (#!13 & sel) #a3bdd2ff
> color (#!13 & sel) #a5bdd2ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #afbdd2ff
> color (#!13 & sel) #aebdd2ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abb9d2ff
> color (#!13 & sel) #abb6d2ff
> color (#!13 & sel) #abb5d2ff
> color (#!13 & sel) #abb7d2ff
> color (#!13 & sel) #abb9d2ff
> color (#!13 & sel) #abbad2ff
> color (#!13 & sel) #abbbd2ff
> color (#!13 & sel) #abbdd2ff
> select subtract #13.27
1 model selected
> select add #13.27
1542 atoms, 278 residues, 1 model selected
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abbdd5ff
> color (#!13 & sel) #abbdd8ff
> color (#!13 & sel) #abbdddff
> color (#!13 & sel) #abbde3ff
> color (#!13 & sel) #abbde9ff
> color (#!13 & sel) #abbdeeff
> color (#!13 & sel) #abbdecff
> color (#!13 & sel) #abbdebff
> color (#!13 & sel) #abbde1ff
> color (#!13 & sel) #abbdd4ff
> color (#!13 & sel) #abbdd3ff
> color (#!13 & sel) #abbdd2ff
> color (#!13 & sel) #abbdd7ff
> select subtract #13.27
1 model selected
> select clear
> select #13/Z:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 11 atom styles
> select clear
> select add #13.10
527 atoms, 73 residues, 1 model selected
> select add #13.11
1062 atoms, 147 residues, 2 models selected
> select add #13.12
1597 atoms, 221 residues, 3 models selected
> select add #13.13
2132 atoms, 295 residues, 4 models selected
> select add #13.14
2667 atoms, 369 residues, 5 models selected
> select add #13.15
3202 atoms, 443 residues, 6 models selected
> select add #13.16
3737 atoms, 517 residues, 7 models selected
> select add #13.17
4272 atoms, 591 residues, 8 models selected
> select add #13.18
4799 atoms, 664 residues, 9 models selected
Alignment identifier is 2
Alignment identifier is 3
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #13/I,Q:59-60
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #13/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> style (#!13 & sel) stick
Changed 18 atom styles
> select clear
> select #13/P,O,N,L-M,K,J:59
63 atoms, 56 bonds, 7 residues, 1 model selected
> select #13/P,O,N,L-M,K,J:59
63 atoms, 56 bonds, 7 residues, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 63 atom styles
> select clear
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #10/T:290 #12/Z:290
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains T,Z [266] RMSD: 1.278
> show #!5-6,13 atoms
> hide #!5-6,13 atoms
> undo
Drag select of 4 atoms, 5 bonds
> select clear
> select add #13.9
535 atoms, 74 residues, 1 model selected
> select subtract #13.9
1 model selected
> select add #13.10
527 atoms, 73 residues, 1 model selected
> select subtract #13.10
1 model selected
> select add #13.9
535 atoms, 74 residues, 1 model selected
Alignment identifier is 13/H
> select #13/H:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/H:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style (#!13 & sel) stick
Changed 9 atom styles
> select clear
> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb
Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb #14
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H J K L M N O P | No description available
I Q | No description available
R | No description available
S W | No description available
T | No description available
U X | No description available
V | No description available
Y | No description available
Z | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5-6,13-14 atoms
> select add #14
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #14.2
34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected
> select subtract #14.3
30980 atoms, 31384 bonds, 3 pseudobonds, 4355 residues, 27 models selected
> select subtract #14.4
27158 atoms, 27504 bonds, 3 pseudobonds, 3855 residues, 26 models selected
> select subtract #14.5
23561 atoms, 23844 bonds, 3 pseudobonds, 3386 residues, 25 models selected
> select subtract #14.6
19956 atoms, 20176 bonds, 3 pseudobonds, 2916 residues, 24 models selected
> select subtract #14.7
16370 atoms, 16527 bonds, 3 pseudobonds, 2448 residues, 23 models selected
> select subtract #14.8
14088 atoms, 14217 bonds, 3 pseudobonds, 2159 residues, 22 models selected
> select subtract #14.27
12546 atoms, 12667 bonds, 2 pseudobonds, 1881 residues, 21 models selected
> select subtract #14.26
11334 atoms, 11445 bonds, 2 pseudobonds, 1730 residues, 20 models selected
> select subtract #14.25
10269 atoms, 10378 bonds, 2 pseudobonds, 1580 residues, 19 models selected
> select subtract #14.24
9904 atoms, 10014 bonds, 2 pseudobonds, 1506 residues, 18 models selected
> select subtract #14.23
9140 atoms, 9251 bonds, 2 pseudobonds, 1354 residues, 17 models selected
> select subtract #14.22
8393 atoms, 8505 bonds, 2 pseudobonds, 1204 residues, 16 models selected
> select subtract #14.21
6805 atoms, 6902 bonds, 939 residues, 14 models selected
> select subtract #14.20
6440 atoms, 6538 bonds, 865 residues, 13 models selected
> select subtract #14.19
5548 atoms, 5636 bonds, 748 residues, 12 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> color (#!14 & sel) #f5ccdcff
Cell requested for row 13 is out of bounds for table with 41 rows! Resizing
table model.
> select add #14
38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected
> select subtract #14
26 models selected
> hide #!13 models
> hide #!6 models
> hide #!5 models
Drag select of 738 residues
Alignment identifier is 1
Alignment identifier is 4
> show #!13 models
> show #!5 models
> show #!6 models
> select #14/P,O,N,L-M,K,J,H:76
64 atoms, 56 bonds, 8 residues, 1 model selected
> select #14/P,O,N,L-M,K,J,H
4280 atoms, 4344 bonds, 592 residues, 1 model selected
> hide sel cartoons
> select #14/P,O,N,L-M,K,J,H:59
72 atoms, 64 bonds, 8 residues, 1 model selected
> select #14/P,O,N,L-M,K,J,H:59
72 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #14/I,Q:75
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #14/I,Q
1054 atoms, 1070 bonds, 146 residues, 1 model selected
> hide sel cartoons
> select #14/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #14/I,Q:59
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select clear
> style #5-6,13-14 ball
Changed 89937 atom styles
> style #5-6,13-14 stick
Changed 89937 atom styles
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX63CH/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 46天3小时39分钟
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Redmi 27 NU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Resolution: 3024 x 1964
UI Looks like: 1512 x 982 @ 120.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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