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Opened 7 months ago
Closed 7 months ago
#17143 closed defect (can't reproduce)
Crash deleting atoms
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001fe124840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 818 in delete
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py", line 50 in delete_atoms
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1428 in
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, 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 (total: 100)
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{
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "Mac15,3",
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"build" : "24D81",
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"captureTime" : "2025-03-20 17:20:34.5316 +0800",
"codeSigningMonitor" : 1,
"incident" : "DE0ED329-534D-4808-B9FF-507008BF50C7",
"pid" : 31575,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-20 17:19:44.1484 +0800",
"procStartAbsTime" : 2543305012344,
"procExitAbsTime" : 2544513831790,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F197DFDE-47C9-9A85-79E8-078C72A2A357",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "D5CB6B22-F3F8-4368-8D14-83C9A672666E",
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4364451840\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104244000-104248000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31575},
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[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6781566976,
"size" : 4865835008,
"uuid" : "5700d77a-6190-36e0-884d-fee6d586d62f"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.1G written=1927K(0%) resident=1927K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 224K 12 \nColorSync 640K 32 \nCoreAnimation 1856K 100 \nCoreGraphics 80K 5 \nCoreUI image data 3888K 28 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 2.3G 110 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 560K 35 \nStack 191.2M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 256.2M 188 \nVM_ALLOCATE (reserved) 384.0M 6 reserved VM address space (unallocated)\n__AUTH 5217K 666 \n__AUTH_CONST 70.3M 913 \n__CTF 824 1 \n__DATA 35.9M 1140 \n__DATA_CONST 35.4M 1149 \n__DATA_DIRTY 2761K 339 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 649.9M 231 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1170 \n__TPRO_CONST 272K 2 \ndyld private memory 304K 3 \nmapped file 284.0M 56 \nowned unmapped memory 1936K 1 \npage table in kernel 1927K 1 \nshared memory 3280K 31 \n=========== ======= ======= \nTOTAL 5.5G 6288 \nTOTAL, minus reserved VM space 5.2G 6288 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "810dc9cabec53a63e10f43526a8e42a1f039b743",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
},
{
"rolloutId" : "658361a603dc58766bab2d2a",
"factorPackIds" : {
"SIRI_TTS_DEVICE_TRAINING" : "6736733a26c1270f5a9ef53d"
},
"deploymentId" : 240000045
}
],
"experiments" : [
{
"treatmentId" : "a5ebf88d-4e1a-4ce6-91a7-ffa0f0af997d",
"experimentId" : "67cf8ce544f1a3655d87001a",
"deploymentId" : 400000001
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/cavity all.cxs"
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Populating font family aliases took 123 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
Log from Thu Mar 20 17:02:46 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/All 21h and
> Oseltamivir reference (wt).cxs"
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Log from Thu Mar 20 16:03:03 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/All 21h and
> Oseltamivir reference (wt).cxs"
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Log from Thu Mar 20 14:14:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/All 21h and
> Oseltamivir reference (wt).cxs"
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Log from Thu Mar 20 11:56:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/1 wt+21h vs
> h275y+21h .cxs"
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Log from Tue Mar 18 15:54:31 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/25.3.16-5 275+21h vs
> wt+21h.cxs"
Error opening map "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/25.3.16-5
275+21h vs wt+21h.cxs": File 25.3.16-5 275+21h vs wt+21h.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened 275y+21h density as #6, grid size 140,140,140, pixel 1.32, shown at
level 0.0709, step 1, values float32
Log from Sun Mar 16 18:21:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/hp/坚果云/科研/研二/TEXAS/建模/25.3.16 画图/25.3.16 -3 wt21h vs
> 2hu4.cxs"
Opened 25.3.14 wt_21h.mrc 21h density as #5, grid size 140,140,140, pixel
1.32, shown at level 0.0894, step 1, values float32
Opened 25.3.14 wt_21h.mrc as #3, grid size 140,140,140, pixel 1.32, shown at
level 0.0922, step 1, values float32
Opened 25.3.14 wt_21h.mrc copy as #7, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
Log from Sun Mar 16 15:13:15 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.15 21h-wt.cxs"
Opened 25.3.14 wt_21h.mrc copy as #5, grid size 140,140,140, pixel 1.32, shown
at level 0.0894, step 1, values float32
Log from Sat Mar 15 15:10:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\hp\Desktop\temporary file\25.3.14 refine\25.3.15 21h-wt all
> view.cxs" format session
Log from Sat Mar 15 13:19:14 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt 21h.pdb"
Chain information for 25.3.14 wt 21h.pdb #1
---
Chain | Description
D | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 275Y
> 21h.pdb"
Chain information for 25.3.14 275Y 21h.pdb #2
---
Chain | Description
D | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 275APO.pdb"
Chain information for 25.3.14 275APO.pdb #3
---
Chain | Description
D | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> set bgColor white
> set bgColor #ffffff00
> ui tool show "Command Line Interface"
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> view orient
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> align #1 toAtoms #2
Unequal number of atoms to pair, 3061 and 3063
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 25.3.14 wt 21h.pdb, chain D (#1) with 25.3.14 275Y 21h.pdb, chain D
(#2), sequence alignment score = 1999.1
RMSD between 387 pruned atom pairs is 0.324 angstroms; (across all 387 pairs:
0.324)
> matchmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 25.3.14 wt 21h.pdb, chain D (#1) with 25.3.14 275APO.pdb, chain D
(#3), sequence alignment score = 1991.6
RMSD between 387 pruned atom pairs is 0.364 angstroms; (across all 387 pairs:
0.364)
> hide #1 models
> hide #2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #1 models
> show #2 models
> show #3 models
> hide #1 models
> hide #3 models
> show #1 models
> close
> close #
Expected a models specifier or a keyword
> open "C:/Users/hp/Desktop/temporary file/25.2.9 274apo/25.2.9
> H5N1-APO-274-TERA.pdb"
Chain information for 25.2.9 H5N1-APO-274-TERA.pdb #1
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt_21h.mrc"
Opened 25.3.14 wt_21h.mrc as #2, grid size 140,140,140, pixel 1.32, shown at
level 0.15, step 1, values float32
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-0.71014,0,1,0,-1.0647,0,0,1,24.039
> select subtract #2
Nothing selected
> select add #1
12252 atoms, 12632 bonds, 1572 residues, 1 model selected
> view matrix models #1,1,0,0,6.8891,0,1,0,-3.0198,0,0,1,-45.744
> view matrix models #1,1,0,0,2.7469,0,1,0,4.2044,0,0,1,-0.8542
> view matrix models #1,1,0,0,-1.6281,0,1,0,-2.0361,0,0,1,-1.3732
> view matrix models
> #1,0.98817,-0.15334,0.0018364,13.34,0.15333,0.98816,0.0047055,-15.687,-0.0025362,-0.0043683,0.99999,-0.73564
> view matrix models
> #1,0.98817,-0.15334,0.0018364,14.526,0.15333,0.98816,0.0047055,-16.837,-0.0025362,-0.0043683,0.99999,-0.68414
> view matrix models
> #1,0.98979,-0.12595,-0.066777,19.257,0.12603,0.99202,-0.0030002,-13.839,0.066622,-0.0054467,0.99776,-6.7346
> view matrix models
> #1,0.97219,-0.22503,-0.064857,29.824,0.22508,0.97432,-0.0066573,-20.961,0.06469,-0.0081258,0.99787,-6.3204
> fitmap #1 inMap #2
Fit molecule 25.2.9 H5N1-APO-274-TERA.pdb (#1) to map 25.3.14 wt_21h.mrc (#2)
using 12252 atoms
average map value = 0.2203, steps = 72
shifted from previous position = 2.23
rotated from previous position = 4.31 degrees
atoms outside contour = 3838, contour level = 0.15019
Position of 25.2.9 H5N1-APO-274-TERA.pdb (#1) relative to 25.3.14 wt_21h.mrc
(#2) coordinates:
Matrix rotation and translation
0.96521608 -0.26145349 -0.00000313 27.36331187
0.26145349 0.96521608 -0.00001537 -20.92404374
0.00000704 0.00001401 1.00000000 -25.10689376
Axis 0.00005618 -0.00001945 1.00000000
Axis point 92.32202072 92.38125036 0.00000000
Rotation angle (degrees) 15.15632453
Shift along axis -25.10494943
> close #2
> close
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt_21h.mrc"
Opened 25.3.14 wt_21h.mrc as #1, grid size 140,140,140, pixel 1.32, shown at
level 0.15, step 1, values float32
> open "C:/Users/hp/Desktop/temporary file/25.2.9 274apo/25.2.9
> H5N1-APO-274-TERA.pdb"
Chain information for 25.2.9 H5N1-APO-274-TERA.pdb #2
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
12252 atoms, 12632 bonds, 1572 residues, 1 model selected
> view matrix models #2,1,0,0,-8.8859,0,1,0,-9.3602,0,0,1,-15.246
> view matrix models
> #2,0.97173,-0.22891,0.0578,8.6224,0.23233,0.97068,-0.061677,-21.46,-0.041986,0.073362,0.99642,-17.755
> view matrix models
> #2,0.97173,-0.22891,0.0578,16.97,0.23233,0.97068,-0.061677,-11.976,-0.041986,0.073362,0.99642,-22.25
> view matrix models
> #2,0.97173,-0.22891,0.0578,16.533,0.23233,0.97068,-0.061677,-12.322,-0.041986,0.073362,0.99642,-26.135
> fitmap #2 inMap #1
Fit molecule 25.2.9 H5N1-APO-274-TERA.pdb (#2) to map 25.3.14 wt_21h.mrc (#1)
using 12252 atoms
average map value = 0.2203, steps = 64
shifted from previous position = 1.78
rotated from previous position = 5.18 degrees
atoms outside contour = 3843, contour level = 0.15019
Position of 25.2.9 H5N1-APO-274-TERA.pdb (#2) relative to 25.3.14 wt_21h.mrc
(#1) coordinates:
Matrix rotation and translation
0.96509004 -0.26191833 -0.00004220 27.42736600
0.26191833 0.96509004 -0.00001683 -20.96803728
0.00004513 0.00000519 1.00000000 -25.10722655
Axis 0.00004204 -0.00016671 0.99999999
Axis point 92.38817006 92.40725382 0.00000000
Rotation angle (degrees) 15.18392000
Shift along axis -25.10257762
> save "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.2.9 tert
> apo274.pdb"
> close
> open "C:/Users/hp/Desktop/temporary file/25.2.9 274apo/25.2.9
> H5N1-APO-274-TERA.pdb"
Chain information for 25.2.9 H5N1-APO-274-TERA.pdb #1
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 tert
> 275apo.pdb"
Chain information for 25.3.14 tert 275apo.pdb #1
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides slab
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> close
> open C:/Users/hp/Downloads/h52G5oo.pdb
Summary of feedback from opening C:/Users/hp/Downloads/h52G5oo.pdb
---
warnings | End residue of secondary structure not found: SHEET 3 3 1 ILE D 122 UNK D 124 0
Start residue of secondary structure not found: SHEET 4 4 1 UNK D 129 LEU D
139 0
Chain information for h52G5oo.pdb #1
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Color Actions"
> color bychain
> select ::name="21H"
136 atoms, 144 bonds, 4 residues, 1 model selected
> color sel byhetero
> ui tool show "Color Actions"
> color sel red
> color sel byhetero
> color sel yellow
> color sel byhetero
> color sel gold
> color sel crimson
> color sel orange red
> color sel yellow green
> color sel olive
> color sel chartreuse
> color sel spring green
> color sel saddle brown
> color sel maroon
> color sel yellow
> color sel byhetero
> view matrix models #1,1,0,0,-0.10137,0,1,0,0.016025,0,0,1,0.010116
> select clear
> lighting simple
> lighting soft
> hide atoms
> select ::name="21H"
136 atoms, 144 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> view
> volume region all imageMode "full region"
No volumes specified
> view orient
> save C:\Users\hp/Desktop\image1.png supersample 3
> show target m
> view clip false
> select /C
3061 atoms, 3145 bonds, 393 residues, 1 model selected
> select ~sel & ##selected
9183 atoms, 9445 bonds, 1179 residues, 1 model selected
> hide target m
[Repeated 1 time(s)]
> close
> open C:\Users\hp\Downloads\h52G5oo.pdb format pdb
Summary of feedback from opening C:\Users\hp\Downloads\h52G5oo.pdb
---
warnings | End residue of secondary structure not found: SHEET 3 3 1 ILE D 122 UNK D 124 0
Start residue of secondary structure not found: SHEET 4 4 1 UNK D 129 LEU D
139 0
Chain information for h52G5oo.pdb #1
---
Chain | Description
A B C D | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> hide atoms
> ui tool show "Color Actions"
> color bychain
> select ::name="21H"
136 atoms, 144 bonds, 4 residues, 1 model selected
> color sel yellow
> show sel atoms
> color sel byhetero
> view orient
> lighting soft
> select clear
> save C:\Users\hp/Desktop\image2.png supersample 3
> save "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.15 21h-wt all
> view.cxs"
——— End of log from Sat Mar 15 13:19:14 2025 ———
opened ChimeraX session
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt 21h.pdb"
Chain information for 25.3.14 wt 21h.pdb #2
---
Chain | Description
D | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #2/D
3061 atoms, 3155 bonds, 393 residues, 1 model selected
> color sel forest green
> ui tool show "Color Actions"
> color sel chartreuse
> color sel green
> color sel lime
> color sel spring green
> color sel lime green
> color sel medium sea green
> color sel sea green
> color sel olive drab
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel dark cyan
> color sel medium aquamarine
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel light slate gray
> color sel slate gray
> color sel dark slate gray
> color sel midnight blue
> color sel hot pink
> color sel orange
> color sel orange red
> color sel red
> color sel yellow green
> color sel dark goldenrod
> color sel medium spring green
> color sel byelement
[Repeated 1 time(s)]
> color sel bychain
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel medium turquoise
> color sel cornflower blue
> color sel light sea green
> color sel byelement
> color sel byhetero
> color sel bychain
> hide #1 models
> hide sel atoms
> select ::name="21H"
170 atoms, 180 bonds, 5 residues, 2 models selected
> hide sel & #2 atoms
> show sel & #2 atoms
> color (#2 & sel) yellow
> color (#2 & sel) byhetero
> select add #1
12278 atoms, 12626 bonds, 1573 residues, 2 models selected
> select subtract #1
34 atoms, 36 bonds, 1 residue, 1 model selected
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt_21h.mrc"
Opened 25.3.14 wt_21h.mrc as #3, grid size 140,140,140, pixel 1.32, shown at
level 0.15, step 1, values float32
> volume #3 level 0.06894
> volume #3 style mesh
> select ::name="21H"
170 atoms, 180 bonds, 5 residues, 2 models selected
> volume zone #1 centerSelected true radius 5
Expected a keyword
> volume zone #3 centerSelected true radius 5
Expected a keyword
> volume zone #3 nearAtoms sel & #2 range 7.92
> volume #3 level 0.0931
> color zone #3 near sel & #2 distance 7.92
> undo
> surface dust #3 size 13.2
> undo
[Repeated 1 time(s)]
> volume zone #3 nearAtoms sel & #2 range 7.92
> volume #3 orthoplanes xyz positionPlanes 70,70,70 style image region all
> mousemode rightMode "move planes"
> undo
> volume zone #3 nearAtoms sel & #2 range 7.92
> undo
[Repeated 1 time(s)]
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> undo
[Repeated 2 time(s)]
> volume style surface
> volume style mesh
> redo
[Repeated 4 time(s)]
> volume zone #3 nearAtoms sel & #2 range 7.92
> volume #3 region 0,0,0,139,136,139
> volume showOutlineBox false
> volume zone #3 nearAtoms sel & #2 range 5
> volume #3 change image level -0.0124,0 level 0.1501,0.8 level 0.7728,1
> volume #3 level 0.07773
> volume zone #3 nearAtoms sel & #2 range 3
> volume zone #3 nearAtoms sel & #2 range 2
> volume zone #3 nearAtoms sel & #2 range 2.5
> volume zone #3 nearAtoms sel & #2 range 2.3
> volume zone #3 nearAtoms sel & #2 range 2.4
> vop gaussian #3 sdev 3.96
Opened 25.3.14 wt_21h.mrc gaussian as #4, grid size 140,140,140, pixel 1.32,
shown at step 1, values float32
> undo
> volume zone #3 nearAtoms sel & #2 range 2.4
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> volume zone #4 nearAtoms sel & #2 range 7.92
> volume #!4 style surface
> volume #!4 style mesh
> volume #4 region 0,0,0,139,139,139
> close #4
> show #!3 models
> volume zone #3 nearAtoms sel & #2 range 2.4
> volume zone #3 nearAtoms sel & #2 range 2.5
> volume zone #3 nearAtoms sel & #2 range 2.3
> volume zone #3 nearAtoms sel & #2 range 2.5
> volume zone #3 nearAtoms sel & #2 range 2.6
> volume #3 step 2
> volume #3 step 1
> transparency 50
> volume style mesh
> volume style image
> volume style mesh
> volume style surface
> volume style mesh
> volume hide
> volume show
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume show
> volume hide
> volume show
> volume zone #3 nearAtoms sel & #2 range 7.92
> volume zone #3 nearAtoms sel & #2 range 2.6
> volume style surface
> volume style mesh
> volume #3 level 0.1293
> volume zone #3 nearAtoms sel & #2 range 2.6
> volume zone #3 nearAtoms sel & #2 range 2.5
> volume zone #3 nearAtoms sel & #2 range 2.3
> volume zone #3 nearAtoms sel & #2 range 2
> volume style surface
> select clear
> volume zone #3 nearAtoms sel & #2 range 2.3
no atoms specified for zone
> select ::name="21H"
170 atoms, 180 bonds, 5 residues, 2 models selected
> volume zone #3 nearAtoms sel & #2 range 2.3
> volume zone #3 nearAtoms sel & #2 range 2.5
> volume zone #3 nearAtoms sel & #2 range 2.6
> volume zone #3 nearAtoms sel & #2 range 2.7
> volume zone #3 nearAtoms sel & #2 range 3
> ui tool show "Volume Viewer"
> ui mousemode right "map eraser"
> volume erase #3 center 61.064,98.558,92.625 radius 2.6964
Opened 25.3.14 wt_21h.mrc copy as #5, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> hide #!5 models
> hide #4 models
> show #4 models
> show #!3 models
> show #!5 models
Can only have one displayed volume when erasing
> hide #!3 models
> hide #4 models
> show #4 models
> volume erase #5 center 55.434,101.74,92.709 radius 2.6796 outside true
> undo
[Repeated 1 time(s)]
> hide #!5 models
> show #!3 models
> volume copy #3 subregion 43,72,69,48,77,74
Opened 25.3.14 wt_21h.mrc copy as #6, grid size 6,6,6, pixel 1.32, shown at
step 1, values float32
> undo
> close #6
> show #!5 models
> close #5
> show #!3 models
> volume erase #3 center 61.457,99.29,91.494 radius 2.5872
Opened 25.3.14 wt_21h.mrc copy as #5, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> hide #!5 models
> show #!3 models
> select add #3
170 atoms, 180 bonds, 5 residues, 5 models selected
> select add #3
170 atoms, 180 bonds, 5 residues, 5 models selected
> select add #3
170 atoms, 180 bonds, 5 residues, 5 models selected
> select add #2
3197 atoms, 3299 bonds, 397 residues, 5 models selected
> select add #3
3197 atoms, 3299 bonds, 397 residues, 5 models selected
> select subtract #2
136 atoms, 144 bonds, 4 residues, 4 models selected
> select add #3
136 atoms, 144 bonds, 4 residues, 4 models selected
> show #!5 models
> select clear
Can only have one displayed volume when erasing
> hide #!3 models
> volume erase #5 center 51.528,102.57,89.589 radius 2.5872
> hide #!5 models
> show #!3 models
> volume erase #3 center 60.316,99.236,88.608 radius 2.5872
Opened 25.3.14 wt_21h.mrc copy as #6, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> hide #!6 models
> show #!6 models
> close #5-6
> show #!3 models
> hide #4 models
> show #4 models
> hide #!3 models
> show #!3 models
> volume zone #3 nearAtoms sel & #2 range 2.7
no atoms specified for zone
> select ::name="21H"
170 atoms, 180 bonds, 5 residues, 2 models selected
> volume zone #3 nearAtoms sel & #2 range 5
> volume #3 level 0.09062
> close #4
> ui mousemode right "map eraser"
> volume erase #3 center 61.446,97.572,81.679 radius 2.587
Opened 25.3.14 wt_21h.mrc copy as #5, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> volume erase #5 center 61.446,97.572,81.679 radius 2.587
> volume erase #5 center 62.975,102.89,92.894 radius 2.587 outside true
> volume erase #5 center 62.975,102.89,92.894 radius 5.9136 outside true
> volume copy #5 subregion 36,74,59,46,84,69
Opened 25.3.14 wt_21h.mrc copy as #6, grid size 11,11,11, pixel 1.32, shown at
step 1, values float32
> close #6
> close #5
> show #!3 models
> ui mousemode right "pick blobs"
> measure blob #!3.1 triangleNumber 122911 color #0000ccff outline true
Surface 25.3.14 wt_21h.mrc #3.1 blob:
volume = 86966
area = 1.0243e+05
size = 107.18 107.18 66.96
> hide #!3 models
> show #!3 models
> hide #!3 target m
> close #3
> close #4
> open "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.14 wt_21h.mrc"
Opened 25.3.14 wt_21h.mrc as #3, grid size 140,140,140, pixel 1.32, shown at
level 0.15, step 1, values float32
> volume #3 level 0.09218
> volume zone #3 nearAtoms sel & #2 range 5
> ui mousemode right "map eraser"
> volume erase #3 center 65.186,103.07,92.398 radius 9.9792 outside true
Opened 25.3.14 wt_21h.mrc copy as #5, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> volume erase #5 center 60.525,96.343,91.916 radius 3.8808
> volume erase #5 center 55.484,102.75,91.722 radius 2.9568
> volume erase #5 center 58.525,100.41,96.734 radius 2.9568
> volume erase #5 center 62.237,108.25,100.02 radius 2.9568
> volume erase #5 center 57.521,99.772,90.463 radius 2.9568
> volume erase #5 center 66.263,94.957,88.061 radius 7.2072
> volume erase #5 center 61.286,98.365,82.255 radius 8.4084
> volume #3 level 0.1223
> volume #5 level 0.08021
> hide #!3 models
> hide #!5 models
> show #!3 models
> volume erase #3 center 61.286,98.365,82.255 radius 8.4084
Opened 25.3.14 wt_21h.mrc copy as #6, grid size 140,140,140, pixel 1.32, shown
at step 1, values float32
> close #6
> show #!5 models
> volume #5 level 0.09047
> volume erase #5 center 62.602,108.27,84.121 radius 4.0656
> volume erase #5 center 59.315,109.9,85.976 radius 4.0656
> volume #5 level 0.1007
> volume erase #5 center 69.232,108.52,96.691 radius 4.0656
> volume erase #5 center 67.403,105.5,98.516 radius 4.0656
> volume erase #5 center 68.509,97.638,98.61 radius 4.0656
> volume #5 level 0.05455
> volume #5 level 0.09047
> volume erase #5 center 60.767,97.947,97.969 radius 4.0656
> volume #5 style mesh
> volume #5 style image
> volume #5 style surface
> volume erase #5 center 65.772,112.15,94.619 radius 4.0656
> volume erase #5 center 62.908,113.75,90.217 radius 4.0656
> volume erase #5 center 69.913,109.49,86.52 radius 4.0656
> volume erase #5 center 70.694,109.41,91.18 radius 4.0656
> volume erase #5 center 69.266,110.31,90.464 radius 4.0656
> volume erase #5 center 69.468,104.14,85.347 radius 4.0656
> volume erase #5 center 73.641,101.75,87.342 radius 4.0656
> volume erase #5 center 71.502,97.007,92.743 radius 3.696
> volume erase #5 center 67.169,98.522,91.44 radius 3.696
> volume erase #5 center 74.962,107.11,93.794 radius 3.696
> volume erase #5 center 67.306,112.06,85.746 radius 3.696
> volume erase #5 center 72.403,107.84,87.289 radius 3.696
> volume erase #5 center 55.617,110.08,90.885 radius 3.696
> volume erase #5 center 57.444,110.11,95.639 radius 3.696
> hide #!5 models
> show #!5 models
> hide #4 models
> volume #5 style mesh
> close #3
> save "C:/Users/hp/Desktop/temporary file/25.3.14 refine/25.3.15 21h-wt.cxs"
> volume #5 color cyan
> volume #5 color #00aaff
[Repeated 1 time(s)]
> volume #5 color #0055ff
> volume #5 color #00aaff
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #5 level 0.09047
> volume #5 level 0.08936
> ui mousemode right "map eraser"
> volume erase #5 center 64.232,93.834,94.963 radius 1.0167
> volume erase #5 center 64.721,108.19,93.473 radius 1.0167
> volume erase #5 center 68.835,101.83,89.468 radius 1.0167
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> select ::name="21H"
170 atoms, 180 bonds, 5 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel dark goldenrod
> color sel peru
> color sel dark salmon
> color sel green
> color sel orange
> color sel light sea green
[deleted to fit within ticket limits]
> select #!1.7.2,4,7,10-12,16,19-20
3032 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.2-5,7,10-12,16-20,22
> select #!1.7.2-5,7,10-12,16-20,22
3454 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.2-5,7,10-13,16-20,22
> select #!1.7.2-5,7,10-13,16-20,22
3528 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.2-5,7,10-13,15-20,22
> select #!1.7.2-5,7,10-13,15-20,22
3585 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.2-7,10-13,15-20,22
> select #!1.7.2-7,10-13,15-20,22
3642 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.1-7,10-13,15-20,22
> select #!1.7.1-7,10-13,15-20,22
3692 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.1-7,10-13,15-22
> select #!1.7.1-7,10-13,15-22
3731 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.1-7,10-13,15-23
> select #!1.7.1-7,10-13,15-23
3765 atoms, 20 residues, 20 models selected
> ~surface #1.7
> surface #!1.7.1-7,9-13,15-23
> select #!1.7.1-7,9-13,15-23
3798 atoms, 21 residues, 21 models selected
> ~surface #1.7
> surface #!1.7.1-13,15-23
> select #!1.7.1-13,15-23
3828 atoms, 22 residues, 22 models selected
> surface hidePatches (#!1.7.1-13,15-23 & sel)
[Repeated 1 time(s)]
> surface (#!1.7.1-13,15-23 & sel)
> cartoon hide (#!1.7.1-13,15-23 & sel)
> ~label (#!1.7.1-13,15-23 & sel) residues
> delete atoms (#!1.7.1-13,15-23 & sel)
> ~surface #1.7
> surface #!1.7.1,3-13,15-23
> select #!1.7.1,3-13,15-23
3424 atoms, 21 residues, 21 models selected
> ~surface #1.7
> surface #!1.7.15
> select #!1.7.15
57 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.1,15
> select #!1.7.1,15
107 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.1,4,15
> select #!1.7.1,4,15
368 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.1,4,15,17
> select #!1.7.1,4,15,17
446 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.1,4,15,17,21
> select #!1.7.1,4,15,17,21
485 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,15,17,21
> select #!1.7.1,4,10,15,17,21
814 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,15,17-18,21
> select #!1.7.1,4,10,15,17-18,21
892 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,13,15,17-18,21
> select #!1.7.1,4,10,13,15,17-18,21
966 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-18,21
> select #!1.7.1,4,10-11,13,15,17-18,21
1466 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-18,20-21
> select #!1.7.1,4,10-11,13,15,17-18,20-21
1704 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-21
> select #!1.7.1,4,10-11,13,15,17-21
1920 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-11,13,15,17-21
> select #!1.7.1,4-5,10-11,13,15,17-21
2002 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15,17-21
> select #!1.7.1,4-5,10-13,15,17-21
2202 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15,17-21,23
> select #!1.7.1,4-5,10-13,15,17-21,23
2236 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15-21,23
> select #!1.7.1,4-5,10-13,15-21,23
2417 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,10-13,15-21,23
> select #!1.7.1,3-5,10-13,15-21,23
2506 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7,10-13,15-21,23
> select #!1.7.1,3-5,7,10-13,15-21,23
3209 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.1,3-7,10-13,15-21,23
> select #!1.7.1,3-7,10-13,15-21,23
3266 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.1,3-7,9-13,15-21,23
> select #!1.7.1,3-7,9-13,15-21,23
3299 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.1,3-7,9-13,15-23
> select #!1.7.1,3-7,9-13,15-23
3394 atoms, 20 residues, 20 models selected
> ~surface #1.7
> surface #!1.7.1,3-13,15-23
> select #!1.7.1,3-13,15-23
3424 atoms, 21 residues, 21 models selected
> ~surface #1.7
> surface #!1.7.1,3-13,15-23
> select #!1.7.1,3-13,15-23
3424 atoms, 21 residues, 21 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7-13,15-23
> select #!1.7.1,3-5,7-13,15-23
3367 atoms, 20 residues, 20 models selected
> ~surface #1.7
> surface #!1.7.15
> select #!1.7.15
57 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.1,15
> select #!1.7.1,15
107 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.1,4,15
> select #!1.7.1,4,15
368 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.1,4,15,17
> select #!1.7.1,4,15,17
446 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.1,4,15,17,21
> select #!1.7.1,4,15,17,21
485 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,15,17,21
> select #!1.7.1,4,10,15,17,21
814 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,15,17-18,21
> select #!1.7.1,4,10,15,17-18,21
892 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.1,4,10,13,15,17-18,21
> select #!1.7.1,4,10,13,15,17-18,21
966 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-18,21
> select #!1.7.1,4,10-11,13,15,17-18,21
1466 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-18,20-21
> select #!1.7.1,4,10-11,13,15,17-18,20-21
1704 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.1,4,10-11,13,15,17-21
> select #!1.7.1,4,10-11,13,15,17-21
1920 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-11,13,15,17-21
> select #!1.7.1,4-5,10-11,13,15,17-21
2002 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15,17-21
> select #!1.7.1,4-5,10-13,15,17-21
2202 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15,17-21,23
> select #!1.7.1,4-5,10-13,15,17-21,23
2236 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.1,4-5,10-13,15-21,23
> select #!1.7.1,4-5,10-13,15-21,23
2417 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,10-13,15-21,23
> select #!1.7.1,3-5,10-13,15-21,23
2506 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7,10-13,15-21,23
> select #!1.7.1,3-5,7,10-13,15-21,23
3209 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7,9-13,15-21,23
> select #!1.7.1,3-5,7,9-13,15-21,23
3242 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7,9-13,15-23
> select #!1.7.1,3-5,7,9-13,15-23
3337 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7-13,15-23
> select #!1.7.1,3-5,7-13,15-23
3367 atoms, 20 residues, 20 models selected
> ~surface #1.7
> surface #!1.7.1,3-5,7-13,15-23
> select #!1.7.1,3-5,7-13,15-23
3367 atoms, 20 residues, 20 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-13,15-23
> select #!1.7.1,3,5,7-13,15-23
3106 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.15
> select #!1.7.15
57 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.1,15
> select #!1.7.1,15
107 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.1,15,17
> select #!1.7.1,15,17
185 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.1,15,17,21
> select #!1.7.1,15,17,21
224 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.1,10,15,17,21
> select #!1.7.1,10,15,17,21
553 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.1,10,15,17-18,21
> select #!1.7.1,10,15,17-18,21
631 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.1,10-11,15,17-18,21
> select #!1.7.1,10-11,15,17-18,21
1131 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.1,10-11,15,17-18,20-21
> select #!1.7.1,10-11,15,17-18,20-21
1369 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.1,10-11,15,17-21
> select #!1.7.1,10-11,15,17-21
1585 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.1,5,10-11,15,17-21
> select #!1.7.1,5,10-11,15,17-21
1667 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.1,5,10-12,15,17-21
> select #!1.7.1,5,10-12,15,17-21
1867 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.1,5,10-12,15,17-21,23
> select #!1.7.1,5,10-12,15,17-21,23
1901 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.1,5,10-12,15-21,23
> select #!1.7.1,5,10-12,15-21,23
2082 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,10-12,15-21,23
> select #!1.7.1,3,5,10-12,15-21,23
2171 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7,10-12,15-21,23
> select #!1.7.1,3,5,7,10-12,15-21,23
2874 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-8,10-12,15-21,23
> select #!1.7.1,3,5,7-8,10-12,15-21,23
2904 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-12,15-21,23
> select #!1.7.1,3,5,7-12,15-21,23
2937 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-12,15-23
> select #!1.7.1,3,5,7-12,15-23
3032 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-13,15-23
> select #!1.7.1,3,5,7-13,15-23
3106 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.1,3,5,7-13,15-23
> select #!1.7.1,3,5,7-13,15-23
3106 atoms, 19 residues, 19 models selected
> ~surface #1.7
> surface #!1.7.3,5,7-13,15-23
> select #!1.7.3,5,7-13,15-23
3056 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7-8,17,21
> select #!1.7.7-8,17,21
850 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7-8,15,17,21
> select #!1.7.7-8,15,17,21
907 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7-8,15,17-18,21
> select #!1.7.7-8,15,17-18,21
985 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7-8,15,17-19,21
> select #!1.7.7-8,15,17-19,21
1201 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7-8,13,15,17-19,21
> select #!1.7.7-8,13,15,17-19,21
1275 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7-8,13,15-19,21
> select #!1.7.7-8,13,15-19,21
1456 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.5,7-8,13,15-19,21
> select #!1.7.5,7-8,13,15-19,21
1538 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.5,7-9,13,15-19,21
> select #!1.7.5,7-9,13,15-19,21
1571 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.5,7-10,13,15-19,21
> select #!1.7.5,7-10,13,15-19,21
1900 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.5,7-10,12-13,15-19,21
> select #!1.7.5,7-10,12-13,15-19,21
2100 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-19,21
> select #!1.7.5,7-13,15-19,21
2600 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-19,21-22
> select #!1.7.5,7-13,15-19,21-22
2695 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-19,21-23
> select #!1.7.5,7-13,15-19,21-23
2729 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.3,5,7-13,15-19,21-23
> select #!1.7.3,5,7-13,15-19,21-23
2818 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.3,5,7-13,15-23
> select #!1.7.3,5,7-13,15-23
3056 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.3,5,7-13,15-23
> select #!1.7.3,5,7-13,15-23
3056 atoms, 18 residues, 18 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-23
> select #!1.7.5,7-13,15-23
2967 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,21
> select #!1.7.7,15,17,21
877 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-18,21
> select #!1.7.7,15,17-18,21
955 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-19,21
> select #!1.7.7,15,17-19,21
1171 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7,13,15,17-19,21
> select #!1.7.7,13,15,17-19,21
1245 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7,13,15-19,21
> select #!1.7.7,13,15-19,21
1426 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7,9,13,15-19,21
> select #!1.7.7,9,13,15-19,21
1459 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-19,21
> select #!1.7.7,9-10,13,15-19,21
1788 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.5,7,9-10,13,15-19,21
> select #!1.7.5,7,9-10,13,15-19,21
1870 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.5,7,9-10,12-13,15-19,21
> select #!1.7.5,7,9-10,12-13,15-19,21
2070 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.5,7,9-13,15-19,21
> select #!1.7.5,7,9-13,15-19,21
2570 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.5,7,9-13,15-19,21-22
> select #!1.7.5,7,9-13,15-19,21-22
2665 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.5,7,9-13,15-19,21-23
> select #!1.7.5,7,9-13,15-19,21-23
2699 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-19,21-23
> select #!1.7.5,7-13,15-19,21-23
2729 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-23
> select #!1.7.5,7-13,15-23
2967 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.5,7-13,15-23
> select #!1.7.5,7-13,15-23
2967 atoms, 17 residues, 17 models selected
> ~surface #1.7
> surface #!1.7.7-13,15-23
> select #!1.7.7-13,15-23
2885 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,21
> select #!1.7.7,15,17,21
877 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-18,21
> select #!1.7.7,15,17-18,21
955 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-19,21
> select #!1.7.7,15,17-19,21
1171 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7,13,15,17-19,21
> select #!1.7.7,13,15,17-19,21
1245 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7,13,15-19,21
> select #!1.7.7,13,15-19,21
1426 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7,9,13,15-19,21
> select #!1.7.7,9,13,15-19,21
1459 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-19,21
> select #!1.7.7,9-10,13,15-19,21
1788 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12-13,15-19,21
> select #!1.7.7,9-10,12-13,15-19,21
1988 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12-13,15-19,21-22
> select #!1.7.7,9-10,12-13,15-19,21-22
2083 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7,9-13,15-19,21-22
> select #!1.7.7,9-13,15-19,21-22
2583 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7,9-13,15-19,21-23
> select #!1.7.7,9-13,15-19,21-23
2617 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.7-13,15-19,21-23
> select #!1.7.7-13,15-19,21-23
2647 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.7-13,15-23
> select #!1.7.7-13,15-23
2885 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.7-13,15-23
> select #!1.7.7-13,15-23
2885 atoms, 16 residues, 16 models selected
> ~surface #1.7
> surface #!1.7.7-10,12-13,15-23
> select #!1.7.7-10,12-13,15-23
2385 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,21
> select #!1.7.7,15,17,21
877 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-18,21
> select #!1.7.7,15,17-18,21
955 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7,15,17-19,21
> select #!1.7.7,15,17-19,21
1171 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7,15-19,21
> select #!1.7.7,15-19,21
1352 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7,12,15-19,21
> select #!1.7.7,12,15-19,21
1552 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7,9,12,15-19,21
> select #!1.7.7,9,12,15-19,21
1585 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12,15-19,21
> select #!1.7.7,9-10,12,15-19,21
1914 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12,15-19,21-22
> select #!1.7.7,9-10,12,15-19,21-22
2009 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12-13,15-19,21-22
> select #!1.7.7,9-10,12-13,15-19,21-22
2083 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,12-13,15-19,21-23
> select #!1.7.7,9-10,12-13,15-19,21-23
2117 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7-10,12-13,15-19,21-23
> select #!1.7.7-10,12-13,15-19,21-23
2147 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.7-10,12-13,15-23
> select #!1.7.7-10,12-13,15-23
2385 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.7-10,12-13,15-23
> select #!1.7.7-10,12-13,15-23
2385 atoms, 15 residues, 15 models selected
> ~surface #1.7
> surface #!1.7.7-10,13,15-23
> select #!1.7.7-10,13,15-23
2185 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7-8,17,21
> select #!1.7.7-8,17,21
850 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7-8,15,17,21
> select #!1.7.7-8,15,17,21
907 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7-8,15,17,19,21
> select #!1.7.7-8,15,17,19,21
1123 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7-9,15,17,19,21
> select #!1.7.7-9,15,17,19,21
1156 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7-10,15,17,19,21
> select #!1.7.7-10,15,17,19,21
1485 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7-10,15,17-19,21
> select #!1.7.7-10,15,17-19,21
1563 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7-10,15,17-19,21-22
> select #!1.7.7-10,15,17-19,21-22
1658 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.7-10,15-19,21-22
> select #!1.7.7-10,15-19,21-22
1839 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.7-10,15-19,21-23
> select #!1.7.7-10,15-19,21-23
1873 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7-10,13,15-19,21-23
> select #!1.7.7-10,13,15-19,21-23
1947 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7-10,13,15-23
> select #!1.7.7-10,13,15-23
2185 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.7-10,13,15-23
> select #!1.7.7-10,13,15-23
2185 atoms, 14 residues, 14 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-23
> select #!1.7.7,9-10,13,15-23
2155 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,21
> select #!1.7.7,15,17,21
877 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,19,21
> select #!1.7.7,15,17,19,21
1093 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7,9,15,17,19,21
> select #!1.7.7,9,15,17,19,21
1126 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,15,17,19,21
> select #!1.7.7,9-10,15,17,19,21
1455 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,15,17-19,21
> select #!1.7.7,9-10,15,17-19,21
1533 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,15,17-19,21-22
> select #!1.7.7,9-10,15,17-19,21-22
1628 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,15-19,21-22
> select #!1.7.7,9-10,15-19,21-22
1809 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,15-19,21-23
> select #!1.7.7,9-10,15-19,21-23
1843 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-19,21-23
> select #!1.7.7,9-10,13,15-19,21-23
1917 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-23
> select #!1.7.7,9-10,13,15-23
2155 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7,9-10,13,15-23
> select #!1.7.7,9-10,13,15-23
2155 atoms, 13 residues, 13 models selected
> ~surface #1.7
> surface #!1.7.7,10,13,15-23
> select #!1.7.7,10,13,15-23
2122 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7
> select #!1.7.7
703 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.7,17
> select #!1.7.7,17
781 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.7,17,21
> select #!1.7.7,17,21
820 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,21
> select #!1.7.7,15,17,21
877 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.7,15,17,19,21
> select #!1.7.7,15,17,19,21
1093 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.7,10,15,17,19,21
> select #!1.7.7,10,15,17,19,21
1422 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.7,10,15,17,19,21-22
> select #!1.7.7,10,15,17,19,21-22
1517 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.7,10,15,17-19,21-22
> select #!1.7.7,10,15,17-19,21-22
1595 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.7,10,15,17-19,21-23
> select #!1.7.7,10,15,17-19,21-23
1629 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.7,10,15-19,21-23
> select #!1.7.7,10,15-19,21-23
1810 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.7,10,13,15-19,21-23
> select #!1.7.7,10,13,15-19,21-23
1884 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.7,10,13,15-23
> select #!1.7.7,10,13,15-23
2122 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.7,10,13,15-23
> select #!1.7.7,10,13,15-23
2122 atoms, 12 residues, 12 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-23
> select #!1.7.10,13,15-23
1419 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.17,21
> select #!1.7.17,21
117 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.15,17,21
> select #!1.7.15,17,21
174 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.15,17,19,21
> select #!1.7.15,17,19,21
390 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,19,21
> select #!1.7.10,15,17,19,21
719 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,19,21-22
> select #!1.7.10,15,17,19,21-22
814 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-19,21-22
> select #!1.7.10,15,17-19,21-22
892 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-19,21-23
> select #!1.7.10,15,17-19,21-23
926 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.10,15-19,21-23
> select #!1.7.10,15-19,21-23
1107 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-19,21-23
> select #!1.7.10,13,15-19,21-23
1181 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-23
> select #!1.7.10,13,15-23
1419 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-23
> select #!1.7.10,13,15-23
1419 atoms, 11 residues, 11 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,20-23
> select #!1.7.10,13,15-18,20-23
1203 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.17,21
> select #!1.7.17,21
117 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.15,17,21
> select #!1.7.15,17,21
174 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,21
> select #!1.7.10,15,17,21
503 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,21-22
> select #!1.7.10,15,17,21-22
598 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,21-22
> select #!1.7.10,15,17-18,21-22
676 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,21-23
> select #!1.7.10,15,17-18,21-23
710 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,15-18,21-23
> select #!1.7.10,15-18,21-23
891 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,21-23
> select #!1.7.10,13,15-18,21-23
965 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,20-23
> select #!1.7.10,13,15-18,20-23
1203 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,20-23
> select #!1.7.10,13,15-18,20-23
1203 atoms, 10 residues, 10 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,21-23
> select #!1.7.10,13,15-18,21-23
965 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.17,21
> select #!1.7.17,21
117 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.15,17,21
> select #!1.7.15,17,21
174 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,21
> select #!1.7.10,15,17,21
503 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,21-22
> select #!1.7.10,15,17,21-22
598 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,21-22
> select #!1.7.10,15,17-18,21-22
676 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,21-23
> select #!1.7.10,15,17-18,21-23
710 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,15-18,21-23
> select #!1.7.10,15-18,21-23
891 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,21-23
> select #!1.7.10,13,15-18,21-23
965 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,21-23
> select #!1.7.10,13,15-18,21-23
965 atoms, 9 residues, 9 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,22-23
> select #!1.7.10,13,15-18,22-23
926 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.15,17
> select #!1.7.15,17
135 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,15,17
> select #!1.7.10,15,17
464 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,22
> select #!1.7.10,15,17,22
559 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,22
> select #!1.7.10,15,17-18,22
637 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,22-23
> select #!1.7.10,15,17-18,22-23
671 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,15-18,22-23
> select #!1.7.10,15-18,22-23
852 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,22-23
> select #!1.7.10,13,15-18,22-23
926 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,22-23
> select #!1.7.10,13,15-18,22-23
926 atoms, 8 residues, 8 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,23
> select #!1.7.10,13,15-18,23
831 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.15,17
> select #!1.7.15,17
135 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,15,17
> select #!1.7.10,15,17
464 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,15,17,23
> select #!1.7.10,15,17,23
498 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18,23
> select #!1.7.10,15,17-18,23
576 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,15-18,23
> select #!1.7.10,15-18,23
757 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,23
> select #!1.7.10,13,15-18,23
831 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18,23
> select #!1.7.10,13,15-18,23
831 atoms, 7 residues, 7 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18
> select #!1.7.10,13,15-18
797 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.15,17
> select #!1.7.15,17
135 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,15,17
> select #!1.7.10,15,17
464 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,15,17-18
> select #!1.7.10,15,17-18
542 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,15-18
> select #!1.7.10,15-18
723 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18
> select #!1.7.10,13,15-18
797 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,13,15-18
> select #!1.7.10,13,15-18
797 atoms, 6 residues, 6 models selected
> ~surface #1.7
> surface #!1.7.10,13,16-18
> select #!1.7.10,13,16-18
740 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.17
> select #!1.7.17
78 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.10,17
> select #!1.7.10,17
407 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,17-18
> select #!1.7.10,17-18
485 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,16-18
> select #!1.7.10,16-18
666 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,13,16-18
> select #!1.7.10,13,16-18
740 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,13,16-18
> select #!1.7.10,13,16-18
740 atoms, 5 residues, 5 models selected
> ~surface #1.7
> surface #!1.7.10,13,17-18
> select #!1.7.10,13,17-18
559 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.13
> select #!1.7.13
74 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.13,17
> select #!1.7.13,17
152 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,13,17
> select #!1.7.10,13,17
481 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,13,17-18
> select #!1.7.10,13,17-18
559 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,13,17-18
> select #!1.7.10,13,17-18
559 atoms, 4 residues, 4 models selected
> ~surface #1.7
> surface #!1.7.10,13,18
> select #!1.7.10,13,18
481 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.13
> select #!1.7.13
74 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.10,13
> select #!1.7.10,13
403 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,13,18
> select #!1.7.10,13,18
481 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,13,18
> select #!1.7.10,13,18
481 atoms, 3 residues, 3 models selected
> ~surface #1.7
> surface #!1.7.10,13
> select #!1.7.10,13
403 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.13
> select #!1.7.13
74 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.10,13
> select #!1.7.10,13
403 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10,13
> select #!1.7.10,13
403 atoms, 2 residues, 2 models selected
> ~surface #1.7
> surface #!1.7.10
> select #!1.7.10
329 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.10
> select #!1.7.10
329 atoms, 1 residue, 1 model selected
> ~surface #1.7
> surface #!1.7.10
> select #!1.7.10
329 atoms, 1 residue, 1 model selected
> delete bonds (#!1.7.1-13,15-23 & sel)
> ~surface #1.7
> surface #!1.7.14
> select #!1.7.14
2590 atoms, 1 residue, 1 model selected
> surface (#!1.7.14 & sel)
> transparency (#!1.7.14 & sel) 70
> save "/Users/gulhabib/Documents/CryoEM/25.3.16 画图/edited/cavity all.cxs"
——— End of log from Thu Mar 20 17:02:46 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: MTL73CH/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 6 hours, 5 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Mi Monitor:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-clix: 0.1.10
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-GenomeTools: 0.9
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.2.7
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 19.0.1
pycollada: 0.8
pydantic: 2.10.6
pydantic_core: 2.27.2
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.18
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
starfile: 0.5.12
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Core |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash deleting atoms |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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