![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15859 closed defect (duplicate)
Crash on Mac waking from sleep
| 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
The following bug report has been submitted:
Platform: macOS-14.6.1-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 0x00000001fad44f40 (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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, 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 (total: 120)
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{
"uptime" : 250000,
"procRole" : "Background",
"version" : 2,
"userID" : 14957534,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 7784,
"osVersion" : {
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"build" : "23G93",
"releaseType" : "User"
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"captureTime" : "2024-09-01 15:41:47.1369 +0200",
"codeSigningMonitor" : 1,
"incident" : "7A2D8D7B-DEDD-4A49-A14F-75A8FA856ACA",
"pid" : 29214,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-27 17:56:17.1931 +0200",
"procStartAbsTime" : 4328485691017,
"procExitAbsTime" : 6208789065083,
"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":"937A1F87-3F5F-5CF1-B028-24189B743BE7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BAEDB363-C37C-C78A-C18F-90C2D3C5CDD9",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "6F8E90E9-DA95-4D94-BAC9-EDB864A904A7",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4301422231\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100628000-10062c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29214},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4301422231\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100628000-10062c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
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 /Users/yufy/Downloads/eLORE_AF-O64782-F1-model_v2.pdb
eLORE_AF-O64782-F1-model_v2.pdb title:
AF-O64782-F1-model_v2_cut [more info...]
Chain information for eLORE_AF-O64782-F1-model_v2.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> open /Users/yufy/Downloads/eLORE_SD1-29_Model_1_SRK8.pdb
eLORE_SD1-29_Model_1_SRK8.pdb title:
At1g61380_SD1-29.B99990001_SRK8 [more info...]
Chain information for eLORE_SD1-29_Model_1_SRK8.pdb #2
---
Chain | Description
A | No description available
> open /Users/yufy/Downloads/eLORE_SD1-29_Model_SRK9.pdb
eLORE_SD1-29_Model_SRK9.pdb title:
At1g61380_SD1-29.B99990001_SRK9 [more info...]
Chain information for eLORE_SD1-29_Model_SRK9.pdb #3
---
Chain | Description
A | No description available
> hide #2 models
> hide #3 models
> mlp #1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A #2/A #3/A
Alignment identifier is 1
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
1 [ID: 1] region 3 chains [116-259] RMSD: 2.808
> show #2 models
> hide #!1 models
> mlp sel & #2
Map values for surface "eLORE_SD1-29_Model_1_SRK8.pdb_A SES surface": minimum
-27.19, mean -4.328, maximum 24.21
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!2 models
> show #3 models
> mlp sel & #3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.34, mean -4.476, maximum 26.37
To also show corresponding color key, enter the above mlp command and add key
true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!3 models
> show #!1 models
> mlp sel & #!1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> select add #1
5347 atoms, 5497 bonds, 684 residues, 6 models selected
> select add #2
7283 atoms, 7484 bonds, 936 residues, 6 models selected
> select subtract #1
4210 atoms, 4331 bonds, 540 residues, 5 models selected
> select subtract #2
1137 atoms, 1172 bonds, 144 residues, 3 models selected
> select add #3
3073 atoms, 3159 bonds, 396 residues, 2 models selected
> select subtract #3
1 model selected
> mlp #!1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #!1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #!1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!1 surfaces
> show #!1 surfaces
> color #!1 bychain
> mlp #!1
Map values for surface "eLORE_AF-O64782-F1-model_v2.pdb_A SES surface":
minimum -27.94, mean -5.194, maximum 25.3
To also show corresponding color key, enter the above mlp command and add key
true
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-282 #2/A:137-282 #3/A:137-282
3453 atoms, 3558 bonds, 438 residues, 3 models selected
1 [ID: 1] region 3 chains [116-261] RMSD: 2.791
> hide #!1 models
> show #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide sel surfaces
> select add #1
5375 atoms, 5525 bonds, 688 residues, 6 models selected
> select add #2
7297 atoms, 7498 bonds, 938 residues, 6 models selected
> select add #3
9219 atoms, 9471 bonds, 1188 residues, 6 models selected
> select subtract #3
6146 atoms, 6312 bonds, 792 residues, 5 models selected
> select subtract #2
3073 atoms, 3153 bonds, 396 residues, 3 models selected
> select subtract #1
1 model selected
> hide surfaces
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with
eLORE_SD1-29_Model_1_SRK8.pdb, chain A (#2), sequence alignment score = 1889
RMSD between 203 pruned atom pairs is 1.228 angstroms; (across all 396 pairs:
3.289)
Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with
eLORE_SD1-29_Model_SRK9.pdb, chain A (#3), sequence alignment score = 1911.5
RMSD between 225 pruned atom pairs is 1.176 angstroms; (across all 396 pairs:
3.154)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with
eLORE_SD1-29_Model_1_SRK8.pdb, chain A (#2), sequence alignment score = 1889
RMSD between 203 pruned atom pairs is 1.228 angstroms; (across all 396 pairs:
3.289)
Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with
eLORE_SD1-29_Model_SRK9.pdb, chain A (#3), sequence alignment score = 1911.5
RMSD between 225 pruned atom pairs is 1.176 angstroms; (across all 396 pairs:
3.154)
> hide #!1 models
> hide #!2 models
> show #!3 surfaces
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
1 [ID: 1] region 3 chains [116-259] RMSD: 2.813
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:212-213 #2/A:212-213 #3/A:212-213
51 atoms, 51 bonds, 6 residues, 3 models selected
1 [ID: 1] region 3 chains [191-192] RMSD: 3.033
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [191] RMSD: 1.970
> select #1/A:226 #2/A:226 #3/A:226
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:226 #2/A:226 #3/A:226
33 atoms, 33 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [205] RMSD: 1.419
> select #1/A:212-213 #2/A:212-213 #3/A:212-213
51 atoms, 51 bonds, 6 residues, 3 models selected
> select #1/A:212-213 #2/A:212-213 #3/A:212-213
51 atoms, 51 bonds, 6 residues, 3 models selected
1 [ID: 1] region 3 chains [191-192] RMSD: 3.033
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [191] RMSD: 1.970
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:212-213 #2/A:212-213 #3/A:212-213
51 atoms, 51 bonds, 6 residues, 3 models selected
1 [ID: 1] region 3 chains [191-192] RMSD: 3.033
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:202 #2/A:202 #3/A:202
42 atoms, 45 bonds, 3 residues, 3 models selected
> select #1/A:202-295 #2/A:202-295 #3/A:202-295
2208 atoms, 2279 bonds, 282 residues, 3 models selected
1 [ID: 1] region 3 chains [181-274] RMSD: 3.123
> ui mousemode right select
> select clear
> select #1/A:202-295 #2/A:202-295 #3/A:202-295
2208 atoms, 2279 bonds, 282 residues, 3 models selected
> select #1/A:296 #2/A:296 #3/A:296
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:295-296 #2/A:295-296 #3/A:295-296
51 atoms, 48 bonds, 6 residues, 3 models selected
1 [ID: 1] region 3 chains [274-275] RMSD: 1.852
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #1/A:296 #2/A:296 #3/A:296
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:295-296 #2/A:295-296 #3/A:295-296
51 atoms, 48 bonds, 6 residues, 3 models selected
1 [ID: 1] region 3 chains [274-275] RMSD: 1.852
> select clear
> select #1/A:295-296 #2/A:295-296 #3/A:295-296
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [274] RMSD: 2.169
> show sel & #!3 atoms
> hide sel & #!3 surfaces
> show sel & #!3 surfaces
> select clear
> hide #!3 surfaces
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A #2/A #3/A
Alignment identifier is 2
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:273 #2/A:273 #3/A:273
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:273 #2/A:273 #3/A:273
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:273 #2/A:273 #3/A:273
30 atoms, 30 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [252] RMSD: 2.171
> show sel & #!3 atoms
> select clear
> show #!3 surfaces
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [274] RMSD: 2.169
> hide sel & #!3 surfaces
> select clear
> hide #!3 surfaces
> show #!2 models
> show #!1 models
> show surfaces
> hide surfaces
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> select clear
> ui mousemode right translate
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!1 surfaces
> show #!3 models
> hide #!1 models
> show #!3 surfaces
> hide #!3 surfaces
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!3 surfaces
> coulombic #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> mlp #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> select add #3
3073 atoms, 3159 bonds, 396 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> show sel surfaces
> hide #!3 models
> show #!3 models
> color sel bychain
> color sel bypolymer
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> ~hbonds
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> select #1/A:87 #2/A:87 #3/A:87
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1/A:87-388 #2/A:87-388 #3/A:87-388
7032 atoms, 7222 bonds, 906 residues, 3 models selected
2 [ID: 2] region 3 chains [66-367] RMSD: 3.044
> coulombic sel & #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> hide sel & #!3 surfaces
> show sel & #!3 surfaces
> color sel & #!3 bychain
> coulombic sel & #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> select #1/A:417 #2/A:417 #3/A:417
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:417 #2/A:417 #3/A:417
18 atoms, 15 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [396] RMSD: 1.307
> color sel & #!3 byhetero
> ui mousemode right select
> select clear
> mlp #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 17874 of 367328
triangles, 6 atoms, 29 residues, 7 bonds
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 4132 of 367328
triangles, 19 residues
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 40125 of 367328
triangles, 7 atoms, 63 residues, 7 bonds
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3810 of 367328
triangles, 13 residues
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 75448 of 367328
triangles, 7 atoms, 128 residues, 7 bonds
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> select clear
> select #3/A:266@CA
1 atom, 1 residue, 1 model selected
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 64837 of 367328
triangles, 7 atoms, 88 residues, 7 bonds
> show sel atoms
> hide sel surfaces
> select clear
> hide #!3 atoms
> show #!3 surfaces
> ui mousemode right translate
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:212 #2/A:212 #3/A:212
33 atoms, 33 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [191] RMSD: 1.970
> hide sel & #!3 surfaces
> show sel & #!3 atoms
> select #1/A:226 #2/A:226 #3/A:226
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:226 #2/A:226 #3/A:226
33 atoms, 33 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [205] RMSD: 1.419
> show sel & #!3 atoms
> hide sel & #!3 surfaces
> select #1/A:241 #2/A:241 #3/A:241
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1/A:241 #2/A:241 #3/A:241
36 atoms, 36 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [220] RMSD: 0.403
> hide sel & #!3 surfaces
> show sel & #!3 atoms
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A #2/A #3/A
9219 atoms, 9471 bonds, 1188 residues, 3 models selected
2 [ID: 2] region 3 chains [1-396] RMSD: 2.850
> hide sel & #!3 surfaces
> show sel & #!3 surfaces
> hide sel & #!3 surfaces
> ui mousemode right select
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:239 #2/A:239 #3/A:239
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:239 #2/A:239 #3/A:239
33 atoms, 33 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [218] RMSD: 1.304
> select #1/A:273 #2/A:273 #3/A:273
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:273 #2/A:273 #3/A:273
30 atoms, 30 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [252] RMSD: 2.171
> show sel & #!3 atoms
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [274] RMSD: 2.169
> show sel & #!3 atoms
> select #1/A:216 #2/A:216 #3/A:216
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:216 #2/A:216 #3/A:216
18 atoms, 15 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [195] RMSD: 4.411
> show sel & #!3 atoms
> select #1/A:221 #2/A:221 #3/A:221
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:221 #2/A:221 #3/A:221
18 atoms, 15 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [200] RMSD: 8.119
> select #1/A:224 #2/A:224 #3/A:224
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:224 #2/A:224 #3/A:224
18 atoms, 15 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [203] RMSD: 6.161
> show sel & #!3 atoms
> select #1/A:202 #2/A:202 #3/A:202
42 atoms, 45 bonds, 3 residues, 3 models selected
> select #1/A:202 #2/A:202 #3/A:202
42 atoms, 45 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [181] RMSD: 1.864
> show sel & #!3 atoms
> select #1/A:270 #2/A:270 #3/A:270
42 atoms, 45 bonds, 3 residues, 3 models selected
> select #1/A:270 #2/A:270 #3/A:270
42 atoms, 45 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [249] RMSD: 2.665
> select #1/A:264 #2/A:264 #3/A:264
42 atoms, 45 bonds, 3 residues, 3 models selected
> select #1/A:264 #2/A:264 #3/A:264
42 atoms, 45 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [243] RMSD: 1.921
> show sel & #!3 atoms
> select #1/A:222 #2/A:222 #3/A:222
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1/A:222 #2/A:222 #3/A:222
36 atoms, 36 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [201] RMSD: 7.915
> show sel & #!3 atoms
> mlp sel & #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel & #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel & #!3 surfaces
> ui mousemode right select
> select #3/A:222@CB
1 atom, 1 residue, 1 model selected
> select #3/A:222
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:273@CA
1 atom, 1 residue, 1 model selected
> select #3/A:273@CA
1 atom, 1 residue, 1 model selected
> select #3/A:273
10 atoms, 10 bonds, 1 residue, 1 model selected
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/A:222
12 atoms, 12 bonds, 1 residue, 1 model selected
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> select #3/A:222@CD1
1 atom, 1 residue, 1 model selected
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 1162 of 367328
triangles, 18 atoms, 19 residues, 20 bonds
> hide sel surfaces
> select clear
Drag select of 1 residues
> select clear
> open /Users/yufy/switchdrive/Fan-
> Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json
Failed opening file /Users/yufy/switchdrive/Fan-
Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json:
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/yufy/switchdrive/Fan-
Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json
format pae structure #1
> open /Users/yufy/switchdrive/Fan-
> Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_model_0.cif
Chain information for fold_2024_08_23_lomi_dimer_model_0.cif #4
---
Chain | Description
A | .
B | .
> hide #!3 models
Drag select of 108 residues
Drag select of 57 residues
> ui mousemode right translate
> ui mousemode right select
> select clear
> hide #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/yufy/switchdrive/Fan-
> Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lore_dimer/fold_2024_08_25_lore_dimer_model_0.cif
Chain information for fold_2024_08_25_lore_dimer_model_0.cif #5
---
Chain | Description
A B | .
Drag select of 37 residues
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> hide #5 models
> show #5 models
> open /Users/yufy/switchdrive/Fan-
> Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/AthLOREdimer_67ef4/AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#6
---
Chain | Description
A B | No description available
> hide #5 models
> set bgColor black
> set bgColor transparent
> mlp #6
Map values for surface
"AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A
SES surface": minimum -28.76, mean -4.06, maximum 25.4
Map values for surface
"AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface": minimum -30.26, mean -4.011, maximum 26.74
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!6 surfaces
> hide #!6 models
> show #!3 models
> coulombic #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> coulombic #!3 reassignCharges true
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> ui mousemode right select
> select clear
Drag select of 68 atoms, 136 residues, 68 bonds
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:359 #2/A:359 #3/A:359
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:359-360 #2/A:359-360 #3/A:359-360
54 atoms, 54 bonds, 6 residues, 3 models selected
2 [ID: 2] region 3 chains [338-339] RMSD: 3.580
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #3/A:244@CD1
1 atom, 1 residue, 1 model selected
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 120408 of 367328
triangles, 69 atoms, 158 residues, 69 bonds
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> set bgColor white
> set bgColor #ffffff00
> color #3 black
> color #3 Coral
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3 coral
> select #1/A:224 #2/A:224 #3/A:224
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:224 #2/A:224 #3/A:224
18 atoms, 15 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [203] RMSD: 6.161
> color #3:222 red
> color #3:222 blue
> color #3:224 blue
> color #3:216 blue
> select clear
> color #3:212 blue
> color #3:241 hot pink
> color #3:239 hot pink
> select #1/A:239 #2/A:239 #3/A:239
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1/A:239 #2/A:239 #3/A:239
33 atoms, 33 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [218] RMSD: 1.304
> show sel & #!3 atoms
> color #3:226 hot pink
> show sel & #!3 atoms
> select clear
> color #3:184 turquoise
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [163] RMSD: 2.154
> show sel & #!3 atoms
> color #3:237 turquoise
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [216] RMSD: 1.000
> show sel & #!3 atoms
> select #1/A:241 #2/A:241 #3/A:241
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1/A:241 #2/A:241 #3/A:241
36 atoms, 36 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [220] RMSD: 0.403
> save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/AthLORE-
> BindingPocket.cxs
> select clear
> select #3/A:273
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:202@CA
1 atom, 1 residue, 1 model selected
> select clear
> open /Users/yufy/switchdrive/Fan-
> Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/AthLOREdimer_67ef4/AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#7
---
Chain | Description
A B | No description available
> hide #!3 models
> hide #7 models
> show #7 models
Drag select of 56 residues
Drag select of 103 residues
> ui mousemode right translate
> ui mousemode right select
> select clear
Drag select of 39 residues
> select clear
> ui mousemode right translate
> hide #7 models
> show #!3 models
> hide #!3 models
> show #7 models
> hide #7 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> show #6.1 models
> hide #6.2 models
> show #6.2 models
Cell requested for row 6 is out of bounds for table with 9 rows! Resizing
table model.
> hide #!6 models
> show #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #3.1 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> coulombic #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom
that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA
417 C)
> hide #!3 models
> hide #3.1 models
> show #!1 models
> coulombic #!1
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of eLORE_AF-O64782-F1-model_v2.pdb #/A ALA 417 HXT bonded to
atom that should not have hydrogens (copy of eLORE_AF-O64782-F1-model_v2.pdb
#/A ALA 417 C)
> hide #!1 models
> show #!3 models
> color #3:239 coral
> color #3:226 coral
> color #3:241 #8B008B
> color #3:241 #FF00FF
> save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/AthLORE-
> BindingPocket.cxs
> save /Users/yufy/Desktop/image1.png supersample 3
> save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/LORE-
> BindingPocket.ppm width 1257 height 850 supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A #2/A #3/A
Alignment identifier is 2
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:203 #2/A:203 #3/A:203
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:203-204 #2/A:203-204 #3/A:203-204
51 atoms, 48 bonds, 6 residues, 3 models selected
2 [ID: 2] region 3 chains [182-183] RMSD: 2.237
> select #1/A:225 #2/A:225 #3/A:225
21 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:203-225 #2/A:203-225 #3/A:203-225
516 atoms, 531 bonds, 69 residues, 3 models selected
2 [ID: 2] region 3 chains [182-204] RMSD: 4.786
> save /Users/yufy/Desktop/image2.png supersample 3
> color (#!3 & sel) cornflower blue
> undo
> ui mousemode right select
> select clear
> mlp #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!3 surfaces
> ui mousemode right select
Drag select of 80 atoms, 133 residues, 79 bonds
> select #3/A:247
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 81 atoms, 141 residues, 81 bonds
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-276 #2/A:137-276 #3/A:137-276
3318 atoms, 3417 bonds, 420 residues, 3 models selected
2 [ID: 2] region 3 chains [116-255] RMSD: 2.846
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
Drag select of 2 residues
> select #1/A:137-138 #2/A:137-138 #3/A:137-138
66 atoms, 69 bonds, 6 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
> mlp sel & #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.58, mean -4.477, maximum 26.66
To also show corresponding color key, enter the above mlp command and add key
true
> surface style #3 solid
> surface style #3 mesh
> surface style #3 dot
> surface style #3 solid
> transparency (#!3 & sel) 50
> select clear
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
> open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.asnt
Unrecognized file suffix '.asnt'
> open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.json
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command, for example
open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.json format pae
structure #1
> open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.sdf
PubChem entry 26612
> hide #!3 models
Drag select of 9 atoms, 7 bonds
Drag select of 8 atoms, 9 bonds
> ui mousemode right translate
> ui mousemode right select
> select clear
> show #!3 models
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 4502 of 367328
triangles, 9 atoms, 28 residues, 6 bonds
> select clear
> select #1/A:137 #2/A:137 #3/A:137
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
> color (#!3 & sel) light gray
> undo
> color (#!3 & sel) light gray
> select clear
Drag select of 28 atoms, 29 bonds
> select clear
Drag select of 33 atoms, 32 bonds
> ui mousemode right translate
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,24.008,0,1,0,-5.6817,0,0,1,25.149
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.68499,-0.57923,0.44192,24.18,0.58568,0.79856,0.13885,-6.1185,-0.43332,0.16372,0.88625,25.474
> view matrix models
> #8,0.83894,-0.32902,0.4335,24.088,0.29244,0.94432,0.15079,-5.8988,-0.45897,0.00026563,0.88845,25.48
> view matrix models
> #8,0.87287,-0.19526,0.44718,24.073,-0.078378,0.84844,0.52345,-5.6507,-0.48162,-0.49196,0.72528,25.466
> ui mousemode right select
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328
triangles, 103 atoms, 396 residues, 100 bonds
> select clear
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A #2/A #3/A
9219 atoms, 9471 bonds, 1188 residues, 3 models selected
2 [ID: 2] region 3 chains [1-396] RMSD: 2.850
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 12 of 367328
triangles
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A #2/A #3/A
9219 atoms, 9471 bonds, 1188 residues, 3 models selected
2 [ID: 2] region 3 chains [1-396] RMSD: 2.850
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98822,0.14155,-0.058171,-0.91946,-0.14052,0.98984,0.021525,4.5149,0.060628,-0.013097,0.99807,-1.8909,#2,0.99173,0.11249,-0.061722,-0.60774,-0.11208,0.99365,0.010095,3.9696,0.062465,-0.0030941,0.99804,-2.1042,#3,0.99047,0.12806,-0.050768,-0.99518,-0.12764,0.99175,0.011501,4.4523,0.051822,-0.0049116,0.99864,-1.962
> view matrix models
> #1,0.99126,0.066335,-0.11403,2.0168,-0.075762,0.99388,-0.080417,4.9314,0.108,0.088354,0.99022,-5.3208,#2,0.99249,0.03656,-0.11669,2.3803,-0.047457,0.99463,-0.092011,4.4329,0.1127,0.096858,0.9889,-5.5645,#3,0.993,0.052312,-0.10593,1.95,-0.061956,0.99402,-0.089901,4.8709,0.10059,0.095835,0.9903,-5.4019
> color (#!3 & sel) gray
> view matrix models
> #1,0.99272,0.034361,-0.11547,2.6336,-0.049897,0.98966,-0.13448,5.5742,0.10965,0.13926,0.98417,-6.2651,#2,0.99303,0.0045432,-0.11775,3.0138,-0.021846,0.98903,-0.14607,5.1005,0.1158,0.14762,0.98224,-6.5319,#3,0.99404,0.02031,-0.10707,2.5692,-0.035684,0.98898,-0.14369,5.5158,0.10297,0.14666,0.98381,-6.3496
> transparency (#!3 & sel) 40
> ui mousemode right select
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 239 of 367328
triangles, 33 atoms, 32 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #3.1,1,8.5001e-17,2.3592e-16,-6.62,-1.3357e-16,1,-3.3307e-16,4.2002,-6.9389e-17,-1.6852e-34,1,-2.2772,#8,0.87287,-0.19526,0.44718,17.821,-0.078378,0.84844,0.52345,-0.9334,-0.48162,-0.49196,0.72528,23.16
> view matrix models
> #3.1,1,8.5001e-17,2.3592e-16,0.055566,-1.3357e-16,1,-3.3307e-16,-3.4356,-6.9389e-17,-1.6852e-34,1,-2.5932,#8,0.87287,-0.19526,0.44718,24.336,-0.078378,0.84844,0.52345,-8.6778,-0.48162,-0.49196,0.72528,22.417
> undo
> ui mousemode right select
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
Drag select of 33 atoms, 32 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87287,-0.19526,0.44718,17.873,-0.078378,0.84844,0.52345,12.976,-0.48162,-0.49196,0.72528,38.696
> ui mousemode right select
> select clear
> undo
> select #1/A:154 #2/A:154 #3/A:154
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:154-280 #2/A:154-280 #3/A:154-280
2997 atoms, 3087 bonds, 381 residues, 3 models selected
2 [ID: 2] region 3 chains [133-259] RMSD: 2.972
> select #1/A:149-150 #2/A:149-150 #3/A:149-150
45 atoms, 45 bonds, 6 residues, 3 models selected
> select #1/A:149-280 #2/A:149-280 #3/A:149-280
3105 atoms, 3198 bonds, 396 residues, 3 models selected
2 [ID: 2] region 3 chains [128-259] RMSD: 2.920
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 629 of 367328
triangles, 5 residues
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 130056 of 367328
triangles, 85 atoms, 166 residues, 83 bonds
> select #1/A:149 #2/A:149 #3/A:149
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:149-280 #2/A:149-280 #3/A:149-280
3105 atoms, 3198 bonds, 396 residues, 3 models selected
2 [ID: 2] region 3 chains [128-259] RMSD: 2.920
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #8 target m
> show #8 models
> select clear
Drag select of 33 atoms, 32 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87287,-0.19526,0.44718,13.507,-0.078378,0.84844,0.52345,-18.133,-0.48162,-0.49196,0.72528,-6.9555
> hide #8 models
> select subtract #8
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right select
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328
triangles, 90 atoms, 394 residues, 88 bonds
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328
triangles, 90 atoms, 396 residues, 88 bonds
> color #3 coral
> select #1/A:137-138 #2/A:137-138 #3/A:137-138
66 atoms, 69 bonds, 6 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
> mlp sel & #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.83, mean -4.481, maximum 26.5
To also show corresponding color key, enter the above mlp command and add key
true
> color (#!3 & sel) light sea green
> color (#!3 & sel) orange
> color (#!3 & sel) dark gray
> color (#!3 & sel) dim gray
> transparency (#!3 & sel) 50
> hide sel & #!3 cartoons
> hide sel & #!3 atoms
> hide sel & #!3 cartoons
> show sel & #!3 cartoons
> cartoon style (#!3 & sel) modeHelix tube sides 20
> undo
> show sel & #!3 atoms
> hide sel & #!3 atoms
> hide sel & #!3 cartoons
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> style sel & #!3 ball
Changed 1137 atom styles
> style sel & #!3 stick
Changed 1137 atom styles
> color (#!3 & sel) light gray
> color (#!3 & sel) gray
> ui tool show "Side View"
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> undo
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting simple
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> cofr sel
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Render/Select by Attribute"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> transparency (#!3 & sel) 50
> transparency (#!3 & sel) 80
> select #3/A:222@CE1
1 atom, 1 residue, 1 model selected
> select #3/A:222@N
1 atom, 1 residue, 1 model selected
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 14426 of 367328
triangles
> select #3/A:222@CE1
1 atom, 1 residue, 1 model selected
> select #3/A:221@CB
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select #3/A:222@CB
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select #3/A:222@CD2
1 atom, 1 residue, 1 model selected
> select #3/A:220@O
1 atom, 1 residue, 1 model selected
> show sel cartoons
> select #1/A:241 #2/A:241 #3/A:241
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1/A:187-241 #2/A:187-241 #3/A:187-241
1257 atoms, 1296 bonds, 165 residues, 3 models selected
2 [ID: 2] region 3 chains [166-220] RMSD: 3.646
> show sel & #!3 cartoons
> select clear
> select #1/A:242 #2/A:242 #3/A:242
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:242-280 #2/A:242-280 #3/A:242-280
963 atoms, 990 bonds, 117 residues, 3 models selected
2 [ID: 2] region 3 chains [221-259] RMSD: 2.524
> show sel & #!3 cartoons
> select clear
> transparency #3 60
> graphics silhouettes false
> graphics silhouettes true
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:184-185 #2/A:184-185 #3/A:184-185
45 atoms, 42 bonds, 6 residues, 3 models selected
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [163] RMSD: 2.154
> show sel & #!3 cartoons
> show sel & #!3 atoms
> hide sel & #!3 atoms
> select clear
> select #1/A:137-138 #2/A:137-138 #3/A:137-138
66 atoms, 69 bonds, 6 residues, 3 models selected
> select #1/A:137-280 #2/A:137-280 #3/A:137-280
3411 atoms, 3516 bonds, 432 residues, 3 models selected
2 [ID: 2] region 3 chains [116-259] RMSD: 2.813
> show sel & #!3 cartoons
> select clear
> mlp #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.83, mean -4.481, maximum 26.5
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A:22-135 #2/A:22-135 #3/A:22-135
2607 atoms, 2664 bonds, 342 residues, 3 models selected
2 [ID: 2] region 3 chains [1-114] RMSD: 2.913
> hide #8 target m
> hide sel & #!3 atoms
> hide sel & #!3 cartoons
> hide sel & #!3 surfaces
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:136 #2/A:136 #3/A:136
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1/A:136-137 #2/A:136-137 #3/A:136-137
51 atoms, 48 bonds, 6 residues, 3 models selected
2 [ID: 2] region 3 chains [115-116] RMSD: 2.468
> select #1/A:136 #2/A:136 #3/A:136
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1/A:136 #2/A:136 #3/A:136
27 atoms, 24 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [115] RMSD: 2.625
> hide sel & #!3 cartoons
> hide sel & #!3 surfaces
> select #3/A:138@CH2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A:22-138 #2/A:22-138 #3/A:22-138
2700 atoms, 2763 bonds, 351 residues, 3 models selected
2 [ID: 2] region 3 chains [1-117] RMSD: 2.897
> select #3/A:257@OE1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:281 #2/A:281 #3/A:281
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:281-417 #2/A:281-417 #3/A:281-417
3174 atoms, 3258 bonds, 411 residues, 3 models selected
2 [ID: 2] region 3 chains [260-396] RMSD: 2.835
> hide sel & #!3 cartoons
> hide sel & #!3 surfaces
> hide sel & #!3 atoms
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 1109 of 367328
triangles, 3 residues
> select clear
> select #3/A:266@OD2
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 105 of 367328
triangles
> ui mousemode right translate
> ui mousemode right select
> select #3/A:262@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> show sel cartoons
> show sel atoms
> hide sel surfaces
> show sel surfaces
> select clear
> hide #!3 atoms
> select clear
> ui mousemode right translate
> ui mousemode right clip
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [216] RMSD: 1.000
> ui mousemode right "move planes"
> ui mousemode right select
> select clear
> ui mousemode right "contour level"
> ui mousemode right "rotate slab"
> ui mousemode right "crop volume"
> ui mousemode right translate
> mlp #!3
Map values for surface "eLORE_SD1-29_Model_SRK9.pdb_A SES surface": minimum
-27.83, mean -4.481, maximum 26.5
To also show corresponding color key, enter the above mlp command and add key
true
> transparency #3 60
> select #1/A:22-23 #2/A:22-23 #3/A:22-23
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #1/A:22-136 #2/A:22-136 #3/A:22-136
2634 atoms, 2691 bonds, 345 residues, 3 models selected
2 [ID: 2] region 3 chains [1-115] RMSD: 2.911
> hide sel & #!3 surfaces
> ui mousemode right select
> select #3/A:138@CH2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #3/A:137@CD2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #1/A:281 #2/A:281 #3/A:281
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:281-417 #2/A:281-417 #3/A:281-417
3174 atoms, 3258 bonds, 411 residues, 3 models selected
2 [ID: 2] region 3 chains [260-396] RMSD: 2.835
> hide sel & #!3 surfaces
> select #1/A:295 #2/A:295 #3/A:295
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:280-295 #2/A:280-295 #3/A:280-295
363 atoms, 374 bonds, 48 residues, 3 models selected
2 [ID: 2] region 3 chains [259-274] RMSD: 1.281
> show sel & #!3 surfaces
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2032 of 367328
triangles
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3847 of 367328
triangles
> select #3/A:290@OH
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #3/A:290@CE2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #3/A:290@CZ
1 atom, 1 residue, 1 model selected
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3301 of 367328
triangles
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2354 of 367328
triangles
Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2265 of 367328
triangles
> select #3/A:290@CA
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #1/A:292 #2/A:292 #3/A:292
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:292-296 #2/A:292-296 #3/A:292-296
114 atoms, 111 bonds, 15 residues, 3 models selected
2 [ID: 2] region 3 chains [271-275] RMSD: 1.279
> hide sel & #!3 surfaces
> select clear
> select #3/A:290@CE1
1 atom, 1 residue, 1 model selected
> select clear
> select #3/A:290@CD2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #3/A:290@CE1
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #3/A:290@CZ
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> hide #!3 surfaces
> show #!3 surfaces
> select #1/A:23 #2/A:23 #3/A:23
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:23-136 #2/A:23-136 #3/A:23-136
2619 atoms, 2676 bonds, 342 residues, 3 models selected
2 [ID: 2] region 3 chains [2-115] RMSD: 2.882
> hide sel & #!3 surfaces
> select #1/A:22 #2/A:22 #3/A:22
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1/A:22-136 #2/A:22-136 #3/A:22-136
2634 atoms, 2691 bonds, 345 residues, 3 models selected
2 [ID: 2] region 3 chains [1-115] RMSD: 2.911
> hide sel & #!3 surfaces
> select #1/A:281-282 #2/A:281-282 #3/A:281-282
42 atoms, 39 bonds, 6 residues, 3 models selected
> select #1/A:281-417 #2/A:281-417 #3/A:281-417
3174 atoms, 3258 bonds, 411 residues, 3 models selected
2 [ID: 2] region 3 chains [260-396] RMSD: 2.835
> hide sel & #!3 surfaces
> select #3/A:138@CH2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:180-184 #2/A:180-184 #3/A:180-184
126 atoms, 126 bonds, 15 residues, 3 models selected
2 [ID: 2] region 3 chains [159-163] RMSD: 1.720
> hide sel & #!3 cartoons
> show sel & #!3 cartoons
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:184-185 #2/A:184-185 #3/A:184-185
45 atoms, 42 bonds, 6 residues, 3 models selected
> select #1/A:184-185 #2/A:184-185 #3/A:184-185
45 atoms, 42 bonds, 6 residues, 3 models selected
2 [ID: 2] region 3 chains [163-164] RMSD: 2.295
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [163] RMSD: 2.154
> show sel & #!3 atoms
> select
> #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
> #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416
3762 atoms, 3794 bonds, 453 residues, 3 models selected
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1/A:237 #2/A:237 #3/A:237
12 atoms, 9 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [216] RMSD: 1.000
> show sel & #!3 atoms
> select clear
> transparency #3 30
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:184 #2/A:184 #3/A:184
24 atoms, 21 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [163] RMSD: 2.154
> hide sel & #!3 atoms
> select clear
> transparency #3 20
> transparency #3 10
> transparency #3 20
> save /Users/yufy/Desktop/image3.png supersample 3
> show #8 models
> ui mousemode right "translate selected models"
> ui mousemode right select
Drag select of 33 atoms, 32 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.87287,-0.19526,0.44718,13.046,-0.078378,0.84844,0.52345,9.5173,-0.48162,-0.49196,0.72528,40.263
> view matrix models
> #8,0.87287,-0.19526,0.44718,11.832,-0.078378,0.84844,0.52345,11.633,-0.48162,-0.49196,0.72528,41.559
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.8058,-0.52171,0.2802,11.862,0.33667,0.79283,0.50801,11.333,-0.48718,-0.31502,0.81451,41.573
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.8058,-0.52171,0.2802,11.767,0.33667,0.79283,0.50801,11.307,-0.48718,-0.31502,0.81451,41.341
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.75896,-0.62551,0.18087,11.796,0.49983,0.7377,0.45383,11.188,-0.4173,-0.25404,0.87254,41.294
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.75896,-0.62551,0.18087,12.424,0.49983,0.7377,0.45383,9.7686,-0.4173,-0.25404,0.87254,40.057
> view matrix models
> #8,0.75896,-0.62551,0.18087,12.25,0.49983,0.7377,0.45383,10.076,-0.4173,-0.25404,0.87254,40.251
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.58296,-0.79671,-0.15941,12.373,0.80507,0.53991,0.24569,9.8491,-0.10968,-0.27156,0.95615,40.028
> view matrix models
> #8,0.74877,-0.43468,0.50039,12.262,0.46519,0.8824,0.07044,10.121,-0.47217,0.18003,0.86293,40.321
> hide #8 models
> select subtract #8
Nothing selected
> ui mousemode right translate
> save /Users/yufy/Desktop/image4.png supersample 3
> volume planes z style image imageMode "full region"
No volumes specified
===== 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 - 88.1
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: Z11C0002BSM/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 13 days, 6 hours, 6 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2422HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 14 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt bug, crashing in _NSViewHierarchyDidChangeBackingProperties, on connecting or disconnecting external display or waking from sleep.