![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16898 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-15.3-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 0x00000001ec4bc840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, torch._C, torch._C._dynamo.autograd_compiler, torch._C._dynamo.eval_frame, torch._C._dynamo.guards, torch._C._dynamo.utils, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree (total: 71)
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{
"uptime" : 230000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 2678,
"osVersion" : {
"train" : "macOS 15.3",
"build" : "24D60",
"releaseType" : "User"
},
"captureTime" : "2025-02-18 17:15:00.2291 -0500",
"codeSigningMonitor" : 1,
"incident" : "1BD4852E-9542-4F54-ACB1-06665CDFCEDA",
"pid" : 15886,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-18 15:51:38.4576 -0500",
"procStartAbsTime" : 5532419686678,
"procExitAbsTime" : 5603475979516,
"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":"84D25F55-7B2C-552D-9D35-07B1F74F5F8D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2E93C3E2-1DC4-1036-43B4-8E316F1B9D98",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "AD3A9485-C358-4F91-8249-DE9AC5ECD64A",
"sleepWakeUUID" : "25396CB0-8F7B-4D60-B5C5-414F810D1311",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x00005deb28c227e8","rawCodes":[1,103264582510568],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005deb28c227e8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":15886},
"vmregioninfo" : "0x5deb28c227e8 is not in any region. Bytes after previous region: 102783546173417 Bytes before following region: 2288533755928\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Log from Fri Feb 14 16:04:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.236, step 1, values float32
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.25, step 1, values float32
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.25, step 1, values float32
Log from Fri Feb 14 14:36:16 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
> open /Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
> main/calc_level.py
/Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
main/calc_level.py:96: FutureWarning: You are using `torch.load` with
`weights_only=False` (the current default value), which uses the default
pickle module implicitly. It is possible to construct malicious pickle data
which will execute arbitrary code during unpickling (See
https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for
more details). In a future release, the default value for `weights_only` will
be flipped to `True`. This limits the functions that could be executed during
unpickling. Arbitrary objects will no longer be allowed to be loaded via this
mode unless they are explicitly allowlisted by the user via
`torch.serialization.add_safe_globals`. We recommend you start setting
`weights_only=True` for any use case where you don't have full control of the
loaded file. Please open an issue on GitHub for any issues related to this
experimental feature.
checkpoint = torch.load(os.path.join(dir, 'weights_5e6.pth'), map_location =
device)
executed calc_level.py
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/gabriellalopezperez/Downloads/masks_J861/YjgA_2_align420.pdb
Chain information for YjgA_2_align420.pdb #1
---
Chain | Description
8 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/tRNA_align420.pdb
Chain information for tRNA_align420.pdb #2
---
Chain | Description
7 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RsfS_align420.pdb
Chain information for RsfS_align420.pdb #3
---
Chain | Description
6 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RluD_align420.pdb
Chain information for RluD_align420.pdb #4
---
Chain | Description
7 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/ObgE_align420.pdb
Chain information for ObgE_align420.pdb #5
---
Chain | Description
9 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/YjgA_align420.pdb
YjgA_align420.pdb title:
Structural genomics, the crystal structure of A conserved putative protein
from pseudomonas syringae PV. Tomato STR. DC3000 [more info...]
Chain information for YjgA_align420.pdb #6
---
Chain | Description | UniProt
A | UPF0307 protein pspto_4464 | Y4464_PSESM 1-173
Non-standard residues in YjgA_align420.pdb #6
---
FMT — formic acid
PEG — di(hydroxyethyl)ether
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA5S_align420.pdb
Chain information for RNA5S_align420.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA4_align420.pdb
Chain information for RNA4_align420.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA3_align420.pdb
Chain information for RNA3_align420.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA2_align420.pdb
Chain information for RNA2_align420.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA1_align420.pdb
Chain information for RNA1_align420.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/prots2_align420.pdb
Chain information for prots2_align420.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/prots1_align420.pdb
Chain information for prots1_align420.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J261_004_volume_map.mrc
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.216, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J263_004_volume_map.mrc
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.219, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J271_005_volume_map.mrc
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.208, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J273_006_volume_map.mrc
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.201, step 2, values float32
> surface dust #14 size 10.6
> surface dust #15 size 10.6
> surface dust #16 size 10.6
> surface dust #17 size 10.6
> set bgColor white
> lighting soft
> select #1-13
100386 atoms, 108540 bonds, 68 pseudobonds, 7564 residues, 22 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #14
Fit molecules YjgA_2_align420.pdb (#1), tRNA_align420.pdb (#2),
RsfS_align420.pdb (#3), RluD_align420.pdb (#4), ObgE_align420.pdb (#5),
YjgA_align420.pdb (#6), RNA5S_align420.pdb (#7), RNA4_align420.pdb (#8),
RNA3_align420.pdb (#9), RNA2_align420.pdb (#10), RNA1_align420.pdb (#11),
prots2_align420.pdb (#12), prots1_align420.pdb (#13) to map
cryosparc_P250_J261_004_volume_map.mrc (#14) using 100386 atoms
average map value = 0.4524, steps = 100
shifted from previous position = 0.778
rotated from previous position = 6.34 degrees
atoms outside contour = 22181, contour level = 0.21626
Position of YjgA_2_align420.pdb (#1) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of tRNA_align420.pdb (#2) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RsfS_align420.pdb (#3) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RluD_align420.pdb (#4) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of ObgE_align420.pdb (#5) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of YjgA_align420.pdb (#6) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA5S_align420.pdb (#7) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA4_align420.pdb (#8) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA3_align420.pdb (#9) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA2_align420.pdb (#10) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA1_align420.pdb (#11) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of prots2_align420.pdb (#12) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of prots1_align420.pdb (#13) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
> ~select #1-13
Nothing selected
> ~view #1-13
Unknown command: ~view #1-13
> hide #13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #1-13
> hide #!8 models
> hide #!7 models
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #3 models
> hide #2 models
> hide #1 models
> view #1-13
No displayed objects specified.
> view #1-13 models
Expected an integer >= 1 or a keyword
> show #1 models
> hide #1 models
> show #!7 models
> show #1-13 models
> show #1-13
> hide #1-13
> hide #1 models
> hide #2 models
> hide #3 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #13 models
> volume calc_level all
/Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
main/calc_level.py:103: FutureWarning: `torch.cuda.amp.autocast(args...)` is
deprecated. Please use `torch.amp.autocast('cuda', args...)` instead.
with torch.cuda.amp.autocast():
predicted contour level is [0.24087214]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.23630011]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.20290649]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.21415067]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #3 models
> select add #3
780 atoms, 787 bonds, 102 residues, 1 model selected
> fitmap #3 inMap #17
Fit molecule RsfS_align420.pdb (#3) to map
cryosparc_P250_J273_006_volume_map.mrc (#17) using 780 atoms
average map value = 0.1819, steps = 68
shifted from previous position = 1.14
rotated from previous position = 1.45 degrees
atoms outside contour = 462, contour level = 0.21415
Position of RsfS_align420.pdb (#3) relative to
cryosparc_P250_J273_006_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.99873401 0.00017451 -0.05030249 11.67593399
0.00363211 0.99713364 0.07557322 -17.96658316
0.05017149 -0.07566025 0.99587065 7.22475191
Axis -0.83278369 -0.55327101 0.01903968
Axis point 0.00000000 82.39613522 238.26787639
Rotation angle (degrees) 5.20963037
Shift along axis 0.35441914
> fitmap #5 inMap #17
Fit molecule ObgE_align420.pdb (#5) to map
cryosparc_P250_J273_006_volume_map.mrc (#17) using 2611 atoms
average map value = 0.2221, steps = 84
shifted from previous position = 1.26
rotated from previous position = 2.01 degrees
atoms outside contour = 1220, contour level = 0.21415
Position of ObgE_align420.pdb (#5) relative to
cryosparc_P250_J273_006_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.99652737 0.02312754 -0.07998952 15.03793269
-0.01828537 0.99798573 0.06074647 -8.64718245
0.08123332 -0.05907289 0.99494298 -4.36890390
Axis -0.58421011 -0.78608342 -0.20191930
Axis point 67.54885003 0.00000000 176.99038389
Rotation angle (degrees) 5.88592465
Shift along axis -1.10573951
> show #!5 models
> select add #5
3391 atoms, 3444 bonds, 4 pseudobonds, 442 residues, 3 models selected
> hide #!14 models
> hide #!15 models
> hide #!16 models
> color #17 #666666ff models
> color #17 #999999ff models
> color #17 #ccccccff models
> color #17 #999999ff models
> color #16 #999999ff models
> color #15 #999999ff models
> color #14 #999999ff models
> color #14 #ccccccff models
> color #14 #999999ff models
> color #17 #ccccccff models
> color #17 #999999ff models
> volume #17 level 0.23
> select subtract #5
780 atoms, 787 bonds, 102 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> volume #16 level 0.22
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!16 models
> volume #17 level 0.25
> volume #16 level 0.25
> show #8/L
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8/L
1129 atoms, 1260 bonds, 53 residues, 1 model selected
> fitmap sel inMap #16
Fit molecule RNA4_align420.pdb (#8) to map
cryosparc_P250_J271_005_volume_map.mrc (#16) using 1129 atoms
average map value = 0.2581, steps = 108
shifted from previous position = 3.68
rotated from previous position = 10.6 degrees
atoms outside contour = 549, contour level = 0.25
Position of RNA4_align420.pdb (#8) relative to
cryosparc_P250_J271_005_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99394003 0.08301145 0.07205774 -24.59292312
-0.09577383 0.97570474 0.19704727 -12.42669093
-0.05394990 -0.20275442 0.97774233 61.12162945
Axis -0.87729092 0.27650050 -0.39231125
Axis point 0.00000000 280.33959281 89.43527729
Rotation angle (degrees) 13.17120319
Shift along axis -5.83954068
> select add #8
14554 atoms, 16263 bonds, 5 pseudobonds, 678 residues, 2 models selected
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #3#!5,8 cartoons
> hide #3#!5,8 cartoons
> cartoon #8/L
> hide #!8 models
> show #!8 models
> hide #8/L
> cartoon #13/K
> show #13 models
> volume #14 level 0.25
> volume #14 level 0.26
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> color #15 #00ff66ff models
> show #!15 models
> color #16 #3300ffff models
> show #!16 models
> hide #!15 models
> color #16 #3300ffab models
> color #16 #3300ff2c models
> color #16 #3300ff35 models
> color #16 #3300ffff models
> color #16 #6633ffff models
> color #16 #cc99ffff models
> color #14 #99999933 models
> select subtract #13
Nothing selected
> hide #13 models
> color #14 #99999972 models
> color #14 #99999969 models
> ui tool show "Side View"
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> ui tool show "Fit in Map"
> ui tool show "Color Zone"
> color zone #14 near sel distance 6.36
> color zone #14 near sel distance 6.01
> color zone #14 near sel distance 2.19
> color single #14
> color #14 #9999999d models
> color #14 #9999997f models
> color #16 #999999ff models
> color #14 #9966ffff models
> color #14 #9966ff80 models
> color #14 #9966ff76 models
> color #14 #9966ff54 models
> color #14 #9966ff45 models
> color #14 #9966ff35 models
> color #14 #9966ff62 models
> color #14 #999999ff models
> color #14 #9999997d models
> color #16 #ff99ffff models
> color #16 #330033ff models
> color #16 #cc99ccff models
> color #16 #ffccffff models
> color #16 #cc99ccff models
> color #16 #996699ff models
> color #16 #663366ff models
> color #16 #330033ff models
> color #16 #663366ff models
> color #16 #996699ff models
> color #16 #663366ff models
> color #14 #999999a1 models
> color #14 #999999b9 models
> color #14 #999999b5 models
> color #17 #ccccccff models
> color #17 #cc9999ff models
> color #17 #ff3333ff models
> color #17 #660066ff models
> color #17 #9966ccff models
> color #17 #3300ccff models
> show #!17 models
> hide #!16 models
> color #17 #3300ffff models
> color #17 #6633ffff models
> color #17 #330099ff models
> color #17 #cc99ffff models
> color #17 #330099ff models
> color #17 #9966ccff models
> color #17 #330099ff models
> color #17 #000099ff models
> color #17 #0000ccff models
> color #17 #000099ff models
No map chosen to save
> save /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
——— End of log from Fri Feb 14 14:36:16 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> ui mousemode right zoom
> ui mousemode right translate
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #!8 models
> color #14 #99999982 models
> color #14 #999999ff models
> hide #!17 models
> show #!17 models
> hide #!14 models
> show #!14 models
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!14 models
> show #!14 models
> hide #!14 models
> lighting simple
> lighting full
> lighting simple
> set bgColor white
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> show #!14 models
> hide #!14 models
> cartoon #13/K
> show #13 models
> hide #!17 models
> show #!14 models
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> color #14 #999999d8 models
> color #14 #999999c9 models
> color #14 #999999bd models
> color #14 #99999948 models
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> color #14 #999999ff models
> color #14 #99999980 models
> ui tool show "Color Zone"
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> color zone #14 near sel distance 6.36
> color zone #14 near sel distance 6.26
> color zone #14 near sel distance 6.16
> color zone #14 near sel distance 6.06
> color zone #14 near sel distance 5.96
> color zone #14 near sel distance 5.86
> color zone #14 near sel distance 5.76
> color zone #14 near sel distance 5.66
> color zone #14 near sel distance 5.56
> color zone #14 near sel distance 5.46
> color zone #14 near sel distance 5.36
> color zone #14 near sel distance 5.26
> color zone #14 near sel distance 5.16
> color zone #14 near sel distance 5.06
> color zone #14 near sel distance 4.96
> color zone #14 near sel distance 4.86
> color zone #14 near sel distance 4.76
> color zone #14 near sel distance 4.66
> color zone #14 near sel distance 4.56
> color zone #14 near sel distance 4.46
> color zone #14 near sel distance 4.36
> color zone #14 near sel distance 4.26
> color zone #14 near sel distance 4.16
> color zone #14 near sel distance 4.06
> color zone #14 near sel distance 3.96
> color zone #14 near sel distance 3.86
> color zone #14 near sel distance 3.76
> color zone #14 near sel distance 3.66
> color zone #14 near sel distance 3.56
> color zone #14 near sel distance 3.46
> color zone #14 near sel distance 3.36
> color zone #14 near sel distance 3.26
> color zone #14 near sel distance 3.16
> color zone #14 near sel distance 3.06
> color zone #14 near sel distance 2.96
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.76
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #13 models
> hide #!14 models
> show #!16 models
> color #16 #999999ff models
No atoms selected for color zoning
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> color zone #16 near sel distance 6.36
> color zone #16 near sel distance 6.24
> color zone #16 near sel distance 2.68
> hide #!16 models
> show #!14 models
> hide #!14 models
> show #!16 models
> color #16 #99999982 models
> color zone #16 near sel distance 2.68
> hide #!16 models
> show #!14 models
> color zone #14 near sel distance 2.76
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.96
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.76
> color zone #14 near sel distance 2.66
> color zone #14 near sel distance 2.56
> color zone #14 near sel distance 2.66
> color zone #14 near sel distance 2.76
[Repeated 1 time(s)]
> color zone #16 near sel distance 2.78
[Repeated 1 time(s)]
> show #!16 models
> hide #!14 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!14 models
> save /Users/gabriellalopezperez/Desktop/image18.png supersample 3
> show #!16 models
> hide #!14 models
> save /Users/gabriellalopezperez/Desktop/image19.png supersample 3
> volume #16 level 0.26
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!15 models
> show #!14 models
> volume #15 level 0.26
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> volume #17 level 0.26
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> save /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
——— End of log from Fri Feb 14 16:04:09 2025 ———
opened ChimeraX session
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J275_005_volume_map.mrc
Opened cryosparc_P250_J275_005_volume_map.mrc as #18, grid size 440,440,440,
pixel 1.06, shown at level 0.202, step 2, values float32
> hide #!17 models
> show #!15 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> volume calc_level #18
/Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
main/calc_level.py:103: FutureWarning: `torch.cuda.amp.autocast(args...)` is
deprecated. Please use `torch.amp.autocast('cuda', args...)` instead.
with torch.cuda.amp.autocast():
predicted contour level is [0.16981167]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
> surface dust #15 size 10.6
> surface dust #18 size 10.6
> hide #!15 models
> show #!15 models
> hide #!15 models
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J278_006_volume_map.mrc
Opened cryosparc_P250_J278_006_volume_map.mrc as #19, grid size 440,440,440,
pixel 1.06, shown at level 0.217, step 2, values float32
> select add #19
2 models selected
> volume calc_level #19
predicted contour level is [0.18340528]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
> surface dust #19 size 10.6
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.68483,-0.42119,0.59465,24.859,0.52266,0.85254,0.0019351,-88.717,-0.50778,0.30948,0.80398,95.522
> view matrix models
> #19,0.99065,0.086513,0.10551,-42.671,0.11227,-0.95631,-0.26995,478.84,0.077545,0.27927,-0.95708,390.08
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.99065,0.086513,0.10551,-39.544,0.11227,-0.95631,-0.26995,492.87,0.077545,0.27927,-0.95708,373.88
> ui tool show "Side View"
> ui mousemode right translate
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #19 inMap #18
Fit map cryosparc_P250_J278_006_volume_map.mrc in map
cryosparc_P250_J275_005_volume_map.mrc using 1038326 points
correlation = 0.9433, correlation about mean = 0.7006, overlap = 1.085e+05
steps = 112, shift = 4.55, angle = 5.35 degrees
Position of cryosparc_P250_J278_006_volume_map.mrc (#19) relative to
cryosparc_P250_J275_005_volume_map.mrc (#18) coordinates:
Matrix rotation and translation
0.98335312 0.03419589 0.17845807 -41.61312150
0.07906407 -0.96480744 -0.25078974 496.28597923
0.16360170 0.26072449 -0.95145008 352.78197362
Axis 0.99575829 0.02892072 0.08734431
Axis point 0.00000000 225.63135012 210.75805067
Rotation angle (degrees) 165.11696854
Shift along axis 3.72983438
> select add #19
4 models selected
> select subtract #19
Nothing selected
> hide #!18 models
> volume #19 level 0.2
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J281_006_volume_map.mrc
Opened cryosparc_P250_J281_006_volume_map.mrc as #20, grid size 440,440,440,
pixel 1.06, shown at level 0.225, step 2, values float32
> select add #20
2 models selected
> surface dust #20 size 10.6
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.96182,-0.0077182,-0.27357,72.225,-0.20431,0.64483,-0.73651,292.79,0.18209,0.76428,0.61864,-127.27
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.96182,-0.0077182,-0.27357,72.557,-0.20431,0.64483,-0.73651,317.96,0.18209,0.76428,0.61864,-136.06
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.956,0.10975,-0.27206,47.253,-0.28568,0.55913,-0.77831,365.37,0.066702,0.82179,0.56588,-110.39
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.956,0.10975,-0.27206,36.358,-0.28568,0.55913,-0.77831,359.67,0.066702,0.82179,0.56588,-116.03
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.956,0.10975,-0.27206,51.132,-0.28568,0.55913,-0.77831,354.38,0.066702,0.82179,0.56588,-106.07
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.956,0.10975,-0.27206,57.672,-0.28568,0.55913,-0.77831,382.19,0.066702,0.82179,0.56588,-97.118
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.95599,0.10927,-0.27228,57.828,-0.28573,0.55746,-0.77949,382.84,0.066607,0.82298,0.56415,-96.974
> view matrix models
> #20,0.9256,0.26605,-0.26923,29.049,-0.37425,0.53688,-0.75611,402.63,-0.056616,0.80061,0.59651,-70.791
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.9256,0.26605,-0.26923,25.355,-0.37425,0.53688,-0.75611,386.49,-0.056616,0.80061,0.59651,-78.171
> view matrix models
> #20,0.9256,0.26605,-0.26923,21.194,-0.37425,0.53688,-0.75611,376.76,-0.056616,0.80061,0.59651,-93.616
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.9256,0.26605,-0.26923,98.975,-0.37425,0.53688,-0.75611,378.22,-0.056616,0.80061,0.59651,-218.92
> view matrix models
> #20,0.9256,0.26605,-0.26923,119.41,-0.37425,0.53688,-0.75611,455.92,-0.056616,0.80061,0.59651,-253.67
> view matrix models
> #20,0.9256,0.26605,-0.26923,115.09,-0.37425,0.53688,-0.75611,353.83,-0.056616,0.80061,0.59651,-88.534
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.98434,-0.025448,-0.17446,145.44,-0.11911,0.63357,-0.76446,275.12,0.12999,0.77327,0.62061,-130.95
> view matrix models
> #20,0.98234,-0.11793,-0.14522,160.02,-0.039285,0.62892,-0.77647,260.43,0.18291,0.76847,0.61319,-140.43
> view matrix models
> #20,0.99062,-0.0071278,-0.13645,131.31,-0.087426,0.7344,-0.67307,224.61,0.10501,0.67868,0.72689,-127.96
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.99062,-0.0071278,-0.13645,39.58,-0.087426,0.7344,-0.67307,241.14,0.10501,0.67868,0.72689,-124.31
> fitmap #20 inMap #19
Fit map cryosparc_P250_J281_006_volume_map.mrc in map
cryosparc_P250_J278_006_volume_map.mrc using 106407 points
correlation = 0.6843, correlation about mean = 0.1076, overlap = 7284
steps = 124, shift = 8.16, angle = 4.68 degrees
Position of cryosparc_P250_J281_006_volume_map.mrc (#20) relative to
cryosparc_P250_J278_006_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99454922 0.08690371 -0.05761572 -4.79920701
0.09433066 -0.51448963 0.85229227 122.34986886
0.04442467 -0.85308155 -0.51988295 538.19624086
Axis -0.99820527 -0.05972723 0.00434721
Axis point 0.00000000 212.82904413 234.64732944
Rotation angle (degrees) 121.32632780
Shift along axis -0.17737147
> select add #20
3 models selected
> select subtract #20
Nothing selected
> select add #20
3 models selected
> select subtract #20
Nothing selected
> select add #20
3 models selected
> view matrix models
> #20,0.98915,-0.084376,-0.12029,-34.772,-0.023519,0.7172,-0.69647,408.91,0.14504,0.69174,0.70743,-188.43
> view matrix models
> #20,0.98915,-0.084376,-0.12029,-56.227,-0.023519,0.7172,-0.69647,369.36,0.14504,0.69174,0.70743,-151.42
> hide #!19 models
> show #!18 models
> volume calc_level #20
predicted contour level is [0.21112768]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
> volume #20 level 0.24
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.98146,0.16387,-0.099403,-114.64,-0.1873,0.71001,-0.67883,404.85,-0.040661,0.68486,0.72754,-111.49
> view matrix models
> #20,0.96267,0.25299,-0.096279,-130.92,-0.25193,0.7073,-0.6605,416.27,-0.098999,0.6601,0.74463,-96.323
> vop zflip #20
> volume zflip #20
Expected a density maps specifier or a keyword
> volume flip #20 axis z
Opened cryosparc_P250_J281_006_volume_map.mrc z flip as #21, grid size
440,440,440, pixel 1.06, shown at step 1, values float32
> select subtract #20
Nothing selected
> select add #21
2 models selected
> surface dust #21 size 10.6
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.96267,0.25299,-0.096279,-133.09,-0.25193,0.7073,-0.6605,292.44,-0.098999,0.6601,0.74463,-73.916
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.62162,-0.63802,0.45445,12.888,-0.008215,-0.58544,-0.81068,560.98,0.78328,0.5002,-0.36916,24.764
> view matrix models
> #21,0.97368,-0.015816,0.22735,-153.13,-0.00058319,-0.99776,-0.066915,473.11,0.2279,0.065021,-0.97151,394.77
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.97368,-0.015816,0.22735,-40.296,-0.00058319,-0.99776,-0.066915,439.03,0.2279,0.065021,-0.97151,367.85
> view matrix models
> #21,0.97368,-0.015816,0.22735,-18.869,-0.00058319,-0.99776,-0.066915,478.16,0.2279,0.065021,-0.97151,378.43
> fitmap #21 inMap #18
Fit map cryosparc_P250_J281_006_volume_map.mrc z flip in map
cryosparc_P250_J275_005_volume_map.mrc using 781665 points
correlation = 0.9357, correlation about mean = 0.5919, overlap = 1.066e+05
steps = 256, shift = 21.5, angle = 14.1 degrees
Position of cryosparc_P250_J281_006_volume_map.mrc z flip (#21) relative to
cryosparc_P250_J275_005_volume_map.mrc (#18) coordinates:
Matrix rotation and translation
0.98095961 0.03066839 0.19177506 -42.84448464
0.08603164 -0.95390338 -0.28751848 500.36121903
0.17411715 0.29854274 -0.93837915 337.09514035
Axis 0.99512008 0.02998278 0.09400568
Axis point 0.00000000 225.35192762 208.41694756
Rotation angle (degrees) 162.87438560
Shift along axis 4.05567223
> select subtract #21
Nothing selected
> close #20
> color #21 #999999ff models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!15 models
> hide #!17 models
> show #!14 models
> hide #!15 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!19 models
> hide #!21 models
> show #!21 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!21 models
> show #!21 models
> color #21 #99cc33ff models
> color #21 #669933ff models
> color #21 #006666ff models
> color #21 #009999ff models
> color #21 #00ccccff models
> color #21 cyan models
> color #21 #00ccccff models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Log from Fri Feb 14 16:04:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.26, step 1, values float32
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.236, step 1, values float32
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.25, step 1, values float32
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.25, step 1, values float32
Log from Fri Feb 14 14:36:16 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
> open /Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
> main/calc_level.py
/Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
main/calc_level.py:96: FutureWarning: You are using `torch.load` with
`weights_only=False` (the current default value), which uses the default
pickle module implicitly. It is possible to construct malicious pickle data
which will execute arbitrary code during unpickling (See
https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for
more details). In a future release, the default value for `weights_only` will
be flipped to `True`. This limits the functions that could be executed during
unpickling. Arbitrary objects will no longer be allowed to be loaded via this
mode unless they are explicitly allowlisted by the user via
`torch.serialization.add_safe_globals`. We recommend you start setting
`weights_only=True` for any use case where you don't have full control of the
loaded file. Please open an issue on GitHub for any issues related to this
experimental feature.
checkpoint = torch.load(os.path.join(dir, 'weights_5e6.pth'), map_location =
device)
executed calc_level.py
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/gabriellalopezperez/Downloads/masks_J861/YjgA_2_align420.pdb
Chain information for YjgA_2_align420.pdb #1
---
Chain | Description
8 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/tRNA_align420.pdb
Chain information for tRNA_align420.pdb #2
---
Chain | Description
7 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RsfS_align420.pdb
Chain information for RsfS_align420.pdb #3
---
Chain | Description
6 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RluD_align420.pdb
Chain information for RluD_align420.pdb #4
---
Chain | Description
7 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/ObgE_align420.pdb
Chain information for ObgE_align420.pdb #5
---
Chain | Description
9 | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/YjgA_align420.pdb
YjgA_align420.pdb title:
Structural genomics, the crystal structure of A conserved putative protein
from pseudomonas syringae PV. Tomato STR. DC3000 [more info...]
Chain information for YjgA_align420.pdb #6
---
Chain | Description | UniProt
A | UPF0307 protein pspto_4464 | Y4464_PSESM 1-173
Non-standard residues in YjgA_align420.pdb #6
---
FMT — formic acid
PEG — di(hydroxyethyl)ether
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA5S_align420.pdb
Chain information for RNA5S_align420.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA4_align420.pdb
Chain information for RNA4_align420.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA3_align420.pdb
Chain information for RNA3_align420.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA2_align420.pdb
Chain information for RNA2_align420.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/RNA1_align420.pdb
Chain information for RNA1_align420.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/prots2_align420.pdb
Chain information for prots2_align420.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/gabriellalopezperez/Downloads/masks_J861/prots1_align420.pdb
Chain information for prots1_align420.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J261_004_volume_map.mrc
Opened cryosparc_P250_J261_004_volume_map.mrc as #14, grid size 440,440,440,
pixel 1.06, shown at level 0.216, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J263_004_volume_map.mrc
Opened cryosparc_P250_J263_004_volume_map.mrc as #15, grid size 440,440,440,
pixel 1.06, shown at level 0.219, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J271_005_volume_map.mrc
Opened cryosparc_P250_J271_005_volume_map.mrc as #16, grid size 440,440,440,
pixel 1.06, shown at level 0.208, step 2, values float32
> open
> /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/cryosparc_P250_J273_006_volume_map.mrc
Opened cryosparc_P250_J273_006_volume_map.mrc as #17, grid size 440,440,440,
pixel 1.06, shown at level 0.201, step 2, values float32
> surface dust #14 size 10.6
> surface dust #15 size 10.6
> surface dust #16 size 10.6
> surface dust #17 size 10.6
> set bgColor white
> lighting soft
> select #1-13
100386 atoms, 108540 bonds, 68 pseudobonds, 7564 residues, 22 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #14
Fit molecules YjgA_2_align420.pdb (#1), tRNA_align420.pdb (#2),
RsfS_align420.pdb (#3), RluD_align420.pdb (#4), ObgE_align420.pdb (#5),
YjgA_align420.pdb (#6), RNA5S_align420.pdb (#7), RNA4_align420.pdb (#8),
RNA3_align420.pdb (#9), RNA2_align420.pdb (#10), RNA1_align420.pdb (#11),
prots2_align420.pdb (#12), prots1_align420.pdb (#13) to map
cryosparc_P250_J261_004_volume_map.mrc (#14) using 100386 atoms
average map value = 0.4524, steps = 100
shifted from previous position = 0.778
rotated from previous position = 6.34 degrees
atoms outside contour = 22181, contour level = 0.21626
Position of YjgA_2_align420.pdb (#1) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of tRNA_align420.pdb (#2) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RsfS_align420.pdb (#3) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RluD_align420.pdb (#4) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of ObgE_align420.pdb (#5) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of YjgA_align420.pdb (#6) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA5S_align420.pdb (#7) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA4_align420.pdb (#8) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA3_align420.pdb (#9) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA2_align420.pdb (#10) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of RNA1_align420.pdb (#11) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of prots2_align420.pdb (#12) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
Position of prots1_align420.pdb (#13) relative to
cryosparc_P250_J261_004_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.99790762 0.01778553 -0.06216147 11.34316333
-0.01214067 0.99586459 0.09003507 -16.62921624
0.06350573 -0.08909200 0.99399680 6.95103058
Axis -0.81108349 -0.56901837 -0.13550521
Axis point 0.00000000 64.05381560 191.93561198
Rotation angle (degrees) 6.33979028
Shift along axis -0.67982390
> ~select #1-13
Nothing selected
> ~view #1-13
Unknown command: ~view #1-13
> hide #13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #1-13
> hide #!8 models
> hide #!7 models
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #3 models
> hide #2 models
> hide #1 models
> view #1-13
No displayed objects specified.
> view #1-13 models
Expected an integer >= 1 or a keyword
> show #1 models
> hide #1 models
> show #!7 models
> show #1-13 models
> show #1-13
> hide #1-13
> hide #1 models
> hide #2 models
> hide #3 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #13 models
> volume calc_level all
/Users/gabriellalopezperez/Documents/calc_level_ChimeraX-
main/calc_level.py:103: FutureWarning: `torch.cuda.amp.autocast(args...)` is
deprecated. Please use `torch.amp.autocast('cuda', args...)` instead.
with torch.cuda.amp.autocast():
predicted contour level is [0.24087214]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.23630011]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.20290649]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
predicted contour level is [0.21415067]
> volume all step 1
> volume all style surface
> volume showOutlineBox false
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #3 models
> select add #3
780 atoms, 787 bonds, 102 residues, 1 model selected
> fitmap #3 inMap #17
Fit molecule RsfS_align420.pdb (#3) to map
cryosparc_P250_J273_006_volume_map.mrc (#17) using 780 atoms
average map value = 0.1819, steps = 68
shifted from previous position = 1.14
rotated from previous position = 1.45 degrees
atoms outside contour = 462, contour level = 0.21415
Position of RsfS_align420.pdb (#3) relative to
cryosparc_P250_J273_006_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.99873401 0.00017451 -0.05030249 11.67593399
0.00363211 0.99713364 0.07557322 -17.96658316
0.05017149 -0.07566025 0.99587065 7.22475191
Axis -0.83278369 -0.55327101 0.01903968
Axis point 0.00000000 82.39613522 238.26787639
Rotation angle (degrees) 5.20963037
Shift along axis 0.35441914
> fitmap #5 inMap #17
Fit molecule ObgE_align420.pdb (#5) to map
cryosparc_P250_J273_006_volume_map.mrc (#17) using 2611 atoms
average map value = 0.2221, steps = 84
shifted from previous position = 1.26
rotated from previous position = 2.01 degrees
atoms outside contour = 1220, contour level = 0.21415
Position of ObgE_align420.pdb (#5) relative to
cryosparc_P250_J273_006_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.99652737 0.02312754 -0.07998952 15.03793269
-0.01828537 0.99798573 0.06074647 -8.64718245
0.08123332 -0.05907289 0.99494298 -4.36890390
Axis -0.58421011 -0.78608342 -0.20191930
Axis point 67.54885003 0.00000000 176.99038389
Rotation angle (degrees) 5.88592465
Shift along axis -1.10573951
> show #!5 models
> select add #5
3391 atoms, 3444 bonds, 4 pseudobonds, 442 residues, 3 models selected
> hide #!14 models
> hide #!15 models
> hide #!16 models
> color #17 #666666ff models
> color #17 #999999ff models
> color #17 #ccccccff models
> color #17 #999999ff models
> color #16 #999999ff models
> color #15 #999999ff models
> color #14 #999999ff models
> color #14 #ccccccff models
> color #14 #999999ff models
> color #17 #ccccccff models
> color #17 #999999ff models
> volume #17 level 0.23
> select subtract #5
780 atoms, 787 bonds, 102 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> volume #16 level 0.22
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!16 models
> volume #17 level 0.25
> volume #16 level 0.25
> show #8/L
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8/L
1129 atoms, 1260 bonds, 53 residues, 1 model selected
> fitmap sel inMap #16
Fit molecule RNA4_align420.pdb (#8) to map
cryosparc_P250_J271_005_volume_map.mrc (#16) using 1129 atoms
average map value = 0.2581, steps = 108
shifted from previous position = 3.68
rotated from previous position = 10.6 degrees
atoms outside contour = 549, contour level = 0.25
Position of RNA4_align420.pdb (#8) relative to
cryosparc_P250_J271_005_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99394003 0.08301145 0.07205774 -24.59292312
-0.09577383 0.97570474 0.19704727 -12.42669093
-0.05394990 -0.20275442 0.97774233 61.12162945
Axis -0.87729092 0.27650050 -0.39231125
Axis point 0.00000000 280.33959281 89.43527729
Rotation angle (degrees) 13.17120319
Shift along axis -5.83954068
> select add #8
14554 atoms, 16263 bonds, 5 pseudobonds, 678 residues, 2 models selected
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #3#!5,8 cartoons
> hide #3#!5,8 cartoons
> cartoon #8/L
> hide #!8 models
> show #!8 models
> hide #8/L
> cartoon #13/K
> show #13 models
> volume #14 level 0.25
> volume #14 level 0.26
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> color #15 #00ff66ff models
> show #!15 models
> color #16 #3300ffff models
> show #!16 models
> hide #!15 models
> color #16 #3300ffab models
> color #16 #3300ff2c models
> color #16 #3300ff35 models
> color #16 #3300ffff models
> color #16 #6633ffff models
> color #16 #cc99ffff models
> color #14 #99999933 models
> select subtract #13
Nothing selected
> hide #13 models
> color #14 #99999972 models
> color #14 #99999969 models
> ui tool show "Side View"
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> ui tool show "Fit in Map"
> ui tool show "Color Zone"
> color zone #14 near sel distance 6.36
> color zone #14 near sel distance 6.01
> color zone #14 near sel distance 2.19
> color single #14
> color #14 #9999999d models
> color #14 #9999997f models
> color #16 #999999ff models
> color #14 #9966ffff models
> color #14 #9966ff80 models
> color #14 #9966ff76 models
> color #14 #9966ff54 models
> color #14 #9966ff45 models
> color #14 #9966ff35 models
> color #14 #9966ff62 models
> color #14 #999999ff models
> color #14 #9999997d models
> color #16 #ff99ffff models
> color #16 #330033ff models
> color #16 #cc99ccff models
> color #16 #ffccffff models
> color #16 #cc99ccff models
> color #16 #996699ff models
> color #16 #663366ff models
> color #16 #330033ff models
> color #16 #663366ff models
> color #16 #996699ff models
> color #16 #663366ff models
> color #14 #999999a1 models
> color #14 #999999b9 models
> color #14 #999999b5 models
> color #17 #ccccccff models
> color #17 #cc9999ff models
> color #17 #ff3333ff models
> color #17 #660066ff models
> color #17 #9966ccff models
> color #17 #3300ccff models
> show #!17 models
> hide #!16 models
> color #17 #3300ffff models
> color #17 #6633ffff models
> color #17 #330099ff models
> color #17 #cc99ffff models
> color #17 #330099ff models
> color #17 #9966ccff models
> color #17 #330099ff models
> color #17 #000099ff models
> color #17 #0000ccff models
> color #17 #000099ff models
No map chosen to save
> save /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
——— End of log from Fri Feb 14 14:36:16 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> ui mousemode right zoom
> ui mousemode right translate
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #!8 models
> color #14 #99999982 models
> color #14 #999999ff models
> hide #!17 models
> show #!17 models
> hide #!14 models
> show #!14 models
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!14 models
> show #!14 models
> hide #!14 models
> lighting simple
> lighting full
> lighting simple
> set bgColor white
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> show #!14 models
> hide #!14 models
> cartoon #13/K
> show #13 models
> hide #!17 models
> show #!14 models
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> color #14 #999999d8 models
> color #14 #999999c9 models
> color #14 #999999bd models
> color #14 #99999948 models
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> color #14 #999999ff models
> color #14 #99999980 models
> ui tool show "Color Zone"
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> color zone #14 near sel distance 6.36
> color zone #14 near sel distance 6.26
> color zone #14 near sel distance 6.16
> color zone #14 near sel distance 6.06
> color zone #14 near sel distance 5.96
> color zone #14 near sel distance 5.86
> color zone #14 near sel distance 5.76
> color zone #14 near sel distance 5.66
> color zone #14 near sel distance 5.56
> color zone #14 near sel distance 5.46
> color zone #14 near sel distance 5.36
> color zone #14 near sel distance 5.26
> color zone #14 near sel distance 5.16
> color zone #14 near sel distance 5.06
> color zone #14 near sel distance 4.96
> color zone #14 near sel distance 4.86
> color zone #14 near sel distance 4.76
> color zone #14 near sel distance 4.66
> color zone #14 near sel distance 4.56
> color zone #14 near sel distance 4.46
> color zone #14 near sel distance 4.36
> color zone #14 near sel distance 4.26
> color zone #14 near sel distance 4.16
> color zone #14 near sel distance 4.06
> color zone #14 near sel distance 3.96
> color zone #14 near sel distance 3.86
> color zone #14 near sel distance 3.76
> color zone #14 near sel distance 3.66
> color zone #14 near sel distance 3.56
> color zone #14 near sel distance 3.46
> color zone #14 near sel distance 3.36
> color zone #14 near sel distance 3.26
> color zone #14 near sel distance 3.16
> color zone #14 near sel distance 3.06
> color zone #14 near sel distance 2.96
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.76
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #13 models
> hide #!14 models
> show #!16 models
> color #16 #999999ff models
No atoms selected for color zoning
> select #13/K
1075 atoms, 1094 bonds, 136 residues, 1 model selected
> color zone #16 near sel distance 6.36
> color zone #16 near sel distance 6.24
> color zone #16 near sel distance 2.68
> hide #!16 models
> show #!14 models
> hide #!14 models
> show #!16 models
> color #16 #99999982 models
> color zone #16 near sel distance 2.68
> hide #!16 models
> show #!14 models
> color zone #14 near sel distance 2.76
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.96
> color zone #14 near sel distance 2.86
> color zone #14 near sel distance 2.76
> color zone #14 near sel distance 2.66
> color zone #14 near sel distance 2.56
> color zone #14 near sel distance 2.66
> color zone #14 near sel distance 2.76
[Repeated 1 time(s)]
> color zone #16 near sel distance 2.78
[Repeated 1 time(s)]
> show #!16 models
> hide #!14 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> select add #13
24911 atoms, 25214 bonds, 3243 residues, 1 model selected
> select subtract #13
Nothing selected
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!14 models
> save /Users/gabriellalopezperez/Desktop/image18.png supersample 3
> show #!16 models
> hide #!14 models
> save /Users/gabriellalopezperez/Desktop/image19.png supersample 3
> volume #16 level 0.26
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!15 models
> show #!14 models
> volume #15 level 0.26
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> volume #17 level 0.26
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> save /Users/gabriellalopezperez/Downloads/J53_25_rep2/OTF/maps/session.cxs
——— End of log from Fri Feb 14 16:04:09 2025 ———
opened ChimeraX session
> hide #3 models
> hide #!5 models
> hide #!16 models
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 13 days, 6 hours, 44 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
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
G247HYU:
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
fsspec: 2024.10.0
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
mpmath: 1.3.0
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
sympy: 1.13.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.5.1
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 , 9 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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