The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00000001e8a4bac0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1979 in _open_dropped_file
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 240 in event
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.dssp._dssp, chimerax.mmcif.mmcif_write, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 62)
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"procRole" : "Foreground",
"version" : 2,
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"captureTime" : "2024-05-02 23:56:52.1895 +0100",
"codeSigningMonitor" : 1,
"incident" : "77C95A51-AB8A-42D7-A866-90E1C4C781B7",
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"cpuType" : "ARM-64",
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"procLaunch" : "2024-05-02 23:52:32.3877 +0100",
"procStartAbsTime" : 8742998057263,
"procExitAbsTime" : 8749233193858,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6013,
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4331175767\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102288000-10228c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":52356},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4331175767\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102288000-10228c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000.cif
Summary of feedback from opening
/Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 329
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "12" near line 154
Bad residue range for struct_conf "13" near line 155
Bad residue range for struct_conf "14" near line 156
Bad residue range for struct_conf "15" near line 157
Bad residue range for struct_conf "16" near line 158
14 messages similar to the above omitted
Invalid residue range for struct_conf "31": invalid entity "B", near line 173
Invalid residue range for struct_conf "32": invalid entity "B", near line 174
Invalid residue range for struct_conf "33": invalid entity "B", near line 175
Invalid residue range for struct_conf "34": invalid entity "B", near line 176
Invalid residue range for struct_conf "35": invalid entity "B", near line 177
25 messages similar to the above omitted
Bad residue range for struct_conf "73" near line 215
Bad residue range for struct_conf "74" near line 216
Bad residue range for struct_conf "75" near line 217
Bad residue range for struct_conf "76" near line 218
Bad residue range for struct_conf "77" near line 219
15 messages similar to the above omitted
Invalid residue range for struct_conf "93": invalid entity "D", near line 235
Invalid residue range for struct_conf "94": invalid entity "D", near line 236
Invalid residue range for struct_conf "95": invalid entity "D", near line 237
Invalid residue range for struct_conf "96": invalid entity "D", near line 238
Invalid residue range for struct_conf "97": invalid entity "D", near line 239
25 messages similar to the above omitted
Bad residue range for struct_conf "134" near line 276
Bad residue range for struct_conf "135" near line 277
Bad residue range for struct_conf "136" near line 278
Bad residue range for struct_conf "137" near line 279
Bad residue range for struct_conf "138" near line 280
15 messages similar to the above omitted
Invalid residue range for struct_conf "154": invalid entity "F", near line 296
Invalid residue range for struct_conf "155": invalid entity "F", near line 297
Invalid residue range for struct_conf "156": invalid entity "F", near line 298
Invalid residue range for struct_conf "157": invalid entity "F", near line 299
Invalid residue range for struct_conf "158": invalid entity "F", near line 300
27 messages similar to the above omitted
Atom H is not in the residue template for LYS /A:266
Atom H is not in the residue template for LYS /B:266
Atom H is not in the residue template for LYS /C:266
Atom H is not in the residue template for LYS /D:266
Atom H is not in the residue template for LYS /E:266
1 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 36715
Chain information for
comp002_frame010-5_comb-3_modified_real_space_refined_000.cif #1
---
Chain | Description
A B C D E F | No description available
S | No description available
> hide atoms
> show cartoons
> color bychain
> dssp #1
> save
> /Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000_dssp.cif
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs
Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.338, step 1, values float32
Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size
213,213,213, pixel 1, shown at level 1.71, step 1, values float32
Restoring stepper: comp002_frame010-5_comb.pdb
Log from Thu May 2 23:31:55 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.338, step 1, values float32
Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size
213,213,213, pixel 1, shown at level 3.3, step 1, values float32
Restoring stepper: comp002_frame010-5_comb.pdb
Log from Tue Apr 30 01:03:15 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> format session
Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.903, step 1, values float32
Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size
213,213,213, pixel 1, shown at level 2.82, step 1, values float32
Restoring stepper: comp002_frame010-5_comb.pdb
Log from Tue Jan 23 18:55:59 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at level 0.903, step 1, values float32
Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size
213,213,213, pixel 1, shown at level 2.17, step 1, values float32
Restoring stepper: comp002_frame010-5_comb.pdb
Log from Tue Jan 23 03:11:45 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp002_frame010-5_comb.pdb
Chain information for comp002_frame010-5_comb.pdb #1
---
Chain | Description
A B C D E F | No description available
S | No description available
> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_002/J332_component_002_frame_010.mrc
Opened J332_component_002_frame_010.mrc as #2, grid size 128,128,128, pixel
1.67, shown at level 0.731, step 1, values float32
> open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP-
> Mg_CGfork/cryosparc_P18_J332_component_002/J332_component_002_frame_010_emready.mrc
Opened J332_component_002_frame_010_emready.mrc as #3, grid size 213,213,213,
pixel 1, shown at level 4.66, step 1, values float32
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp002_frame010-5.pdb
Chain information for comp002_frame010-5.pdb #4
---
Chain | Description
A B C D E F | No description available
S | No description available
> open /Users/tahashahid/Library/CloudStorage/OneDrive-
> UniversityofLeicester/for_taha/Comp002_models/Comp002_Frame10_ssDNA_ISOLDE.pdb
Chain information for Comp002_Frame10_ssDNA_ISOLDE.pdb #5
---
Chain | Description
A B C D E F | No description available
S | No description available
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp002_frame015-7_comb-1.pdb
Chain information for comp002_frame015-7_comb-1.pdb #6
---
Chain | Description
A B C D E F | No description available
S | No description available
> isolde start
> set selectionWidth 4
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Volume Viewer"
> ui tool show "Ramachandran Plot"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for comp002_frame010-5_comb.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | No description available
1.2/S | No description available
> clipper associate #2 toModel #1
Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128,
pixel 1.67, shown at step 1, values float32
> clipper associate #3 toModel #1
Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size
213,213,213, pixel 1, shown at step 1, values float32
> select clear
> select add #6
36101 atoms, 36482 bonds, 2192 residues, 1 model selected
> select add #5
72202 atoms, 72964 bonds, 4384 residues, 2 models selected
> select add #4
108270 atoms, 109411 bonds, 6575 residues, 3 models selected
> color sel bychain
> color sel byhetero
> style sel stick
Changed 108270 atom styles
> hide HC
> select clear
> hide #6 models
> hide #5 models
> hide #4 models
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/S
ISOLDE: started sim
> show #4 models
> hide #4 models
> volume #1.1.1.2 level 3.318
> select clear
> volume #1.1.1.2 level 5.304
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> volume #1.1.1.2 level 2.803
> isolde stepto #1.2/S:2
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
Loading residue template for ATP from internal database
ISOLDE: started sim
> select clear
> volume #1.1.1.2 level 1.231
> volume #1.1.1.2 level 1.556
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:511
> view #!1.2/A:516
> volume #1.1.1.2 level 0.9317
> view #!1.2/A:516
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:516
> volume #1.1.1.2 level 3.028
> volume #1.1.1.2 level 4.7
> volume #1.1.1.2 level 3.427
> view #!1.2/A:349
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:349
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:349
> volume #1.1.1.2 level 4.75
> volume #1.1.1.2 level 4.7
> view #!1.2/A:517
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:517
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
ISOLDE: started sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.554
> volume #1.1.1.2 level 5.249
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> volume #1.1.1.2 level 2.529
> volume #1.1.1.2 level 3.452
> volume #1.1.1.2 level 1.88
> volume #1.1.1.2 level 3.078
> select clear
> volume #1.1.1.2 level 1.056
> view #!1.2/A:515
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.93
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:512
> volume #1.1.1.2 level 1.181
> view #!1.2/A:512
> volume #1.1.1.2 level 2.404
> volume #1.1.1.2 level 1.78
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:513
> volume #1.1.1.2 level 3.402
> show #4 models
> hide #4 models
> volume #1.1.1.2 level 1.581
> volume #1.1.1.2 level 0.782
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.579
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:514
> volume #1.1.1.2 level 1.156
> volume #1.1.1.2 level 0.5574
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:514
> view #!1.2/A:456
> show #6 models
> volume #1.1.1.2 level 0.4327
> volume #1.1.1.2 level 2.529
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> hide #6 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:456
> volume #1.1.1.2 level 0.7071
> volume #1.1.1.2 level 0.2829
> show #6 models
> hide #6 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.154
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:456
> volume #1.1.1.2 level 0.7321
> volume #1.1.1.2 level 0.3578
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.805
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:516
> volume #1.1.1.2 level 0.7321
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim pause
> isolde sim resume
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.154
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> volume #1.1.1.2 level 1.331
> show #4 models
> hide #4 models
> show #5 models
> isolde sim pause
> select clear
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> hide #5 models
> show #4 models
> select clear
> view #!1.2/A:516
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:516
[Repeated 1 time(s)]
> show #6 models
> hide #4 models
> view #!1.2/A:349
> volume #1.1.1.2 level 3.976
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.204
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> hide #6 models
> volume #1.1.1.2 level 3.677
> volume #1.1.1.2 level 1.381
> view #!1.2/A:506
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> volume #1.1.1.2 level 1.955
> select clear
> view #!1.2/A:499
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
ISOLDE: started sim
> view #!1.2/A:505
> select clear
> show #6 models
> view #!1.2/A:520
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.903
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 1.895
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
ISOLDE: started sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/A:507
> volume #1.1.1.2 level 3.816
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.995
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.793
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
ISOLDE: started sim
> select clear
> hide #6 models
> volume #1.1.1.2 level 1.571
> volume #1.1.1.2 level 3.068
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.271
> volume #1.1.1.2 level 2.719
> volume #1.1.1.2 level 1.097
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.87
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.742
> volume #1.1.1.2 level 2.17
> volume #1.1.1.2 level 1.097
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/D:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/D:454-460,509-517
ISOLDE: started sim
> select clear
> volume #1.1.1.2 level 1.865
> show #5 models
> hide #5 models
> show #6 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:458
> volume #1.1.1.2 level 0.5757
> select clear
> hide #6 models
> show #6 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/F:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/F:454-460,509-517
ISOLDE: started sim
> select clear
> hide #6 models
> volume #1.1.1.2 level 1.255
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.294
> volume #1.1.1.2 level 2.129
> volume #1.1.1.2 level 1.304
> show #6 models
> select clear
> isolde sim resume
[Repeated 1 time(s)]
> hide #6 models
> volume #1.1.1.2 level 3.367
> volume #1.1.1.2 level 1.547
> select clear
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.663
> view #!1.2/F:512
> volume #1.1.1.2 level 1.887
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.76
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.692
> show #4 models
> volume #1.1.1.2 level 3.1
> view #!1.2/F:505
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.692
> hide #4 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 0.9641
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.425
> volume #1.1.1.2 level 0.6728
> volume #1.1.1.2 level 1.984
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:514
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.085
> volume #1.1.1.2 level 0.5029
> view #!1.2/F:515
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/S
ISOLDE: started sim
> volume #1.1.1.2 level 3.028
> show #4 models
> volume #1.1.1.2 level 3.322
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/E:510
> volume #1.1.1.2 level 2.17
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
——— End of log from Tue Jan 23 03:11:45 2024 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> view #1/A:800
> hide #4 models
> view #1/B:800
> volume #1.1.1.2 level 4.418
> volume #1.1.1.2 level 3.246
> isolde sim start #1.2/C:498
ISOLDE: started sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:498
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> view #1/C:800
> volume #1.1.1.2 level 5.305
> isolde sim start #1.2/D:498
ISOLDE: started sim
> select clear
> volume #1.1.1.2 level 3.716
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:498
> volume #1.1.1.2 level 4.977
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.959
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/D:800
> volume #1.1.1.2 level 2.822
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> view #!1.2/E:498
> isolde sim start #1.2/E:498
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/E:800
> isolde sim start #1.2/F:498
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
——— End of log from Tue Jan 23 18:55:59 2024 ———
opened ChimeraX session
> select clear
> select add #4
36068 atoms, 36447 bonds, 2191 residues, 1 model selected
> ui tool show "Change Chain IDs"
> select subtract #4
Nothing selected
> close #6
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_001/comp001_frame010-4_comb-2_Rsr/comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif
Summary of feedback from opening
/Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
Mg/3DVA/cs_P18_J332_component_001/comp001_frame010-4_comb-2_Rsr/comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif
---
warnings | Unknown polymer entity '1' near line 194
Unknown polymer entity '2' near line 35954
Atom H is not in the residue template for LYS /A:266
Atom H is not in the residue template for LYS /B:266
Atom H is not in the residue template for LYS /C:266
Atom H is not in the residue template for LYS /D:266
Atom H is not in the residue template for LYS /E:266
1 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif #2
---
Chain | Description
A B C D E F | No description available
S | No description available
> select clear
[Repeated 1 time(s)]
> select add #2
36017 atoms, 36398 bonds, 2186 residues, 1 model selected
> color sel bychain
> color sel byhetero
> style sel stick
Changed 36017 atom styles
> hide HC
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Ramachandran Plot"
> ui tool show "Model-map Q-Score"
> ui tool show "Volume Viewer"
> hide #2 models
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/S
ISOLDE: started sim
> select clear
> show #5 models
> hide #5 models
> show #2 models
> hide #2 models
> select clear
> show #2 models
> hide #2 models
> show #5 models
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> hide #5 models
> show #2 models
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> select #1/B:426-433,473-474,527-529,800/C:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/B:426-433,473-474,527-529,800/C:418,498,540
Loading residue template for ATP from internal database
ISOLDE: started sim
> hide #2 models
> volume #1.1.1.2 level 4.376
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:540
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:540
> volume #1.1.1.2 level 2.695
> show #2 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/C:426-433,473-474,527-529,800/D:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/C:426-433,473-474,527-529,800/D:418,498,540
ISOLDE: started sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 5.619
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:425
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> show #5 models
> volume #1.1.1.2 level 2.362
> hide #5 models
> show #2 models
> volume #1.1.1.2 level 5.902
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:433
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.952
> volume #1.1.1.2 level 5.26
> select clear
[Repeated 1 time(s)]
> show #5 models
> hide #5 models
> show #2 models
> volume #1.1.1.2 level 2.567
> select clear
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:428
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 4.901
> volume #1.1.1.2 level 3.439
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:430
> view #!1.2/D:498
> show #2 models
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/B:471
ISOLDE: started sim
> select clear
> hide #2 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/D:426-433,473-474,527-529,800/E:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/D:426-433,473-474,527-529,800/E:418,498,540
ISOLDE: started sim
> show #2 models
> view #!1.2/E:540
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/E:540
> hide #2 models
> volume #1.1.1.2 level 2.219
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> show #5 models
> hide #5 models
> show #2 models
> hide #2 models
> volume #1.1.1.2 level 5.523
> show #2 models
> volume #1.1.1.2 level 2.727
> volume #1.1.1.2 level 5.549
> volume #1.1.1.2 level 4.507
> select clear
[Repeated 3 time(s)]
> view #!1.2/D:430
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:432
> view #!1.2/D:430
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> hide #2 models
> volume #1.1.1.2 level 2.6
> isolde sim pause
> isolde sim resume
> isolde sim pause
> view #!1.2/E:498
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/E:426-433,473-474,527-529,800/F:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/E:426-433,473-474,527-529,800/F:418,498,540
ISOLDE: started sim
> show #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:499
> volume #1.1.1.2 level 5.216
> volume #1.1.1.2 level 2.237
> volume #1.1.1.2 level 5.07
> volume #1.1.1.2 level 3.23
> hide #2 models
> show #2 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/E:533
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select #1/E,D:509-517,454-460
594 atoms, 594 bonds, 32 residues, 1 model selected
> isolde sim start #1.2/D-E:454-460,509-517
ISOLDE: started sim
> view #!1.2/E:514
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.217
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.645
> volume #1.1.1.2 level 1.723
> select clear
> hide #2 models
> show #2 models
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> hide #2 models
> volume #1.1.1.2 level 1.36
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 4.814
> volume #1.1.1.2 level 1.412
> view #!1.2/E:517
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> show #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 4.97
> view #!1.2/E:349
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/E:349
> volume #1.1.1.2 level 2.321
> hide #2 models
> select clear
> volume #1.1.1.2 level 4.866
> volume #1.1.1.2 level 1.749
> volume #1.1.1.2 level 5.23
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.477
> volume #1.1.1.2 level 0.7884
> volume #1.1.1.2 level 5.931
> volume #1.1.1.2 level 1.568
> volume #1.1.1.2 level 4.139
> volume #1.1.1.2 level 1.438
> view #!1.2/E:517
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.853
> volume #1.1.1.2 level 1.204
> volume #1.1.1.2 level 4.347
> volume #1.1.1.2 level 1.62
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/E:517
> view #!1.2/E:458
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 4.373
> volume #1.1.1.2 level 2.217
> volume #1.1.1.2 level 0.9702
> select clear
> volume #1.1.1.2 level 2.892
> volume #1.1.1.2 level 1.1
> view #!1.2/E:456
> view #!1.2/D:456
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.801
> volume #1.1.1.2 level 1.542
> view #!1.2/E:456
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:349
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> show #2 models
> view #!1.2/D:514
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 4.996
> volume #1.1.1.2 level 2.113
> hide #2 models
> show #2 models
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:512
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:454
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/D:454
> isolde sim pause
> isolde sim resume
> view #!1.2/D:517
> select clear
> view #!1.2/D:517
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/C,B:509-517,454-460
594 atoms, 594 bonds, 32 residues, 1 model selected
> isolde sim start #1.2/B-C:454-460,509-517
ISOLDE: started sim
> view #!1.2/C:513
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:514
> hide #2 models
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:456
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.1
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.646
> show #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 2.009
> volume #1.1.1.2 level 1.308
> volume #1.1.1.2 level 2.944
> volume #1.1.1.2 level 1.412
> select clear
> hide #2 models
> view #!1.2/C:515
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
[Repeated 1 time(s)]
> volume #1.1.1.2 level 4.633
> volume #1.1.1.2 level 1.723
> view #!1.2/C:520
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> view #!1.2/C:265
> select #1/A-F:265
84 atoms, 78 bonds, 6 residues, 1 model selected
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
> select #1/A-F:266
132 atoms, 126 bonds, 6 residues, 1 model selected
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select #1/A-F:266
132 atoms, 126 bonds, 6 residues, 1 model selected
> isolde sim start #1.2/A-F:266
ISOLDE: started sim
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/B:266
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/C:266
> view #!1.2/D:266
> view #!1.2/E:266
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:266
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> clipper isolate #1 maskRadius 16
> select clear
> volume #1.1.1.2 level 3.831
> hide ~@CA
> select clear
> hide #!1.2 models
> show #!1.2 models
> show ~HC
> select #1/C,B:509-517,454-460
594 atoms, 594 bonds, 32 residues, 1 model selected
> isolde sim start #1.2/B-C:454-460,509-517
ISOLDE: started sim
> view #!1.2/C:512
> show #2 models
> hide #2 models
> volume #1.1.1.2 level 2.013
> volume #1.1.1.2 level 1.337
> volume #1.1.1.2 level 2.61
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> show #2 models
> volume #1.1.1.2 level 0.8958
> hide #2 models
> volume #1.1.1.2 level 2.662
> volume #1.1.1.2 level 1.727
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/B:512
> show #2 models
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/B:511
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 0.5321
> show #2 models
> hide #2 models
> show #2 models
> volume #1.1.1.2 level 2.87
> volume #1.1.1.2 level 0.8958
> volume #1.1.1.2 level 3.364
> volume #1.1.1.2 level 1.259
> select clear
> view #!1.2/B:456
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/B:456
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/B:456
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 3.286
> view #!1.2/B:489
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 1.156
> volume #1.1.1.2 level 2.818
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/D:473
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/A:454-460,509-517
ISOLDE: started sim
> view #!1.2/A:513
> volume #1.1.1.2 level 1.538
> view #!1.2/A:455
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> show #5 models
> select clear
> volume #1.1.1.2 level 3.445
> volume #1.1.1.2 level 1.982
> view #!1.2/A:457
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 0.5448
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:514
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 2.295
> view #!1.2/A:506
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 0.4402
> select clear
> volume #1.1.1.2 level 3.079
> hide #5 models
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> view #1/F:509-517,454-460
> select #1/F:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/F:454-460,509-517
ISOLDE: started sim
> select clear
> volume #1.1.1.2 level 1.376
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
> select #1/F:509-517,454-460
297 atoms, 297 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/F:454-460,509-517
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> volume #1.1.1.2 level 1.198
> show #5 models
> hide #5 models
> show #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:456
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:456
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> view #!1.2/F:456
> volume #1.1.1.2 level 3.893
> select clear
> view #!1.2/F:456
> volume #1.1.1.2 level 1.173
> show #5 models
> hide #5 models
> hide #1.3 models
> show #2 models
> show #1.3 models
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/F:510
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> select clear
> volume #1.1.1.2 level 2.291
> volume #1.1.1.2 level 1.224
> select clear
> view #!1.2/F:520
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> volume #1.1.1.2 level 3.308
> view #!1.2/F:507
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.64
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/F:507
> view #!1.2/F:505
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/F:505
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 1.453
> volume #1.1.1.2 level 3.003
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/F:426-433,473-474,527-529,800/A:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/A:418,498,540/F:426-433,473-474,527-529,800
ISOLDE: started sim
> show #5 models
> hide #5 models
> show #2 models
> select clear
> hide #2 models
> volume #1.1.1.2 level 4.765
> open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_000/comp000_frame010_MDFF_ISOLDE-5_comb-5_Rsr/comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif
Summary of feedback from opening
/Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
Mg/3DVA/cs_P18_J332_component_000/comp000_frame010_MDFF_ISOLDE-5_comb-5_Rsr/comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif
---
warnings | Unknown polymer entity '1' near line 194
Unknown polymer entity '2' near line 35954
Atom H is not in the residue template for LYS /A:266
Atom H is not in the residue template for LYS /B:266
Atom H is not in the residue template for LYS /C:266
Atom H is not in the residue template for LYS /D:266
Atom H is not in the residue template for LYS /E:266
1 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif #3
---
Chain | Description
A B C D E F | No description available
S | No description available
> select clear
> hide #3 models
> select add #3
36017 atoms, 36398 bonds, 2186 residues, 1 model selected
> show #3 models
> color sel bychain
> color sel byhetero
> style sel stick
Changed 36017 atom styles
> hide HC
> volume #1.1.1.2 level 2.881
> select clear
> view #!1.2/F:474
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> hide #3 models
> show #2 models
> hide #2 models
> isolde pepflip #1.2/F:474
> select clear
> isolde pepflip #1.2/F:474
> show #3 models
> show #2 models
> hide #2 models
> hide #3 models
> show #3 models
> view #!1.2/F:428
> volume #1.1.1.2 level 1.902
> hide #3 models
> volume #1.1.1.2 level 4.398
> volume #1.1.1.2 level 2.905
> volume #1.1.1.2 level 4.374
> volume #1.1.1.2 level 3.762
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> volume #1.1.1.2 level 2.783
> show #2 models
> volume #1.1.1.2 level 3.884
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> hide #2 models
> volume #1.1.1.2 level 3.297
> select clear
[Repeated 2 time(s)]
> show #2 models
> show #3 models
> select clear
> hide #3 models
> hide #2 models
> show #2 models
> hide #2 models
> select clear
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> select clear
> show #2 models
> hide #2 models
> volume #1.1.1.2 level 1.461
> volume #1.1.1.2 level 2.832
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:535
> volume #1.1.1.2 level 0.9228
> volume #1.1.1.2 level 2.098
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:535
> volume #1.1.1.2 level 3.713
> volume #1.1.1.2 level 1.633
> select clear
> view #!1.2/A:416
[Repeated 2 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 3.223
> view #!1.2/A:418
> isolde sim pause
> isolde sim resume
> volume #1.1.1.2 level 1.388
> show #2 models
> hide #2 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:535
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:535
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> select clear
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/A:426-433,473-474,527-529,800/B:418,540,498
291 atoms, 288 bonds, 17 residues, 1 model selected
> isolde sim start #1.2/A:426-433,473-474,527-529,800/B:418,498,540
ISOLDE: started sim
> volume #1.1.1.2 level 3.604
> show #2 models
> hide #2 models
> volume #1.1.1.2 level 1.886
> show #2 models
> hide #2 models
> show #2 models
> volume #1.1.1.2 level 4.476
> volume #1.1.1.2 level 3.53
> view #!1.2/A:430
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:430
> volume #1.1.1.2 level 2.459
> hide #2 models
> volume #1.1.1.2 level 0.5161
> volume #1.1.1.2 level 1.985
> show #2 models
> volume #1.1.1.2 level 4.7
> volume #1.1.1.2 level 3.43
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 1.487
> hide #2 models
> show #2 models
> select clear
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:474
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 4.252
> volume #1.1.1.2 level 0.8897
> volume #1.1.1.2 level 1.587
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.1 level 0.3377
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:548
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> select clear
> view #!1.2/A:548
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/A:530
> view #!1.2/A:529
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.2 level 3.657
> show #2 models
> hide #2 models
> show #2 models
> show #3 models
> volume #1.1.1.2 level 1.845
> isolde sim start #1.2/B:480
ISOLDE: started sim
> select clear
> hide #3 models
> hide #2 models
> volume #1.1.1.2 level 4.592
> isolde pepflip #1.2/B:480
> volume #1.1.1.2 level 2.351
> volume #1.1.1.2 level 1.652
> isolde pepflip #1.2/B:479
> isolde pepflip #1.2/B:480
> volume #1.1.1.2 level 3.074
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/B:475-490
210 atoms, 210 bonds, 16 residues, 1 model selected
> isolde sim start #1.2/B:475-490
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip #1.2/B:480
> volume #1.1.1.2 level 1.68
> volume #1.1.1.2 level 1.132
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/B:483
[Repeated 1 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/B:483
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> volume #1.1.1.2 level 3.422
> volume #1.1.1.2 level 1.231
> volume #1.1.1.2 level 3.323
> volume #1.1.1.2 level 1.754
> volume #1.1.1.2 level 3.846
> volume #1.1.1.2 level 1.754
> volume #1.1.1.2 level 0.7584
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/B:483
[Repeated 3 time(s)]
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/B:483
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> volume #1.1.1.2 level 3.298
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start #1.2/E:427
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/F:427
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
——— End of log from Tue Apr 30 01:03:15 2024 ———
opened ChimeraX session
> isode start
Unknown command: isode start
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Volume Viewer"
> ui tool show "Ramachandran Plot"
> ui tool show "Model-map Q-Score"
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> view #!1.2/S:8
> select #1.2/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/S
ISOLDE: started sim
> select clear
> isolde stepto #1.2/D:456
> volume #1.1.1.2 level 1.706
> qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
Overall mean Q-Score: 0.65
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> select #1/S
257 atoms, 272 bonds, 8 residues, 1 model selected
> isolde sim start #1.2/S
ISOLDE: started sim
> select #1/S:7
32 atoms, 33 bonds, 1 residue, 1 model selected
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP-
> Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs
> includeMaps true
Taking snapshot of stepper: comp002_frame010-5_comb.pdb
——— End of log from Thu May 2 23:31:55 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: MRW13B/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 14 days, 23 hours, 5 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Taha,
--Eric