![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#15985 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5.1-x86_64-i386-64bit
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 0x0000000204460600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py", line 353 in raw_decode
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py", line 337 in decode
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py", line 346 in loads
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py", line 293 in load
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 990 in read_json_pae_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 977 in read_pae_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 847 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 1188 in alphafold_pae
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/alphafold/pae.py", line 209 in _open_pae_from_file
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 185 in _open_pae
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 172 in _choose_pae_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 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, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mlp._mlp, chimerax.atom_search.ast (total: 61)
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{
"uptime" : 98000,
"procLaunch" : "2024-09-13 11:14:41.5704 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"procStartAbsTime" : 114568048748,
"coalitionID" : 2424,
"osVersion" : {
"train" : "macOS 12.5.1",
"build" : "21G83",
"releaseType" : "User"
},
"captureTime" : "2024-09-20 12:17:46.1416 +0100",
"incident" : "B11D8B9A-1F3C-40A5-98F6-7EFD74BA2187",
"bug_type" : "309",
"pid" : 3406,
"procExitAbsTime" : 2370400547044,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5A474F56-37F1-5EAE-AE4A-716C4B8E9ECA","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "05C48EED-39CC-5B24-BB62-5216644C543A",
"wakeTime" : 12161,
"sleepWakeUUID" : "ABA3011A-687F-4DFF-B5B8-9584C009F087",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722790416215\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc93ef4000-7ffc94530000 [ 6384K] r-x\/r-x SM=COW ...t_id=de16d401",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722790416215\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc93ef4000-7ffc94530000 [ 6384K] r-x\/r-x SM=COW ...t_id=de16d401",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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/joe/projects/depoKP36/depoKP36_cryoEM_models/EPS_depoKP36_c3_trimer.pdb
> format pdb
Chain information for EPS_depoKP36_c3_trimer.pdb #1
---
Chain | Description
A | No description available
B C | No description available
> close
> open /Users/joe/Downloads/cryosparc_P4_J110_007_volume_map.mrc format mrc
Opened cryosparc_P4_J110_007_volume_map.mrc as #1, grid size 336,336,336,
pixel 1.05, shown at level 0.063, step 2, values float32
> volume #1 step 1
> volume #1 level 0.3609
> lighting soft
> volume #1 level 0.3331
> volume #1 level 0.48
> close
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/apo_depoKP36_c3_chainA_WIP.pdb
> format pdb
Chain information for apo_depoKP36_c3_chainA_WIP.pdb #1
---
Chain | Description
A | No description available
> select carboxylate
189 atoms, 126 bonds, 63 residues, 1 model selected
> show sel atoms
> select /A:622@OD2
1 atom, 1 residue, 1 model selected
> select add /A:588@OE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:622@OD2 /A:588@OE2
Distance between /A ASP 622 OD2 and GLU 588 OE2: 5.031Å
> select clear
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J114_005_volume_map_C3_apo.mrc
> format mrc
Opened cryosparc_P4_J114_005_volume_map_C3_apo.mrc as #3, grid size
336,336,336, pixel 1.05, shown at level 0.0535, step 2, values float32
> volume #3 step 1
> volume #3 level 0.6347
> close #3
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J162_006_volume_map_C3_EPS.mrc
Opened cryosparc_P4_J162_006_volume_map_C3_EPS.mrc as #3, grid size
336,336,336, pixel 1.1, shown at level 0.0215, step 2, values float32
> view
> volume #3 step 1
> volume #3 level 0.2975
> fitmap #1 inMap #3
Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map
cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) using 10542 atoms
average map value = 0.1534, steps = 148
shifted from previous position = 12.8
rotated from previous position = 8.73 degrees
atoms outside contour = 8536, contour level = 0.29746
Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to
cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) coordinates:
Matrix rotation and translation
0.99643987 -0.04902652 0.06858560 2.18549632
0.03995467 0.99098216 0.12789829 -15.89245310
-0.07423752 -0.12470264 0.98941298 39.12785882
Axis -0.83224298 0.47055859 0.29316588
Axis point 0.00000000 295.66083173 153.10255089
Rotation angle (degrees) 8.72888423
Shift along axis 2.17375905
> close #2
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8452,0.53228,0.048089,-79.751,-0.53439,0.84295,0.062189,117.4,-0.0074347,-0.078261,0.99691,16.612
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.8452,0.53228,0.048089,-80.344,-0.53439,0.84295,0.062189,122.31,-0.0074347,-0.078261,0.99691,16.946
> fitmap #1 inMap #3
Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map
cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) using 10542 atoms
average map value = 0.1789, steps = 76
shifted from previous position = 3.39
rotated from previous position = 3.97 degrees
atoms outside contour = 8004, contour level = 0.29746
Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to
cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) coordinates:
Matrix rotation and translation
0.83496129 -0.55016356 -0.01263759 137.26469351
0.55023176 0.83500836 0.00245695 -59.16449587
0.00920077 -0.00900506 0.99991712 0.55666186
Axis -0.01041365 -0.01984094 0.99974891
Axis point 167.28392309 199.32164329 0.00000000
Rotation angle (degrees) 33.39005620
Shift along axis 0.30097429
> close #3
> close
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/EPS_depoKP36_c3_chainA.pdb
Chain information for EPS_depoKP36_c3_chainA.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J162_006_volume_map_C3_EPS.mrc
Opened cryosparc_P4_J162_006_volume_map_C3_EPS.mrc as #2, grid size
336,336,336, pixel 1.1, shown at level 0.0215, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3089
> select carboxylate
192 atoms, 128 bonds, 64 residues, 1 model selected
> volume #2 level 0.5575
> volume #2 level 0.2496
> show sel atoms
> hide #!2 models
> close #2
> close
> open /Users/joe/projects/depoKP36/tomo/capsid/run_class001.mrc
Opened run_class001.mrc as #1, grid size 100,100,100, pixel 11.4, shown at
level 0.0149, step 1, values float32
> volume #1 level 0.01135
> volume #1 level 0.01111
> volume #1 level 0.01002
> volume #1 level 0.002496
> volume #1 level 0.00204
> volume #1 level 0.006986
> volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true
> ui mousemode right "tape measure"
> marker segment #2 position 745.8,293.3,558.6 toPosition 382.4,843,558.6
> color yellow radius 2.85 label 659 labelHeight 65.9 labelColor yellow
> marker segment #2 position 875.1,608.6,558.6 toPosition 261.4,536.2,558.6
> color yellow radius 2.85 label 617.9 labelHeight 61.79 labelColor yellow
> close #2
> close
> open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i2.mrc
Opened capsid_i2.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level
0.0159, step 1, values float32
> volume #1 level 0.01131
> close #1
> open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i4.mrc
Opened capsid_i4.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level
0.015, step 1, values float32
> volume #1 level 0.01281
> volume #1 level 0.01093
> volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true
> volume #1 level -0.000816,0 level 0.01606,0.8 level 0.01675,1
> volume #1 level -0.000816,0 level 0.01302,0.5206 level 0.01675,1
> volume #1 level -0.001256,0 level 0.01302,0.5206 level 0.01675,1
> volume #1 level -0.002116,0.01471 level 0.01302,0.5206 level 0.01675,1
> volume #1 region 0,0,0,99,99,99 step 1
> volume #1 style surface region 0,0,0,99,99,99 step 1
> volume #1 style image region 0,0,49,99,99,49 step 1
> ui mousemode right "tape measure"
> marker segment #2 position 466.5,849.8,558.6 toPosition 667.2,289.3,558.6
> color yellow radius 2.85 label 595.3 labelHeight 59.53 labelColor yellow
> volume #1 level -0.002116,0.01471 level 0.007361,0.9118 level 0.01675,1
> marker segment #2 position 252.3,619.4,558.6 toPosition 871,547.8,558.6
> color yellow radius 2.85 label 622.8 labelHeight 62.28 labelColor yellow
> close #1
> close
> open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i4.mrc format mrc
Opened capsid_i4.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level
0.015, step 1, values float32
> volume #1 level 0.01072
> volume #1 level 0.009624
> lighting soft
> lighting simple
> lighting full
> lighting simple
> volume #1 color #73fdff
> volume #1 color #fffb00
> volume #1 color #f0fe48
> volume #1 color #ffff66
> volume #1 color #ffff33
> volume #1 color #ffccff
> volume #1 color #ff99ff
> volume #1 color #ff99ffdc
> volume #1 color #e4c099
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui mousemode right "tape measure"
> volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true
> volume #1 level -0.000816,0 level 0.01606,0.8 level 0.01675,1
> volume #1 level -0.000816,0 level 0.01474,0.8735 level 0.01675,1
> ui mousemode right "tape measure"
> marker segment #2 position 869.5,714.7,558.6 toPosition 272.1,461.6,558.6
> color yellow radius 2.85 label 648.9 labelHeight 64.89 labelColor yellow
> open
> /Users/joe/Downloads/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif
Chain information for
fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif
#3
---
Chain | Description
A B C D E F | .
> close #1
> close #2
> view
> ui tool show "AlphaFold Error Plot"
Must choose path to predicted aligned file
> alphafold pae #3 file
> /Users/joe/Downloads/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_full_data_0.json
> color bfactor #3 palette alphafold
5214 atoms, 684 residues, atom bfactor range 28.8 to 97.4
> alphafold pae #3 colorDomains true
> color bfactor #3 palette alphafold
5214 atoms, 684 residues, atom bfactor range 28.8 to 97.4
> save /Users/joe/projects/depoKP36/AF3_DIT_hexamer_K9L8K4.pdb relModel #3
> open 8xcg
Summary of feedback from opening 8xcg fetched from pdb
---
note | Fetching compressed mmCIF 8xcg from
http://files.rcsb.org/download/8xcg.cif
8xcg title:
Tail tip complex of bacteriophage λ in the open state [more info...]
Chain information for 8xcg #1
---
Chain | Description | UniProt
E K M Y e m | Tail tip protein M | TIPM_LAMBD 1-109
F J Z | Tip attachment protein J | TIPJ_LAMBD 1-1132
I P h | Tail tip assembly protein I | TIPI_LAMBD 1-223
L N f | Tail tip protein L | TIPL_LAMBD 1-232
Non-standard residues in 8xcg #1
---
SF4 — iron/sulfur cluster
> view
> select #1/E
884 atoms, 909 bonds, 109 residues, 1 model selected
> select add #3
6098 atoms, 6243 bonds, 793 residues, 2 models selected
> select add #1
31155 atoms, 31841 bonds, 11 pseudobonds, 3999 residues, 3 models selected
> select subtract #1
5214 atoms, 5334 bonds, 684 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,172.62,0,1,0,37.915,0,0,1,-27.603
> view matrix models #3,1,0,0,192.6,0,1,0,62.955,0,0,1,295.35
> view matrix models #3,1,0,0,169.08,0,1,0,110.17,0,0,1,288.08
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92049,-0.18797,0.34258,169.77,-0.24979,0.39115,0.88578,112.2,-0.3005,-0.90093,0.31309,289.12
> view matrix models
> #3,0.90373,-0.23226,0.35963,169.88,-0.2376,0.42669,0.87263,112.12,-0.35612,-0.87407,0.33043,289.18
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90373,-0.23226,0.35963,171,-0.2376,0.42669,0.87263,117.13,-0.35612,-0.87407,0.33043,288.31
> view matrix models
> #3,0.90373,-0.23226,0.35963,171.51,-0.2376,0.42669,0.87263,116.65,-0.35612,-0.87407,0.33043,276.4
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.857,-0.12267,0.50051,171.55,-0.39798,0.45944,0.79406,116.76,-0.32736,-0.8797,0.34492,276.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.857,-0.12267,0.50051,175.26,-0.39798,0.45944,0.79406,113.44,-0.32736,-0.8797,0.34492,277.01
> hide #3 models
> show #3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.73207,-0.61992,-0.28244,175.4,-0.45463,-0.13583,-0.88026,112.79,0.50732,0.77282,-0.38127,272.84
> view matrix models
> #3,0.78353,-0.50457,-0.36261,175.09,-0.51098,-0.19121,-0.83806,112.99,0.35352,0.84193,-0.40764,272.94
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.78353,-0.50457,-0.36261,170.72,-0.51098,-0.19121,-0.83806,112.74,0.35352,0.84193,-0.40764,272.52
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.86776,-0.43992,-0.23122,170.63,-0.36747,-0.25473,-0.89447,112.57,0.3346,0.86115,-0.38271,272.54
> align #3 toAtoms #1
Unequal number of atoms to pair, 5214 and 25941
> ui tool show Matchmaker
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8xcg, chain e (#1) with
fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif,
chain A (#3), sequence alignment score = 156.9
RMSD between 49 pruned atom pairs is 1.210 angstroms; (across all 104 pairs:
3.747)
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8xcg, chain e (#1) with
fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif,
chain A (#3), sequence alignment score = 156.9
RMSD between 49 pruned atom pairs is 1.210 angstroms; (across all 104 pairs:
3.747)
> select clear
> color #3 #9bb7e5ff
> select #1/I
412 atoms, 415 bonds, 56 residues, 1 model selected
> view matrix models #1,1,0,0,0.67132,0,1,0,1.8325,0,0,1,0.90392
> undo
> select #1/I#1/P#1/h
1276 atoms, 1285 bonds, 173 residues, 1 model selected
> delete sel
> select #1/L#1/N#1/f
5427 atoms, 5544 bonds, 11 pseudobonds, 699 residues, 2 models selected
> delete sel
> select #1/F#1/J#1/Z
13934 atoms, 14224 bonds, 1789 residues, 1 model selected
> delete sel
> show atoms
> show cartoons
> hide surfaces
> style stick
Changed 10518 atom styles
> hide #!1 models
> hide #3 models
> open /Users/joe/projects/depoKP36/tomo/capsid/run_class001.mrc
Opened run_class001.mrc as #2, grid size 512,512,512, pixel 1.9, shown at
level 0.016, step 2, values float32
> volume #2 level 0.01137
> volume #2 step 1
> volume #2 step 2
> volume #2 step 4
> volume #2 level 0.01197
> volume #2 level 0.01077
> volume #2 step 1
> volume #2 level 0.00938
> volume #2 level 0.01
> close #2
> show #3 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #!1 models
> show #!1 models
> open 8xcg
8xcg title:
Tail tip complex of bacteriophage λ in the open state [more info...]
Chain information for 8xcg #2
---
Chain | Description | UniProt
E K M Y e m | Tail tip protein M | TIPM_LAMBD 1-109
F J Z | Tip attachment protein J | TIPJ_LAMBD 1-1132
I P h | Tail tip assembly protein I | TIPI_LAMBD 1-223
L N f | Tail tip protein L | TIPL_LAMBD 1-232
Non-standard residues in 8xcg #2
---
SF4 — iron/sulfur cluster
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> mlp #3#!1
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_A
SES surface": minimum -25.79, mean -5.512, maximum 21.34
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_B
SES surface": minimum -27.68, mean -5.51, maximum 22.43
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_C
SES surface": minimum -25.85, mean -5.525, maximum 22.27
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_D
SES surface": minimum -25.84, mean -5.476, maximum 22.31
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_E
SES surface": minimum -27.47, mean -5.574, maximum 22.39
Map values for surface
"fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_F
SES surface": minimum -26.06, mean -5.532, maximum 22.14
Map values for surface "8xcg_E SES surface": minimum -25.76, mean -4.146,
maximum 21.74
Map values for surface "8xcg_K SES surface": minimum -26.65, mean -3.956,
maximum 24.64
Map values for surface "8xcg_M SES surface": minimum -24.19, mean -3.863,
maximum 22.62
Map values for surface "8xcg_Y SES surface": minimum -25.45, mean -3.962,
maximum 23.48
Map values for surface "8xcg_e SES surface": minimum -25.64, mean -4.067,
maximum 23.15
Map values for surface "8xcg_m SES surface": minimum -24.43, mean -4.146,
maximum 21.51
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #1
5304 atoms, 5454 bonds, 654 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.75795,0.075882,-0.64788,473.4,-0.02055,-0.9955,-0.092553,250.76,-0.65199,-0.056837,0.7561,186.05
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.75795,0.075882,-0.64788,455.53,-0.02055,-0.9955,-0.092553,287.21,-0.65199,-0.056837,0.7561,178.52
> view matrix models
> #1,-0.75795,0.075882,-0.64788,447.76,-0.02055,-0.9955,-0.092553,301.59,-0.65199,-0.056837,0.7561,177.86
> select subtract #1
6 models selected
> select add #3
5214 atoms, 5334 bonds, 684 residues, 1 model selected
> view matrix models
> #3,-0.52059,0.62126,0.58568,191.68,0.82141,0.17726,0.54209,76.755,0.23297,0.76329,-0.60259,276.38
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.63935,0.61509,0.46141,191.82,0.71483,0.25438,0.6514,76.989,0.2833,0.74629,-0.60232,276.29
> view matrix models
> #3,-0.77615,-0.09986,0.6226,193.3,0.62934,-0.061352,0.77471,77.751,-0.039165,0.99311,0.11046,277.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.77615,-0.09986,0.6226,179.55,0.62934,-0.061352,0.77471,70.549,-0.039165,0.99311,0.11046,263.73
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color #!1,3 byhetero
> style #!1,3 stick
Changed 10518 atom styles
> style #!1,3 stick
Changed 10518 atom styles
> hide #!1,3 surfaces
> open
> /Users/joe/Downloads/fold_2024_09_05_15_54_depokp36_timer_k9l8k6/fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif
> format mmcif
Chain information for fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif
#4
---
Chain | Description
A B C | .
> select add #4
19830 atoms, 20169 bonds, 2649 residues, 1 model selected
> view matrix models #4,1,0,0,40.808,0,1,0,-63.945,0,0,1,273.36
> view matrix models #4,1,0,0,29.037,0,1,0,-109.82,0,0,1,268.85
> view matrix models #4,1,0,0,21.452,0,1,0,-129.81,0,0,1,254.06
> show #!2 models
> select #1/E#1/K#1/M#1/Y#1/e#1/m#2/E#2/K#2/M#2/Y#2/e#2/m
10608 atoms, 10908 bonds, 1308 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> select add #4
30438 atoms, 31077 bonds, 3957 residues, 9 models selected
> select subtract #1
25134 atoms, 25623 bonds, 3303 residues, 8 models selected
> select add #2
45771 atoms, 46676 bonds, 11 pseudobonds, 5964 residues, 3 models selected
> select subtract #2
19830 atoms, 20169 bonds, 2649 residues, 1 model selected
> view matrix models #4,1,0,0,30.157,0,1,0,-76.398,0,0,1,183.37
> view matrix models #4,1,0,0,20.936,0,1,0,-92.156,0,0,1,179.05
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.76952,-0.28861,-0.56968,39.566,-0.50702,0.26626,-0.81978,-48.455,0.38828,0.91968,0.05856,135.75
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.76952,-0.28861,-0.56968,95.996,-0.50702,0.26626,-0.81978,84.257,0.38828,0.91968,0.05856,3.0853
> view matrix models
> #4,0.76952,-0.28861,-0.56968,94.028,-0.50702,0.26626,-0.81978,78.69,0.38828,0.91968,0.05856,-12.449
> view matrix models
> #4,0.76952,-0.28861,-0.56968,110.59,-0.50702,0.26626,-0.81978,100.36,0.38828,0.91968,0.05856,-37.238
> view matrix models
> #4,0.76952,-0.28861,-0.56968,110.35,-0.50702,0.26626,-0.81978,98.024,0.38828,0.91968,0.05856,-35.298
> view matrix models
> #4,0.76952,-0.28861,-0.56968,138.64,-0.50702,0.26626,-0.81978,91.507,0.38828,0.91968,0.05856,63.353
> view matrix models
> #4,0.76952,-0.28861,-0.56968,154.03,-0.50702,0.26626,-0.81978,26.604,0.38828,0.91968,0.05856,78.909
> color sel byhetero
> show sel atoms
> hide sel surfaces
> select subtract #4
Nothing selected
> select add #1
5304 atoms, 5454 bonds, 654 residues, 1 model selected
> select subtract #1
6 models selected
> select add #2
25941 atoms, 26507 bonds, 11 pseudobonds, 3315 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> show sel atoms
> hide sel surfaces
> color sel byhetero
> style sel stick
Changed 25941 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select add #4
19830 atoms, 20169 bonds, 2649 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> view matrix models
> #4,0.76952,-0.28861,-0.56968,140.8,-0.50702,0.26626,-0.81978,107.28,0.38828,0.91968,0.05856,69.66
> view matrix models
> #4,0.76952,-0.28861,-0.56968,85.031,-0.50702,0.26626,-0.81978,106.51,0.38828,0.91968,0.05856,60.857
> view matrix models
> #4,0.76952,-0.28861,-0.56968,67.457,-0.50702,0.26626,-0.81978,83.42,0.38828,0.91968,0.05856,70.268
> view matrix models
> #4,0.76952,-0.28861,-0.56968,67.645,-0.50702,0.26626,-0.81978,83.001,0.38828,0.91968,0.05856,68.577
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.65719,-0.52346,-0.54231,79.503,-0.38198,0.38896,-0.83833,74.652,0.64977,0.75809,0.055673,65.741
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,121.89,0.47385,0.3367,-0.81369,48.574,0.69765,-0.70738,0.11357,115.54
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,96.446,0.47385,0.3367,-0.81369,66.635,0.69765,-0.70738,0.11357,255.27
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,218.73,0.47385,0.3367,-0.81369,-3.4628,0.69765,-0.70738,0.11357,258.64
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,290.5,0.47385,0.3367,-0.81369,-45.878,0.69765,-0.70738,0.11357,260.74
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,293.1,0.47385,0.3367,-0.81369,-41.329,0.69765,-0.70738,0.11357,260.22
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,294.18,0.47385,0.3367,-0.81369,-37.074,0.69765,-0.70738,0.11357,274.14
> view matrix models
> #4,-0.53735,-0.62149,-0.57009,294.11,0.47385,0.3367,-0.81369,-38.282,0.69765,-0.70738,0.11357,273.69
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.30586,-0.7008,-0.64446,289.48,0.33699,0.5534,-0.7617,-41.525,0.89044,-0.45015,0.066904,258.46
> view matrix models
> #4,-0.10574,-0.70948,-0.69675,283.36,0.18705,0.67398,-0.71468,-40.958,0.97664,-0.2059,0.061438,247.09
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.10574,-0.70948,-0.69675,302.55,0.18705,0.67398,-0.71468,-71.648,0.97664,-0.2059,0.061438,216.03
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B #4/C
Alignment identifier is 1
> select #4/A-C:83
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #4/A-C:83-883
18054 atoms, 18372 bonds, 2403 residues, 1 model selected
> hide sel
> delete sel
> select add #4
1776 atoms, 1794 bonds, 246 residues, 1 model selected
> view matrix models
> #4,-0.10574,-0.70948,-0.69675,307.19,0.18705,0.67398,-0.71468,-74.228,0.97664,-0.2059,0.061438,149.96
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.43661,-0.68043,-0.58854,346.12,-0.25088,0.72033,-0.64667,-23.694,0.86396,-0.13469,-0.48521,155.47
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.43661,-0.68043,-0.58854,312.84,-0.25088,0.72033,-0.64667,20.614,0.86396,-0.13469,-0.48521,165.67
> view matrix models
> #4,-0.43661,-0.68043,-0.58854,298.2,-0.25088,0.72033,-0.64667,5.8736,0.86396,-0.13469,-0.48521,151.88
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.25513,-0.74018,-0.62213,283.24,-0.051475,0.65291,-0.75568,-10.154,0.96554,-0.16077,-0.20468,141.77
> view matrix models
> #4,-0.45333,-0.72507,-0.51843,306.81,-0.031048,0.59412,-0.80378,-4.0825,0.8908,-0.34828,-0.29184,179.36
> view matrix models
> #4,-0.62166,-0.62306,-0.4747,313.81,-0.31454,0.7536,-0.57719,9.1874,0.71736,-0.20951,-0.66446,182.53
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.62166,-0.62306,-0.4747,314.34,-0.31454,0.7536,-0.57719,10.839,0.71736,-0.20951,-0.66446,180.99
> view matrix models
> #4,-0.62166,-0.62306,-0.4747,314.31,-0.31454,0.7536,-0.57719,10.608,0.71736,-0.20951,-0.66446,181.44
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.50152,-0.69513,-0.51505,309.22,-0.11804,0.64475,-0.75523,1.2077,0.85705,-0.31797,-0.40541,178.48
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.50152,-0.69513,-0.51505,309.29,-0.11804,0.64475,-0.75523,0.9308,0.85705,-0.31797,-0.40541,179.64
> view matrix models
> #4,-0.50152,-0.69513,-0.51505,336.89,-0.11804,0.64475,-0.75523,-53.466,0.85705,-0.31797,-0.40541,189.54
> view matrix models
> #4,-0.50152,-0.69513,-0.51505,337.71,-0.11804,0.64475,-0.75523,-52.535,0.85705,-0.31797,-0.40541,190.84
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.081959,-0.94989,-0.30165,298.11,-0.78748,-0.24724,0.56458,163.69,-0.61086,0.19128,-0.76828,309.47
> view matrix models
> #4,0.017377,-0.8854,-0.46451,297.46,-0.80951,-0.28514,0.51322,172.27,-0.58685,0.36711,-0.72169,280.35
> view matrix models
> #4,-0.52609,-0.83545,-0.1589,360.8,-0.23508,-0.036701,0.97128,59.303,-0.81729,0.54834,-0.17709,282.76
> view matrix models
> #4,-0.083086,-0.87271,0.48111,306.72,0.090771,0.47415,0.87575,-58.418,-0.9924,0.11643,0.039822,368.81
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.083086,-0.87271,0.48111,276.56,0.090771,0.47415,0.87575,-6.0315,-0.9924,0.11643,0.039822,366.92
> view matrix models
> #4,-0.083086,-0.87271,0.48111,280.69,0.090771,0.47415,0.87575,1.4425,-0.9924,0.11643,0.039822,359.44
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.43527,-0.82742,0.35486,320.54,-0.55889,0.55734,0.61401,75.078,-0.70582,0.068935,-0.70503,330.42
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.43527,-0.82742,0.35486,317.48,-0.55889,0.55734,0.61401,69.216,-0.70582,0.068935,-0.70503,326.81
> view matrix models
> #4,-0.43527,-0.82742,0.35486,316.76,-0.55889,0.55734,0.61401,70.486,-0.70582,0.068935,-0.70503,326.38
> view matrix models
> #4,-0.43527,-0.82742,0.35486,318.06,-0.55889,0.55734,0.61401,69.067,-0.70582,0.068935,-0.70503,327.34
> select #2/Z
4650 atoms, 4747 bonds, 597 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4 to #2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8xcg, chain Z (#2) with
fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif, chain A (#4),
sequence alignment score = 71.7
RMSD between 11 pruned atom pairs is 1.051 angstroms; (across all 80 pairs:
10.961)
> matchmaker #4 to #2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8xcg, chain Z (#2) with
fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif, chain A (#4),
sequence alignment score = 71.7
RMSD between 11 pruned atom pairs is 1.051 angstroms; (across all 80 pairs:
10.961)
> select clear
> select #4/A-C:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #4/A-C
1776 atoms, 1794 bonds, 246 residues, 1 model selected
> save /Users/joe/projects/depoKP36/depoKP36_nterm_AF3.pdb models #4
> selectedOnly true
> lighting simple
> lighting soft
> lighting simple
> select #2/N
1809 atoms, 1848 bonds, 4 pseudobonds, 233 residues, 2 models selected
> select #2/Z
4650 atoms, 4747 bonds, 597 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/F #2/J #2/Z
Alignment identifier is 1
> select clear
> select #2/F,J,Z
13934 atoms, 14224 bonds, 1789 residues, 1 model selected
> select #2/F,Z:11-12/J:10-12
61 atoms, 61 bonds, 7 residues, 1 model selected
> select #2/F,J,Z
13934 atoms, 14224 bonds, 1789 residues, 1 model selected
> select clear
> select #2/J:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F,Z:11-28/J:10-28
430 atoms, 430 bonds, 55 residues, 1 model selected
> select
> #2/F,J,Z:21-30,35-38,45-46,64-69,84-94,111-118,135-143,146-155,163-170,179-183,197-206,216-223,235-236,238-241,243-246,249-250,255-256,264-267,311-313,319-321,327-329,348-353,356-361,368-372,386-389,398-405,411-418,430-434,460-463,478-482,492-499,504-507,520-524,530-539,543-546,558-562,570-578,584-590
5298 atoms, 5289 bonds, 663 residues, 1 model selected
> select #2/F,J,Z:594-595
54 atoms, 51 bonds, 6 residues, 1 model selected
> select #2/F,J,Z:594-603
216 atoms, 213 bonds, 30 residues, 1 model selected
> select #2/F,J,Z:557-558
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #2/F,J,Z:557-573
450 atoms, 459 bonds, 51 residues, 1 model selected
> select #2/F,J,Z:225
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #2/F,J,Z:225-488
6321 atoms, 6495 bonds, 792 residues, 1 model selected
> select
> #2/F,J,Z:21-30,35-38,45-46,64-69,84-94,111-118,135-143,146-155,163-170,179-183,197-206,216-223,235-236,238-241,243-246,249-250,255-256,264-267,311-313,319-321,327-329,348-353,356-361,368-372,386-389,398-405,411-418,430-434,460-463,478-482,492-499,504-507,520-524,530-539,543-546,558-562,570-578,584-590
5298 atoms, 5289 bonds, 663 residues, 1 model selected
> select #2/F,J,Z:11-12
54 atoms, 54 bonds, 6 residues, 1 model selected
> select #2/F,J,Z:11-223
4917 atoms, 4992 bonds, 639 residues, 1 model selected
> select #2/F,J,Z:492
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #2/F,J,Z:492-591
2274 atoms, 2301 bonds, 300 residues, 1 model selected
> select clear
> select #2/F,J,Z:21
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #2/F,J,Z:21-224
4695 atoms, 4767 bonds, 612 residues, 1 model selected
> select #2/F,J,Z:492
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #2/F:492-604/J,Z:492-606
2600 atoms, 2635 bonds, 343 residues, 1 model selected
> select #2/F,J,Z:477-478
45 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/F,J,Z:477-603
2868 atoms, 2901 bonds, 381 residues, 1 model selected
> open /Users/joe/Downloads/txtfile/12082/12082.xml
Opened 12082.xml
> close
> set bgColor black
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_0.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_0.cif #1
---
Chain | Description
A B C | .
D | .
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_1.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_1.cif #2
---
Chain | Description
A B C | .
D | .
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_2.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_2.cif #3
---
Chain | Description
A B C | .
D | .
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_3.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_3.cif #4
---
Chain | Description
A B C | .
D | .
> open
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_4.cif
Chain information for fold_2024_09_20_myadm_trail_trimer_model_4.cif #5
---
Chain | Description
A B C | .
D | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select #1/A
2442 atoms, 2500 bonds, 304 residues, 1 model selected
> select clear
> select #1/D
2484 atoms, 2553 bonds, 322 residues, 1 model selected
> color sel cornflower blue
> select clear
> ui tool show Contacts
> contacts resSeparation 5 intraMol false ignoreHiddenModels true color
> #ff9300
1038 contacts
> close #6
> ui tool show Distances
> ui tool show Contacts
> contacts distanceOnly 4.0 resSeparation 5 intraMol false ignoreHiddenModels
> true color #ff9300
1387 distances
> close #6
> select #1/A
2442 atoms, 2500 bonds, 304 residues, 1 model selected
> color sel mauve
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel violet
> select #1/B
2442 atoms, 2500 bonds, 304 residues, 1 model selected
> color sel palegreen pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel pink
> select #1/C
2442 atoms, 2500 bonds, 304 residues, 1 model selected
> color sel fushia
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ui tool show "Color Actions"
> color sel plum
> select clear
Drag select of 17 residues
> show sel atoms
Drag select of 3 atoms, 15 residues, 2 bonds
> show sel atoms
Drag select of 5 residues
> show sel atoms
Drag select of 24 atoms, 16 residues, 23 bonds
> show sel atoms
> select clear
Drag select of 2 atoms, 6 residues, 1 bonds
> show sel atoms
> select #1/B:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/B:151
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> color #1 byhetero
> select #1/B:272
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/B:271
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #1/B:270
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #1/B:153
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #1/B:152
35 atoms, 31 bonds, 5 residues, 1 model selected
> show sel atoms
> select #1/B:151@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/D:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/D:267
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/C:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/D:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> hide #1 models
> show #2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_1.json
> color bfactor #2 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6
> hide #2 models
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json
> color bfactor #2 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6
> show #2 models
> hide #2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json
> color bfactor #2 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6
> show #2 models
> hide #2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json
> color bfactor #1 palette alphafold
9810 atoms, 1234 residues, atom bfactor range 14.7 to 92.7
> hide #1 models
> show #3 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_2.json
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
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: Mac
Model Identifier: Mac14,7
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 7 days 19:04
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-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
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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