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Opened 20 months ago
Last modified 20 months ago
#15254 closed defect
Crash in garbage collection — at Version 1
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-12.7.1-x86_64-i386-64bit
ChimeraX Version: 1.9.dev202405110020 (2024-05-11 00:20:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700004a6e000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001103c0600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 512 in cast
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 223 in set_prop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 273 in _set_atom_colors
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 536 in _set_sequential_residue
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 1068 in color_sequential
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/rainbow.py", line 19 in rainbow
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/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
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, lxml._elementpath, lxml.etree, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 59)
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"usedImages" : [
[deleted to fit within ticket limits]
}
===== 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/pcarlton/Desktop/quickref/DSB_1_2_3relaxed.pdb
Chain information for DSB_1_2_3relaxed.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /C:40
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /C:40-43
56 atoms, 57 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 56 atom styles
> select /C:77
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /C:77-80
70 atoms, 71 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 70 atom styles
> select clear
> style sphere
Changed 16040 atom styles
> select /B:164
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /B:164-166
51 atoms, 52 bonds, 3 residues, 1 model selected
> select /B:266
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /B:266-269
68 atoms, 70 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 17 residues
Drag select of 2 residues
> select up
417 atoms, 425 bonds, 26 residues, 1 model selected
> select clear
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_0.cif
Chain information for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_0.cif #2
---
Chain | Description
A | .
B | .
> close #1
> color bychain
> select clear
> color bypolymer
> select protein
4838 atoms, 4963 bonds, 598 residues, 1 model selected
> select clear
> color dim gray
> select clear
> select protein
4838 atoms, 4963 bonds, 598 residues, 1 model selected
> color sel bypolymer
> color sel bychain
> select clear
> select /A:26
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
123 atoms, 122 bonds, 16 residues, 1 model selected
> select up
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> select clear
Alignment identifier is 2/A
Alignment identifier is 2/B
> ui tool show Contacts
> contacts resSeparation 8 interModel false intraMol false ignoreHiddenModels
> true select true color #c349c3 dashes 0 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
514 contacts
atom1 atom2 overlap distance
/B MET 428 CE /A LEU 16 CD2 1.183 2.577
[deleted to fit within ticket limits]
/A PHE 83 CZ /L OLA 1 C8 -0.399 3.919
514 contacts
> select clear
> hide atoms
> close #2.1
> select clear
Drag select of 18 residues
> select up
709 atoms, 723 bonds, 86 residues, 1 model selected
> select up
4838 atoms, 4963 bonds, 598 residues, 1 model selected
> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
204 contacts
atom1 atom2 overlap distance
/A LEU 16 CD2 /B MET 428 CE 1.183 2.577
[deleted to fit within ticket limits]
/B PRO 37 CA /A ASN 35 O -0.399 3.699
204 contacts
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif
Chain information for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif #1
---
Chain | Description
A | .
B | .
> select protein
4838 atoms, 4963 bonds, 598 residues, 1 model selected
Alignment identifier is 1/A
Alignment identifier is 1/B
> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
143 contacts
atom1 atom2 overlap distance
/A LYS 21 CD /B GLU 398 OE2 1.115 2.185
[deleted to fit within ticket limits]
/B ARG 266 CG /A ARG 22 CZ -0.397 3.887
143 contacts
> color sel red
> color sel bychain
> select clear
> select /A:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
338 atoms, 344 bonds, 43 residues, 1 model selected
> color sel byhetero
> select up
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> select down
338 atoms, 344 bonds, 43 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 338 atom styles
> color sel bychain
> select clear
> select /B:420
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B:368
19 atoms, 17 bonds, 2 residues, 1 model selected
> select /B:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:103-131
252 atoms, 259 bonds, 29 residues, 1 model selected
> color sel cyan
> select /A:92
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
152 atoms, 155 bonds, 19 residues, 1 model selected
> select add /A:118
164 atoms, 167 bonds, 20 residues, 1 model selected
> select up
294 atoms, 301 bonds, 36 residues, 1 model selected
> select /A:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:75-103
239 atoms, 247 bonds, 29 residues, 1 model selected
> color sel cyan
> select /A:119
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
142 atoms, 146 bonds, 17 residues, 1 model selected
> select /B:8
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:8
10 atoms, 9 bonds, 1 residue, 1 model selected
> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
3 contacts
atom1 atom2 overlap distance
/B SEP 8 CB /A PRO 41 CB -0.176 3.816
/B SEP 8 N /A PRO 41 CB -0.201 3.721
/B SEP 8 O2P /A PRO 41 CB -0.261 3.561
3 contacts
> select clear
> select /B:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
260 atoms, 267 bonds, 27 residues, 1 model selected
> select up
3815 atoms, 3914 bonds, 473 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue SEP (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.in.mol2 -fi
mol2 -o
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(SEP) ``
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`
(SEP) ``
(SEP) `Info: Finished reading file
(/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.in.mol2);
atoms read (27), bonds read (26).`
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(SEP) ``
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(SEP) `Info: Total number of electrons: 132; net charge: -2`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(SEP) ``
Charges for residue SEP determined
Coulombic values for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif_B SES surface #1.2:
minimum, -20.78, mean -1.07, maximum 12.52
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface
"fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif_B SES surface":
minimum -28.02, mean 4.821e+12, maximum 1.704e+15
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> select clear
> select /A:14
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
338 atoms, 344 bonds, 43 residues, 1 model selected
> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
126 contacts
atom1 atom2 overlap distance
/A LYS 21 CD /B GLU 398 OE2 1.115 2.185
[deleted to fit within ticket limits]
/A ARG 22 CZ /B ARG 266 CG -0.397 3.887
126 contacts
> select clear
> hide surfaces
> select clear
Drag select of 5 atoms, 6 bonds
> select up
8 atoms, 6 bonds, 2 residues, 1 model selected
> select up
40 atoms, 38 bonds, 2 residues, 1 model selected
> select up
5838 atoms, 5913 bonds, 648 residues, 1 model selected
> select down
40 atoms, 38 bonds, 2 residues, 2 models selected
> select clear
> select protein
4838 atoms, 4963 bonds, 126 pseudobonds, 598 residues, 2 models selected
> select ~sel & ##selected
1000 atoms, 950 bonds, 50 residues, 1 model selected
> hide sel atoms
> select clear
> color bychain
Drag select of 2 residues
> select up
445 atoms, 454 bonds, 54 residues, 2 models selected
> select up
3815 atoms, 3914 bonds, 473 residues, 2 models selected
> select clear
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif
Summary of feedback from opening
/Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif
---
notes | Fetching CCD PLM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif
Fetching CCD MYR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/MYR/MYR.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif
#1
---
Chain | Description
A | .
B C D | .
> color dark gray
> select protein
12468 atoms, 12791 bonds, 1544 residues, 1 model selected
> color sel bychain
> color sel bypolymer
Alignment identifier is 1/A
Alignment identifier is 1
> select clear
> select /A:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> color sel orange
> select clear
Drag select of 34 residues
> select clear
Drag select of 55 residues
> select
> /B,C,D:8-15,18-27,36-43,45-67,69-76,79-105,109-134,144-237,244-251,254-269,276-278,284-286,297-305,310-314,375-377,450-472
6771 atoms, 6888 bonds, 822 residues, 1 model selected
> select clear
> select /B,C,D:101
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /B,C,D:101-143
1083 atoms, 1113 bonds, 129 residues, 1 model selected
> select clear
> select /B,C,D:103
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /B,C,D:103-131
756 atoms, 777 bonds, 87 residues, 1 model selected
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif
#1
---
Chain | Description
A | .
B C D | .
> select protein
12468 atoms, 12791 bonds, 1544 residues, 1 model selected
> color sel bychain
> color sel bypolymer
> select clear
Drag select of 13 residues
> select up
175 atoms, 178 bonds, 23 residues, 1 model selected
> select up
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
401 contacts
atom1 atom2 overlap distance
/A ASN 35 CB /C VAL 319 CG2 1.520 2.240
[deleted to fit within ticket limits]
/A PRO 41 CG /D ARG 4 CZ -0.397 3.887
401 contacts
Alignment identifier is 1/A
Alignment identifier is 1
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue SEP (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.in.mol2 -fi
mol2 -o
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(SEP) ``
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`
(SEP) ``
(SEP) `Info: Finished reading file
(/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.in.mol2);
atoms read (29), bonds read (28).`
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(SEP) ``
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(SEP) `Info: Total number of electrons: 134; net charge: -2`
(SEP) ``
(SEP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(SEP) ``
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(SEP) ``
Charges for residue SEP determined
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_A
SES surface #1.2: minimum, -16.29, mean -1.79, maximum 11.14
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_B
SES surface #1.3: minimum, -18.79, mean -1.13, maximum 11.88
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_C
SES surface #1.4: minimum, -19.34, mean -1.13, maximum 11.59
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_D
SES surface #1.5: minimum, -19.99, mean -1.27, maximum 12.70
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 9 residues
> select up
1243 atoms, 1264 bonds, 170 residues, 4 models selected
> select clear
> select /A:33
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:33-42
83 atoms, 86 bonds, 10 residues, 1 model selected
> select clear
> hide surfaces
> select /B,C,D:103
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /B,C,D:103-131
756 atoms, 777 bonds, 87 residues, 1 model selected
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_2.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_2.cif
#1
---
Chain | Description
A | .
B C D | .
> select /C:260
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> show sel atoms
> style sel sphere
Changed 7 atom styles
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
#1
---
Chain | Description
A | .
B C D | .
Drag select of 7 residues
Alignment identifier is 1
> select clear
Drag select of 2 residues
> select clear
> select /D:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select /D:227@CG1
1 atom, 1 residue, 1 model selected
> select add /D:227@CA
1 atom, 1 bond, 1 residue, 1 model selected
> select add /D:227@C
2 atoms, 1 bond, 1 residue, 1 model selected
> ui mousemode right "bond rotation"
> torsion /D:227@C /D:227@CA /D:227@N /D:226@C -103.11
> torsion /D:227@CD1,CG1,CB,CA -173.00
> torsion /D:227@CG1,CB,CA,N -64.22
> torsion /D:228@N /D:227@C /D:227@CA /D:227@N -30.05
> torsion /D:228@N /D:227@C /D:227@CA /D:227@N -22.69
> torsion /D:228@N /D:227@C /D:227@CA /D:227@N 45.49
> select clear
> select /B:225
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99952,0.019386,0.024107,2.0948,-0.020453,0.99879,0.044825,0.59157,-0.023209,-0.045297,0.9987,-4.0796
> ui mousemode right "bond rotation"
> show sel atoms
> style sel ball
Changed 9 atom styles
> hide sel cartoons
> torsion /B:226@N /B:225@C /B:225@CA /B:225@N -152.18
> torsion /B:226@N /B:225@C /B:225@CA /B:225@N -127.15
> select /C:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> torsion /C:227@CG1,CB,CA,N -1.03
> torsion /C:227@CG1,CB,CA,N -20.17
> hide sel cartoons
> torsion /C:227@CG1,CB,CA,N -4.48
> torsion /C:227@C /C:227@CA /C:227@N /C:226@C -78.98
> torsion /C:227@C /C:227@CA /C:227@N /C:226@C -165.65
> select /B,C,D:103
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /B,C,D:103-159
1428 atoms, 1470 bonds, 171 residues, 1 model selected
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
#1
---
Chain | Description
A | .
B C D | .
Alignment identifier is 1/A
Alignment identifier is 1
> select /B,C,D:103
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /B,C,D:103-131
756 atoms, 777 bonds, 87 residues, 1 model selected
Drag select of 72 residues
> show sel atoms
> hide sel cartoons
> select clear
> color bychain
> color bypolymer
> select clear
> color bychain
> select clear
Drag select of 275 atoms, 276 bonds
> cofr sel
> select clear
Drag select of 18 atoms, 16 bonds
> select clear
> style ball
Changed 15168 atom styles
> color byhetero
> select clear
> select /C:227@O
1 atom, 1 residue, 1 model selected
> select /C:227@C
1 atom, 1 residue, 1 model selected
> select /C:227@CA
1 atom, 1 residue, 1 model selected
> close
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
#1
---
Chain | Description
A | .
B C D | .
> select /A:1-125
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 1023 atom styles
> color sel byhetero
> select clear
Drag select of 27 residues
> select up
3377 atoms, 3442 bonds, 428 residues, 1 model selected
> select up
11445 atoms, 11742 bonds, 1419 residues, 1 model selected
> hide #1 models
> show #1 models
> hide sel cartoons
> select clear
Drag select of 213 atoms, 43 residues
> select up
398 atoms, 404 bonds, 47 residues, 1 model selected
> select up
767 atoms, 783 bonds, 93 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> select clear
Drag select of 43 atoms, 9 residues
> select up
208 atoms, 216 bonds, 25 residues, 1 model selected
> select up
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of 3 residues
> select up
73 atoms, 77 bonds, 8 residues, 1 model selected
> select up
1023 atoms, 1049 bonds, 125 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 3509 atoms, 3348 bonds
> select up
5955 atoms, 5881 bonds, 550 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 358 atoms, 370 bonds
> select clear
Drag select of 218 atoms, 226 bonds
Drag select of 274 atoms, 277 bonds
> select up
505 atoms, 507 bonds, 73 residues, 1 model selected
> select up
567 atoms, 575 bonds, 73 residues, 1 model selected
> select up
2322 atoms, 2376 bonds, 285 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of 32 atoms, 32 bonds
> select up
36 atoms, 32 bonds, 7 residues, 1 model selected
> select up
51 atoms, 50 bonds, 7 residues, 1 model selected
> select up
159 atoms, 159 bonds, 22 residues, 1 model selected
> select protein
12468 atoms, 12791 bonds, 1544 residues, 1 model selected
> hide sel atoms
Drag select of 2700 atoms, 2550 bonds
> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 8 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
3359 contacts
atom1 atom2 overlap distance
/M OLA 1 C18 /GB PLM 1 CG 2.142 1.618
[deleted to fit within ticket limits]
/EC PLM 1 CG /FA OLA 1 C17 -0.400 4.040
3359 contacts
Drag select of 2700 atoms, 2550 bonds, 3359 pseudobonds
> ui tool show Clashes
> clashes sel restrict both interModel false select true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
180 clashes
atom1 atom2 overlap distance
/M OLA 1 C18 /GB PLM 1 CG 2.142 1.618
[deleted to fit within ticket limits]
/IC PLM 1 CG /KC PLM 1 CF 0.601 3.159
180 clashes
> select clear
> close #1.1-2
> select clear
> show cartoons
> color bypolymer
> rainbow
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202405110020 (2024-05-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
#1
---
Chain | Description
A | .
B C D | .
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
System Firmware Version: 522.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.33f12
Software:
System Software Overview:
System Version: macOS 12.7.1 (21G920)
Kernel Version: Darwin 21.6.0
Time since boot: 19 days 23:36
Graphics/Displays:
AMD Radeon R9 M380:
Chipset Model: AMD Radeon R9 M380
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6640
Revision ID: 0x0080
ROM Revision: 113-C6005R-800
VBIOS Version: 113-C6005T-009
EFI Driver Version: 01.00.800
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
EV2336W:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 80101073
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.3
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202405110020
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.1
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.3.3
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.1
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (1)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
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