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Opened 18 months ago
Closed 18 months ago
#15052 closed defect (duplicate)
Crash in python_instances_of_class
| 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
The following bug report has been submitted:
Platform: macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 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 0x00007ff848460100 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.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_Daily.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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._flinalg, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 123)
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{
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"captureTime" : "2024-04-27 16:23:55.4614 +0100",
"codeSigningMonitor" : 0,
"incident" : "7D1D0849-CED6-4972-A0E6-49C3EB1B34C3",
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"procLaunch" : "2024-04-27 14:25:52.3235 +0100",
"procStartAbsTime" : 177903338396559,
"procExitAbsTime" : 184986188012100,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"vmRegionInfo" : "0x101 is not in any region. Bytes before following region: 4531207935\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10e14c000-10e150000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000101","rawCodes":[1,257],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000101"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":93870},
"vmregioninfo" : "0x101 is not in any region. Bytes before following region: 4531207935\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10e14c000-10e150000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gghanim/Desktop/full_structure.cxs
Log from Sat Apr 27 14:05:57 2024
> set bgColor white
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false initialColors dark grey
> saveSettings true
Saved volume settings
> mousemode rightMode "translate selected models"
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; size
> ballscale 0.1; size stickradius 0.07; transparency 70; cofr centerofview;
> clip near -10 far 10 position cofr; color ##~num_residues cornflower blue;
> cofron;
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; style nucleic stick; display nucleic; clip off; set bgColor
> white; size ballscale 0.3 stickradius 0.2; cofroff; color ##~num_residues
> dark grey
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add "Vol. Viewer" command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add "Model Panel" command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add "Default Disp." command default_mol_display
> buttonpanel Shortcuts add "Map Sphere" command map_sphere_15
> buttonpanel Shortcuts add "Map Unsphere" command map_unsphere
> buttonpanel Shortcuts add "Center On" command cofron
> buttonpanel Shortcuts add "Center Off" command cofroff
> buttonpanel Shortcuts add "Coot Mode" command cootmode
> buttonpanel Shortcuts add "Mark Center" command "marker #10000 position
> cofr"
> buttonpanel Shortcuts add "Hide Dust" command "surface dust all"
> buttonpanel Shortcuts add "Show Dust" command "surface undust all"
> buttonpanel Shortcuts add "Color Grey" command "sel; sel sel-residues; sel
> ~sel; color sel dark grey target s; ~sel"
> buttonpanel Shortcuts add "Morph Maps" command "color all cornflower
> blue;material dull;volume morph #1-20 playStep 0.08 frames 200
> constantVolume true"
> alias reset ~tile; view initial; view orient
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gghanim/Desktop/python_script/tp_af_sub_output.pdb
Chain information for tp_af_sub_output.pdb #1
---
Chain | Description
B | No description available
D | No description available
> open /Users/gghanim/Desktop/python_script/tp_af_del_output.pdb
Chain information for tp_af_del_output.pdb #2
---
Chain | Description
B | No description available
D | No description available
> select /B
3674 atoms, 3738 bonds, 488 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 3 time(s)]
> ui tool show "Render by Attribute"
> color byattribute a:bfactor target cabs palette
> -99.66,blue:5.32907e-15,white:18.58,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette
> -100,blue:68.5724,white:100,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette -100,blue:0,white:100,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> hide #2 models
> show #2 models
> hide #1 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> select clear
Already setting window visible!
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> show #1 models
> hide #2 models
> show #2 models
> tile
2 models tiled
> select @@bfactor=0
4037 atoms, 3959 bonds, 520 residues, 2 models selected
> color sel grey
> select clear
> cylinders
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> reset
> hide #2 models
> show #2 models
> hide #1 models
> reset
> view name front
[Repeated 1 time(s)]
> ui tool show "Side View"
> view name front
> turn x 10
> turn x -10
> turn y -10
> turn y 10
> turn y 90
> view name side
> turn y -90
> turn y 45
> view name 45
> turn y -45
[Repeated 1 time(s)]
> view name -45
> vie4 45
Unknown command: vie4 45
> view 45
> view name 45
> view 45
> view -45
> view front
> hide #2 models
> show #1 models
> show #2 models
> save /Users/gghanim/Desktop/full_structure.cxs
> hide #2 models
> view -45
> view 45
> save /Users/gghanim/Desktop/image1.png supersample 3
> view front
> save /Users/gghanim/Desktop/image2.png supersample 3
> view -45
> save /Users/gghanim/Desktop/image3.png supersample 3
> view front
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/gghanim/Desktop/movie1.mp4
Movie saved to /Users/gghanim/Desktop/movie1.mp4
> select #1
5023 atoms, 5134 bonds, 634 residues, 1 model selected
> cofr sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/gghanim/Desktop/movie2.mp4
Movie saved to /Users/gghanim/Desktop/movie2.mp4
> lighting soft
> graphics silhouettes true
> select clear
> view front
> view name front
[Repeated 1 time(s)]
> save /Users/gghanim/Desktop/image1.png supersample 3
> turn y 45
> view 45
> view -45
> view 45
> save /Users/gghanim/Desktop/image2.png supersample 3
> view -45
> save /Users/gghanim/Desktop/image3.png supersample 3
> save /Users/gghanim/Desktop/full_structure.cxs
> show #2 models
> hide #1 models
> view front
> view 45
> view -45
> save /Users/gghanim/Desktop/image1.png supersample 3
> view front
> save /Users/gghanim/Desktop/image2.png supersample 3
> view 45nt
Expected an objects specifier or a view name or a keyword
> view 45
> save /Users/gghanim/Desktop/image3.png supersample 3
> save /Users/gghanim/Desktop/full_structure.cxs
——— End of log from Sat Apr 27 14:05:57 2024 ———
opened ChimeraX session
> ui tool show "Render by Attribute"
> show #1 models
> hide #2 models
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> undo
> redo
> select @@bfactor=0
4039 atoms, 3959 bonds, 522 residues, 2 models selected
> color grey
> color sel grey
> select clear
> show #2 models
> hide #2 models
> reset
> select @@bfactor show sel & #1 cartoons
> show sel & #1 atoms
> select clear
> color #1 byhetero
> select clear
> open 8SH0
Summary of feedback from opening 8SH0 fetched from pdb
---
note | Fetching compressed mmCIF 8sh0 from http://files.rcsb.org/download/8sh0.cif
8sh0 title:
Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated
junction of a telomeric DNA hairpin with a 3'-overhang [more info...]
Chain information for 8sh0 #3
---
Chain | Description | UniProt
A | Protection of telomeres protein 1 | POTE1_HUMAN 1-299
B | DNA (5'-D(P*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3') |
Non-standard residues in 8sh0 #3
---
ACT — acetate ion
> open 8SH1
Summary of feedback from opening 8SH1 fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for DC /B:-9
Atom OP2 has no neighbors to form bonds with according to residue template for
DC /B:-9
note | Fetching compressed mmCIF 8sh1 from http://files.rcsb.org/download/8sh1.cif
8sh1 title:
Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated
junction of a telomeric double-stranded DNA duplex with a 3'-overhang [more
info...]
Chain information for 8sh1 #4
---
Chain | Description | UniProt
A | Protection of telomeres protein 1 | POTE1_HUMAN 1-299
B | DNA (5'-D(*CP*GP*CP*GP*CP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3') |
C | DNA (5'-D(P*CP*TP*AP*AP*CP*GP*CP*GP*CP*G)-3') |
> cylinders
> ui tool show Matchmaker
> matchmaker #!3-4 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 tp_af_sub_output.pdb, chain D (#1) with 8sh0, chain A (#3),
sequence alignment score = 1461.7
RMSD between 281 pruned atom pairs is 0.645 angstroms; (across all 294 pairs:
0.972)
Matchmaker tp_af_sub_output.pdb, chain D (#1) with 8sh1, chain A (#4),
sequence alignment score = 1433.5
RMSD between 280 pruned atom pairs is 0.612 angstroms; (across all 293 pairs:
1.613)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> lighting simple
> select nucleic
1084 atoms, 1214 bonds, 33 pseudobonds, 52 residues, 4 models selected
> hide sel & #!4 cartoons
> nucleotides sel & #!4 fill
> style nucleic & sel & #!4 stick
Changed 664 atom styles
> color cornflower blue
> color nucleic cornflower blue
> select clear
> color byhetero
> select #1
5023 atoms, 5134 bonds, 634 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for tp_af_sub_output.pdb_D SES surface #1.1: minimum, -17.74,
mean -1.83, maximum 13.33
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency #4 50 target s
> transparency #1 50 target s
> select #4
3042 atoms, 3129 bonds, 27 pseudobonds, 370 residues, 2 models selected
> show sel atoms
> select clear
> hide #!1 models
> close #3
> select ::name="HOH"
45 atoms, 45 residues, 1 model selected
> select HOH
Expected an objects specifier or a keyword
> select ::name="HOH"
45 atoms, 45 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4/B:-9@OP1
1 atom, 1 residue, 1 model selected
> select add #4/B:-9@OP2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/gghanim/Desktop/8sh1.pdb models #4 relModel #1
> hide #2#!1,4 target m
> close #2#1,4
> open /Users/gghanim/Desktop/python_script/8sh1_sub_output.pdb
Chain information for 8sh1_sub_output.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/gghanim/Desktop/python_script/8sh1_del_output.pdb
Chain information for 8sh1_del_output.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show "Render by Attribute"
> cylinders
> nucleotides fill
> style nucleic stick
Changed 1328 atom styles
> color byattribute a:bfactor target csab palette -20,blue:0,white:20,red
6084 atoms, 740 residues, atom bfactor range -99.7 to 18.6
> color nucleic cornflower blue
> select clear
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> color byattribute a:bfactor #1 target csab palette
> -99.3818,blue:-1.18266,white:18.58,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette
> -99.3818,blue:-1.18266,white:18.58,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -100,blue:0,white:100,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> show #2 models
> hide #1 models
> color byattribute a:bfactor #2 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 16.6
> show #1 models
> hide #2 models
> select @@bfactor =0
3533 atoms, 3603 bonds, 387 residues, 2 models selected
> color sel grey
> select clear
> save /Users/gghanim/Desktop/pothole.cxs
> select @@bfactor show sel & #1 atoms
> select clear
> color byhetero
> select nucleic
1328 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel grey
> select clear
> select ::name="HOH"
90 atoms, 90 residues, 2 models selected
> delete atoms (#1 & sel)
> delete bonds (#1 & sel)
> select nucleric
Expected an objects specifier or a keyword
> select nucleic
1328 atoms, 1484 bonds, 64 residues, 2 models selected
> hide sel & #1 cartoons
> select clear
> select #1/B:-9@OP1
1 atom, 1 residue, 1 model selected
> select add #1/B:-9@OP2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> coulombic sel & #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8sh1_sub_output.pdb_A SES surface #1.1: minimum, -11.40,
mean -0.12, maximum 14.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency #1 50 target s
> select clear
> hide #1.1 models
> select #1:9,80,82,83
86 atoms, 88 bonds, 6 residues, 1 model selected
> select #1/A:9,80,82,83
44 atoms, 43 bonds, 4 residues, 1 model selected
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel byhetero
> select clear
> undo
> redo
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel grey
> select clear
> select add #1/C:0@O5'
1 atom, 1 residue, 1 model selected
> select add #1/C:0@OP2
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/C:0@OP3
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/C:0@P
4 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/C:0@OP1
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select add #1/A:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:7
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:8
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel cartoons
> cofron
> select #1
2995 atoms, 3129 bonds, 325 residues, 1 model selected
> show sel cartoons
> undo
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> show sel & #!1 cartoons
> select clear
> cofroff
> view name ph
> ui tool show "Side View"
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> show sel & #!1 cartoons
> select clear
> select #1/C:0
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> camera
Camera parameters:
type: orthographic
position: 43.015 -62.988 67.879
view direction: -0.33779 0.32311 -0.88402
field width: 35.056
> camera mono
> view name ph
> show #1.1 models
> hide #!1.1 models
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> mlp sel & #!1
Map values for surface "8sh1_sub_output.pdb_A SES surface": minimum -29.41,
mean -4.283, maximum 21.55
To also show corresponding color key, enter the above mlp command and add key
true
> transparency #1 50 target s
> select clear
> hide #!1.1 models
> view ph
> coulombic #!1
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 162, in copy
m._copy_custom_attrs(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'Chain' object has no attribute '_c_pointer_ref'
AttributeError: 'Chain' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> coulombic sel & #!1
Coulombic values for 8sh1_sub_output.pdb_A SES surface #1.1: minimum, -11.40,
mean -0.12, maximum 14.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency #1 50 target s
> select clear
> hide #!1.1 models
> view ph
> view name ph2
> select add #1/A:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:7
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:8
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #1/A:9
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add #1/A:10
40 atoms, 36 bonds, 5 residues, 2 models selected
> select subtract #1/A:10
32 atoms, 29 bonds, 4 residues, 2 models selected
> hide sel cartoons
> select clear
> view name ph2
> select add #1/A:116
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:115
15 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> view ph2
> save /Users/gghanim/Desktop/image1.png supersample 3
> save /Users/gghanim/Desktop/pothole.cxs
> lighting soft
> select clear
> save /Users/gghanim/Desktop/image1.png supersample 3
> show #1.1 models
> select clear
> view ph
> view ph2
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> show sel & #!1 cartoons
> select clear
> select add #1/A:8@ND2
1 atom, 1 residue, 1 model selected
> select subtract #1/A:8@ND2
1 model selected
> hide #!1.1 models
> select add #1/A:116
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:115
15 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel cartoons
> show #1.1 models
> select clear
> transparency #1 30 target s
> transparency #1 600 target s
> transparency #1 60 target s
> transparency #1 70 target s
> transparency #1 60 target s
> view ph2
> view name ph3
> save /Users/gghanim/Desktop/image1.png supersample 3
> hide #!1.1 models
> save /Users/gghanim/Desktop/image2.png supersample 3
> show #1.1 models
> turn y 10
> turn y -10
> turn y 60
> turn y -60
> turn y 900
> turn y 90
> turn y 45
> turn y 60
> view ph3
> turn y -10
> turn x -10
> turn x 10
> hide #!1.1 models
> select #1/A:113
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:111
11 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:110
19 atoms, 17 bonds, 3 residues, 2 models selected
> select add #1/A:114
27 atoms, 24 bonds, 4 residues, 2 models selected
> hide sel cartoons
> lighting soft
> view name ph4
> show #1.1 models
> select clear
> turn y 30
> view matrix models
> #1,0.99998,0.0042508,-0.0051712,-0.22053,-0.0042243,0.99998,0.0051227,0.28475,0.0051928,-0.0051007,0.99997,-0.082242
> undo
> select add #1/B:-3
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select add #1/B:-4
42 atoms, 45 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> save /Users/gghanim/Desktop/image3.png supersample 3
> view name phview
> turn y -30
> save /Users/gghanim/Desktop/image4.png supersample 3
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> show sel & #!1 cartoons
> undo
> select subtract #1/C:1
1306 atoms, 1461 bonds, 63 residues, 2 models selected
> select #1/B
457 atoms, 513 bonds, 22 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select clear
> save /Users/gghanim/Desktop/image5.png supersample 3
> hide #!1.1 models
> select add #1/A:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/A:118
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #1/A:120
24 atoms, 21 bonds, 3 residues, 2 models selected
> hide sel cartoons
> select clear
> select add #1/A:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:7
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:8
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #1/A:10
28 atoms, 24 bonds, 4 residues, 2 models selected
> select add #1/A:9
40 atoms, 36 bonds, 5 residues, 2 models selected
> hide sel cartoons
> select add #1/A:121
49 atoms, 44 bonds, 6 residues, 2 models selected
> select add #1/A:122
61 atoms, 56 bonds, 7 residues, 2 models selected
> select add #1/A:123
72 atoms, 67 bonds, 8 residues, 2 models selected
> select add #1/A:125
83 atoms, 78 bonds, 9 residues, 2 models selected
> select add #1/A:124
91 atoms, 85 bonds, 10 residues, 2 models selected
> hide sel cartoons
> select clear
> undo
> redo
> select #1/A:112
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> save /Users/gghanim/Desktop/image6.png supersample 3
> show #1.1 models
> save /Users/gghanim/Desktop/image7.png supersample 3
> turn y -60
> turn y 60
> select clear
> save /Users/gghanim/Desktop/image8.png supersample 3
> save /Users/gghanim/Desktop/pothole2.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gghanim/Desktop/pothole.cxs
Log from Sat Apr 27 16:09:14 2024UCSF ChimeraX version: 1.8.dev202403271703
(2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/gghanim/Desktop/full_structure.cxs
Log from Sat Apr 27 14:05:57 2024
> set bgColor white
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false initialColors dark grey
> saveSettings true
Saved volume settings
> mousemode rightMode "translate selected models"
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; size
> ballscale 0.1; size stickradius 0.07; transparency 70; cofr centerofview;
> clip near -10 far 10 position cofr; color ##~num_residues cornflower blue;
> cofron;
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; style nucleic stick; display nucleic; clip off; set bgColor
> white; size ballscale 0.3 stickradius 0.2; cofroff; color ##~num_residues
> dark grey
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add "Vol. Viewer" command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add "Model Panel" command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add "Default Disp." command default_mol_display
> buttonpanel Shortcuts add "Map Sphere" command map_sphere_15
> buttonpanel Shortcuts add "Map Unsphere" command map_unsphere
> buttonpanel Shortcuts add "Center On" command cofron
> buttonpanel Shortcuts add "Center Off" command cofroff
> buttonpanel Shortcuts add "Coot Mode" command cootmode
> buttonpanel Shortcuts add "Mark Center" command "marker #10000 position
> cofr"
> buttonpanel Shortcuts add "Hide Dust" command "surface dust all"
> buttonpanel Shortcuts add "Show Dust" command "surface undust all"
> buttonpanel Shortcuts add "Color Grey" command "sel; sel sel-residues; sel
> ~sel; color sel dark grey target s; ~sel"
> buttonpanel Shortcuts add "Morph Maps" command "color all cornflower
> blue;material dull;volume morph #1-20 playStep 0.08 frames 200
> constantVolume true"
> alias reset ~tile; view initial; view orient
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gghanim/Desktop/python_script/tp_af_sub_output.pdb
Chain information for tp_af_sub_output.pdb #1
---
Chain | Description
B | No description available
D | No description available
> open /Users/gghanim/Desktop/python_script/tp_af_del_output.pdb
Chain information for tp_af_del_output.pdb #2
---
Chain | Description
B | No description available
D | No description available
> select /B
3674 atoms, 3738 bonds, 488 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 3 time(s)]
> ui tool show "Render by Attribute"
> color byattribute a:bfactor target cabs palette
> -99.66,blue:5.32907e-15,white:18.58,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette
> -100,blue:68.5724,white:100,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette -100,blue:0,white:100,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> hide #2 models
> show #2 models
> hide #1 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> select clear
Already setting window visible!
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor target cabs palette -20,blue:0,white:20,red
10046 atoms, 1268 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> color byattribute a:bfactor #2 target cabs palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 16.6
> show #1 models
> hide #2 models
> show #2 models
> tile
2 models tiled
> select @@bfactor=0
4037 atoms, 3959 bonds, 520 residues, 2 models selected
> color sel grey
> select clear
> cylinders
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> reset
> hide #2 models
> show #2 models
> hide #1 models
> reset
> view name front
[Repeated 1 time(s)]
> ui tool show "Side View"
> view name front
> turn x 10
> turn x -10
> turn y -10
> turn y 10
> turn y 90
> view name side
> turn y -90
> turn y 45
> view name 45
> turn y -45
[Repeated 1 time(s)]
> view name -45
> vie4 45
Unknown command: vie4 45
> view 45
> view name 45
> view 45
> view -45
> view front
> hide #2 models
> show #1 models
> show #2 models
> save /Users/gghanim/Desktop/full_structure.cxs
> hide #2 models
> view -45
> view 45
> save /Users/gghanim/Desktop/image1.png supersample 3
> view front
> save /Users/gghanim/Desktop/image2.png supersample 3
> view -45
> save /Users/gghanim/Desktop/image3.png supersample 3
> view front
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/gghanim/Desktop/movie1.mp4
Movie saved to /Users/gghanim/Desktop/movie1.mp4
> select #1
5023 atoms, 5134 bonds, 634 residues, 1 model selected
> cofr sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/gghanim/Desktop/movie2.mp4
Movie saved to /Users/gghanim/Desktop/movie2.mp4
> lighting soft
> graphics silhouettes true
> select clear
> view front
> view name front
[Repeated 1 time(s)]
> save /Users/gghanim/Desktop/image1.png supersample 3
> turn y 45
> view 45
> view -45
> view 45
> save /Users/gghanim/Desktop/image2.png supersample 3
> view -45
> save /Users/gghanim/Desktop/image3.png supersample 3
> save /Users/gghanim/Desktop/full_structure.cxs
> show #2 models
> hide #1 models
> view front
> view 45
> view -45
> save /Users/gghanim/Desktop/image1.png supersample 3
> view front
> save /Users/gghanim/Desktop/image2.png supersample 3
> view 45nt
Expected an objects specifier or a view name or a keyword
> view 45
> save /Users/gghanim/Desktop/image3.png supersample 3
> save /Users/gghanim/Desktop/full_structure.cxs
——— End of log from Sat Apr 27 14:05:57 2024 ———
opened ChimeraX session
> ui tool show "Render by Attribute"
> show #1 models
> hide #2 models
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
5023 atoms, 634 residues, atom bfactor range -99.7 to 18.6
> undo
> redo
> select @@bfactor=0
4039 atoms, 3959 bonds, 522 residues, 2 models selected
> color grey
> color sel grey
> select clear
> show #2 models
> hide #2 models
> reset
> select @@bfactor<0
2962 atoms, 2883 bonds, 362 residues, 2 models selected
> show sel & #1 cartoons
> show sel & #1 atoms
> select clear
> color #1 byhetero
> select clear
> open 8SH0
Summary of feedback from opening 8SH0 fetched from pdb
---
note | Fetching compressed mmCIF 8sh0 from http://files.rcsb.org/download/8sh0.cif
8sh0 title:
Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated
junction of a telomeric DNA hairpin with a 3'-overhang [more info...]
Chain information for 8sh0 #3
---
Chain | Description | UniProt
A | Protection of telomeres protein 1 | POTE1_HUMAN 1-299
B | DNA (5'-D(P*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3') |
Non-standard residues in 8sh0 #3
---
ACT — acetate ion
> open 8SH1
Summary of feedback from opening 8SH1 fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for DC /B:-9
Atom OP2 has no neighbors to form bonds with according to residue template for
DC /B:-9
note | Fetching compressed mmCIF 8sh1 from http://files.rcsb.org/download/8sh1.cif
8sh1 title:
Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated
junction of a telomeric double-stranded DNA duplex with a 3'-overhang [more
info...]
Chain information for 8sh1 #4
---
Chain | Description | UniProt
A | Protection of telomeres protein 1 | POTE1_HUMAN 1-299
B | DNA (5'-D(*CP*GP*CP*GP*CP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3') |
C | DNA (5'-D(P*CP*TP*AP*AP*CP*GP*CP*GP*CP*G)-3') |
> cylinders
> ui tool show Matchmaker
> matchmaker #!3-4 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 tp_af_sub_output.pdb, chain D (#1) with 8sh0, chain A (#3),
sequence alignment score = 1461.7
RMSD between 281 pruned atom pairs is 0.645 angstroms; (across all 294 pairs:
0.972)
Matchmaker tp_af_sub_output.pdb, chain D (#1) with 8sh1, chain A (#4),
sequence alignment score = 1433.5
RMSD between 280 pruned atom pairs is 0.612 angstroms; (across all 293 pairs:
1.613)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> lighting simple
> select nucleic
1084 atoms, 1214 bonds, 33 pseudobonds, 52 residues, 4 models selected
> hide sel & #!4 cartoons
> nucleotides sel & #!4 fill
> style nucleic & sel & #!4 stick
Changed 664 atom styles
> color cornflower blue
> color nucleic cornflower blue
> select clear
> color byhetero
> select #1
5023 atoms, 5134 bonds, 634 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for tp_af_sub_output.pdb_D SES surface #1.1: minimum, -17.74,
mean -1.83, maximum 13.33
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency #4 50 target s
> transparency #1 50 target s
> select #4
3042 atoms, 3129 bonds, 27 pseudobonds, 370 residues, 2 models selected
> show sel atoms
> select clear
> hide #!1 models
> close #3
> select ::name="HOH"
45 atoms, 45 residues, 1 model selected
> select HOH
Expected an objects specifier or a keyword
> select ::name="HOH"
45 atoms, 45 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4/B:-9@OP1
1 atom, 1 residue, 1 model selected
> select add #4/B:-9@OP2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/gghanim/Desktop/8sh1.pdb models #4 relModel #1
> hide #2#!1,4 target m
> close #2#1,4
> open /Users/gghanim/Desktop/python_script/8sh1_sub_output.pdb
Chain information for 8sh1_sub_output.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/gghanim/Desktop/python_script/8sh1_del_output.pdb
Chain information for 8sh1_del_output.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show "Render by Attribute"
> cylinders
> nucleotides fill
> style nucleic stick
Changed 1328 atom styles
> color byattribute a:bfactor target csab palette -20,blue:0,white:20,red
6084 atoms, 740 residues, atom bfactor range -99.7 to 18.6
> color nucleic cornflower blue
> select clear
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> color byattribute a:bfactor #1 target csab palette
> -99.3818,blue:-1.18266,white:18.58,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette
> -99.3818,blue:-1.18266,white:18.58,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -100,blue:0,white:100,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> color byattribute a:bfactor #1 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 18.6
> show #2 models
> hide #1 models
> color byattribute a:bfactor #2 target csab palette -20,blue:0,white:20,red
3042 atoms, 370 residues, atom bfactor range -99.7 to 16.6
> show #1 models
> hide #2 models
> select @@bfactor =0
3533 atoms, 3603 bonds, 387 residues, 2 models selected
> color sel grey
> select clear
> save /Users/gghanim/Desktop/pothole.cxs
> select @@bfactor<0
1420 atoms, 1383 bonds, 181 residues, 2 models selected
> show sel & #1 atoms
> select clear
> color byhetero
> select nucleic
1328 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel grey
> select clear
> select ::name="HOH"
90 atoms, 90 residues, 2 models selected
> delete atoms (#1 & sel)
> delete bonds (#1 & sel)
> select nucleric
Expected an objects specifier or a keyword
> select nucleic
1328 atoms, 1484 bonds, 64 residues, 2 models selected
> hide sel & #1 cartoons
> select clear
> select #1/B:-9@OP1
1 atom, 1 residue, 1 model selected
> select add #1/B:-9@OP2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> coulombic sel & #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8sh1_sub_output.pdb_A SES surface #1.1: minimum, -11.40,
mean -0.12, maximum 14.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency #1 50 target s
> select clear
> hide #1.1 models
> select #1:9,80,82,83
86 atoms, 88 bonds, 6 residues, 1 model selected
> select #1/A:9,80,82,83
44 atoms, 43 bonds, 4 residues, 1 model selected
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel byhetero
> select clear
> undo
[Repeated 1 time(s)]
> redo
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> color sel grey
> select clear
> select add #1/C:0@O5'
1 atom, 1 residue, 1 model selected
> select add #1/C:0@OP2
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #1/C:0@OP3
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/C:0@P
4 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1/C:0@OP1
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select add #1/A:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:7
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:8
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel cartoons
> cofron
> select #1
2995 atoms, 3129 bonds, 325 residues, 1 model selected
> show sel cartoons
> undo
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> show sel & #!1 cartoons
> select clear
> cofroff
> view name ph
> ui tool show "Side View"
> select nucleic
1326 atoms, 1484 bonds, 64 residues, 2 models selected
> show sel & #!1 cartoons
> select clear
> select #1/C:0
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> camera
Camera parameters:
type: orthographic
position: 43.015 -62.988 67.879
view direction: -0.33779 0.32311 -0.88402
field width: 35.056
> camera mono
> view name ph
> show #1.1 models
> hide #!1.1 models
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> mlp sel & #!1
Map values for surface "8sh1_sub_output.pdb_A SES surface": minimum -29.41,
mean -4.283, maximum 21.55
To also show corresponding color key, enter the above mlp command and add key
true
> transparency #1 50 target s
> select clear
> hide #!1.1 models
> view ph
> coulombic #!1
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run
f(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 162, in copy
m._copy_custom_attrs(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'Chain' object has no attribute '_c_pointer_ref'
AttributeError: 'Chain' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select protein
4666 atoms, 4774 bonds, 586 residues, 2 models selected
> coulombic sel & #!1
Coulombic values for 8sh1_sub_output.pdb_A SES surface #1.1: minimum, -11.40,
mean -0.12, maximum 14.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> transparency #1 50 target s
> select clear
> hide #!1.1 models
> view ph
> view name ph2
> select add #1/A:6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/A:7
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #1/A:8
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #1/A:9
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add #1/A:10
40 atoms, 36 bonds, 5 residues, 2 models selected
> select subtract #1/A:10
32 atoms, 29 bonds, 4 residues, 2 models selected
> hide sel cartoons
> select clear
> view name ph2
> select add #1/A:116
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:115
15 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> view ph2
> save /Users/gghanim/Desktop/image1.png supersample 3
> save /Users/gghanim/Desktop/pothole.cxs
——— End of log from Sat Apr 27 16:09:14 2024 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 570X 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: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 64 GB
System Firmware Version: 2020.80.5.0.0
OS Loader Version: 580~1678
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 2 days, 3 hours, 28 minutes
Graphics/Displays:
Radeon Pro 570X:
Chipset Model: Radeon Pro 570X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A14GL-003
EFI Driver Version: 01.B1.042
Metal Support: Metal 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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
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: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
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: 1.8.dev202403271703
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
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-ISOLDE: 1.8.dev0
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: 1.1.4
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: 2.1.3
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
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: 1.13.3
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: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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: 1.0
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: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.1
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: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
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: 3.1.3
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: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
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: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
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: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
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 (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi George,
--Eric