id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15052	Crash in python_instances_of_class	gghanim@…	Eric Pettersen	"{{{
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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}
===== 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

}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX