id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14593	Crash in garbage collection	haaris.safdari@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202307312254 (2023-07-31 22:54:15 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070000fc1e000 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00007ff84a41db80 (most recent call first):
  Garbage-collecting
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 515 in _cursor_position
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 472 in mouse_pause_tracking
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 140 in _redraw_timer_callback
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 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 1044 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, 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, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 53)


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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.0G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           252K       19 \nColorSync                          240K       30 \nCoreAnimation                      788K      109 \nCoreGraphics                        16K        3 \nCoreUI image data                 5344K       45 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.5G      102 \nMALLOC guard page                   96K       24 \nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        116K       29 \nStack                            173.2M       30 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      198.2M      240 \nVM_ALLOCATE (reserved)            96.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            54.9M      784 \n__DATA_CONST                      56.8M      425 \n__DATA_DIRTY                      1701K      225 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       212.7M      146 \n__OBJC_RO                         71.1M        1 \n__OBJC_RW                         2169K        3 \n__TEXT                             1.0G      791 \ndyld private memory                680K        7 \nmapped file                      228.3M       55 \nshared memory                     2988K       27 \n===========                     =======  ======= \nTOTAL                              4.6G     3111 \nTOTAL, minus reserved VM space     4.5G     3111 \n"",
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}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> mousemode shift leftMode ""translate selected models""

> mousemode shift middleMode ""rotate selected models""

> mousemode rightMode zoom

> mousemode control wheelMode ""contour level""

> mousemode setting ""contour level"" speed 0.1

> mousemode shift wheelMode ""rotate selected models""

> camera ortho

> set bgColor grey

> lighting shadows false

> lighting depthCue false

> graphics silhouettes true

> lighting simple

> functionkey F1 cofr sel

> functionkey F2 mousemode rightMode 'mark surface'

> functionkey F3 mousemode rightMode 'move markers'

> functionkey F4 mk 3 1

> functionkey F5 view

> functionkey F6 view sel pad 0.92 clip false

> functionkey F7 mousemode rightMode 'delete markers'

> functionkey F8 mousemode rightMode zoom

> functionkey F9 sequence chain sel

> functionkey F10 transparency sel 65

> functionkey F11 transparency sel 0

> functionkey F12 tool show 'Fit in Map'

> color name f01graublau #BADBED

Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed

  

> color name f02silber #F6FAFC

Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc

  

> color name f03muschel #FFFFE5

Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5

  

> color name f04beige #F3F3A9

Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9

  

> color name f05gelb #f2b701

Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701

  

> color name f06orange #e68310

Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310

  

> color name f07rotorange #FF6A25

Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25

  

> color name f08rot #dd3d2d

Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d

  

> color name f09lachs #f97b72

Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72

  

> color name f10flieder #D57AD5

Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5

  

> color name f11violett #cf1c90

Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90

  

> color name f12lila #4b148f

Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f

  

> color name f13dunkelblau #2E2EF7

Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7

  

> color name f14blau #00AAFF

Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff

  

> color name f15cyan #60e2d6

Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6

  

> color name f16blaugrün #30ffa6

Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6

  

> color name f17grün #00FF00

Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00

  

> color name f18dunkelgrün #228B22

Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  

> color name f19hellgrau #DCDCDC

Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc

  

> color name f20grau #B2B2B2

Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2

  

> color name f21anthrazit #323F45

Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45

  

> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000""
> range $3,$4

> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'

> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'

> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3

> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3

> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3

> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow

> alias chaininfo preset custom chaininfo

> alias foto save browse format tiff height 4000 supersample 4
> transparentBackground false

> alias durch save browse format tiff height 4000 supersample 4
> transparentBackground true

> alias session save browse format session includeMaps true compress lz4

> alias nomapsession save browse format session includeMaps false compress lz4

> alias splitup color zone #$1 near sel sharpEdges true distance $2

> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2

> alias spalt volume splitbyzone #$1

> alias undust surface undust #$1

> alias dust1 surface dust #$1 size 1

> alias dust2 surface dust #$1 size 2

> alias dust3 surface dust #$1 size 3

> alias dust4 surface dust #$1 size 4

> alias dust5 surface dust #$1 size 5

> alias dust6 surface dust #$1 size 6

> alias dust7 surface dust #$1 size 7

> alias dust8 surface dust #$1 size 8

> alias dust9 surface dust #$1 size 9

> alias dust10 surface dust #$1 size 10

> alias dust11 surface dust #$1 size 11

> alias dust12 surface dust #$1 size 12

> alias dust13 surface dust #$1 size 13

> alias dust14 surface dust #$1 size 14

> alias dust15 surface dust #$1 size 15

> alias dust20 surface dust #$1 size 20

> alias dust25 surface dust #$1 size 25

> alias dust30 surface dust #$1 size 30

> alias dust35 surface dust #$1 size 35

> alias dust40 surface dust #$1 size 40

> alias dust45 surface dust #$1 size 45

> alias dust50 surface dust #$1 size 50

> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026""
> range $3,$4

> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true

> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true

> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho

UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Haaris/Desktop/Modelling_Edeine/refined_Ede_Model_correct.pdb

refined_Ede_Model_correct.pdb title:  
Alphafold monomer V2.0 prediction for translation initiation factor if-3
(P0A707) [more info...]  
  
Chain information for refined_Ede_Model_correct.pdb #1  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  
Non-standard residues in refined_Ede_Model_correct.pdb #1  
---  
2MG — (2MG)  
4OC — (4OC)  
5MC — (5MC)  
D2T — (D2T)  
EDE — (EDE)  
G7M — (G7M)  
IAS — (IAS)  
K — (K)  
MA6 — (MA6)  
MG — (MG)  
PSU — (PSU)  
UR3 — (UR3)  
  

> show cartoons

> hide atoms

> close

> open /Users/Haaris/Desktop/Modelling_Ksg/Servalcat/refined_KSG_model-
> coot-4.pdb

Chain information for refined_KSG_model-coot-4.pdb #1  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show cartoons

> hide atoms

> set bgColor white

> select ::name=""KSG""

26 atoms, 27 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 26 atom styles  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 26 atom styles  

> open /Users/Haaris/Desktop/Modelling_Ksg/8cep_aligned.pdb

Chain information for 8cep_aligned.pdb #2  
---  
Chain | Description  
A | No description available  
B C G I V | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show sel cartoons

> hide sel atoms

> select add #2

34852 atoms, 35688 bonds, 432 pseudobonds, 4370 residues, 4 models selected  

> select add #1

68741 atoms, 72351 bonds, 436 pseudobonds, 6930 residues, 5 models selected  

> select subtract #1

34826 atoms, 35661 bonds, 432 pseudobonds, 4369 residues, 3 models selected  

> select add #1

68741 atoms, 72351 bonds, 436 pseudobonds, 6930 residues, 5 models selected  

> select subtract #1

34826 atoms, 35661 bonds, 432 pseudobonds, 4369 residues, 3 models selected  

> select add #1

68741 atoms, 72351 bonds, 436 pseudobonds, 6930 residues, 5 models selected  

> show sel cartoons

> hide sel atoms

> select subtract #1

34826 atoms, 35661 bonds, 432 pseudobonds, 4369 residues, 3 models selected  

> select subtract #2

Nothing selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/B pairing ss

Using Nucleic matrix instead of BLOSUM-62 to match 8cep_aligned.pdb #2/A to
refined_KSG_model-coot-4.pdb #1/B  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 refined_KSG_model-coot-4.pdb, chain B (#1) with 8cep_aligned.pdb,
chain A (#2), sequence alignment score = 3660.8  
RMSD between 1001 pruned atom pairs is 0.803 angstroms; (across all 1046
pairs: 1.262)  
  

> save /Users/Haaris/Desktop/Modelling_Ksg/8cep_aligned.pdb models #2

> hide #!1 models

> close #1

> select ::name=""MG""

54 atoms, 54 residues, 1 model selected  

> select ::name=""K""

25 atoms, 25 residues, 1 model selected  

> close #2

> open /Users/Haaris/Desktop/Modelling_Ksg/8cep_aligned.pdb

Chain information for 8cep_aligned.pdb #1  
---  
Chain | Description  
A | No description available  
B C G I V | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show cartoons

> hide atoms

> select ::name=""MG""

54 atoms, 54 residues, 1 model selected  

> select ::name=""K""

25 atoms, 25 residues, 1 model selected  

> close

> open /Users/Haaris/Desktop/Modelling_Ksg/Servalcat/refined_KSG_model-
> coot-4.pdb

Chain information for refined_KSG_model-coot-4.pdb #1  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show cartoons

> hide atoms

> select ::name=""K""

25 atoms, 25 residues, 1 model selected  

> select ::name=""MG""

53 atoms, 53 residues, 1 model selected  

> close #1

> open /Users/Haaris/Desktop/Modelling_Ksg/8cep_aligned.pdb

Chain information for 8cep_aligned.pdb #1  
---  
Chain | Description  
A | No description available  
B C G I V | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show cartoons

> hide atoms

> select ::name=""HOH""

1933 atoms, 1933 residues, 1 model selected  

> show sel atoms

> open /Users/Haaris/Desktop/Modelling_Ksg/Servalcat/refined_KSG_model-
> coot-4.pdb

Chain information for refined_KSG_model-coot-4.pdb #2  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
  

> show sel cartoons

> hide sel atoms

> select add #2

35848 atoms, 36690 bonds, 4 pseudobonds, 4494 residues, 3 models selected  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> mousemode shift leftMode ""translate selected models""

> mousemode shift middleMode ""rotate selected models""

> mousemode rightMode zoom

> mousemode control wheelMode ""contour level""

> mousemode setting ""contour level"" speed 0.1

> mousemode shift wheelMode ""rotate selected models""

> camera ortho

> set bgColor grey

> lighting shadows false

> lighting depthCue false

> graphics silhouettes true

> lighting simple

> functionkey F1 cofr sel

> functionkey F2 mousemode rightMode 'mark surface'

> functionkey F3 mousemode rightMode 'move markers'

> functionkey F4 mk 3 1

> functionkey F5 view

> functionkey F6 view sel pad 0.92 clip false

> functionkey F7 mousemode rightMode 'delete markers'

> functionkey F8 mousemode rightMode zoom

> functionkey F9 sequence chain sel

> functionkey F10 transparency sel 65

> functionkey F11 transparency sel 0

> functionkey F12 tool show 'Fit in Map'

> color name f01graublau #BADBED

Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed

  

> color name f02silber #F6FAFC

Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc

  

> color name f03muschel #FFFFE5

Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5

  

> color name f04beige #F3F3A9

Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9

  

> color name f05gelb #f2b701

Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701

  

> color name f06orange #e68310

Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310

  

> color name f07rotorange #FF6A25

Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25

  

> color name f08rot #dd3d2d

Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d

  

> color name f09lachs #f97b72

Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72

  

> color name f10flieder #D57AD5

Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5

  

> color name f11violett #cf1c90

Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90

  

> color name f12lila #4b148f

Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f

  

> color name f13dunkelblau #2E2EF7

Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7

  

> color name f14blau #00AAFF

Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff

  

> color name f15cyan #60e2d6

Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6

  

> color name f16blaugrün #30ffa6

Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6

  

> color name f17grün #00FF00

Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00

  

> color name f18dunkelgrün #228B22

Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  

> color name f19hellgrau #DCDCDC

Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc

  

> color name f20grau #B2B2B2

Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2

  

> color name f21anthrazit #323F45

Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45

  

> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000""
> range $3,$4

> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'

> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'

> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3

> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3

> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3

> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow

> alias chaininfo preset custom chaininfo

> alias foto save browse format tiff height 4000 supersample 4
> transparentBackground false

> alias durch save browse format tiff height 4000 supersample 4
> transparentBackground true

> alias session save browse format session includeMaps true compress lz4

> alias nomapsession save browse format session includeMaps false compress lz4

> alias splitup color zone #$1 near sel sharpEdges true distance $2

> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2

> alias spalt volume splitbyzone #$1

> alias undust surface undust #$1

> alias dust1 surface dust #$1 size 1

> alias dust2 surface dust #$1 size 2

> alias dust3 surface dust #$1 size 3

> alias dust4 surface dust #$1 size 4

> alias dust5 surface dust #$1 size 5

> alias dust6 surface dust #$1 size 6

> alias dust7 surface dust #$1 size 7

> alias dust8 surface dust #$1 size 8

> alias dust9 surface dust #$1 size 9

> alias dust10 surface dust #$1 size 10

> alias dust11 surface dust #$1 size 11

> alias dust12 surface dust #$1 size 12

> alias dust13 surface dust #$1 size 13

> alias dust14 surface dust #$1 size 14

> alias dust15 surface dust #$1 size 15

> alias dust20 surface dust #$1 size 20

> alias dust25 surface dust #$1 size 25

> alias dust30 surface dust #$1 size 30

> alias dust35 surface dust #$1 size 35

> alias dust40 surface dust #$1 size 40

> alias dust45 surface dust #$1 size 45

> alias dust50 surface dust #$1 size 50

> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026""
> range $3,$4

> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true

> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true

> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho

UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-5.2.4
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3,7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      System Firmware Version: 2020.40.3.0.0
      OS Loader Version: 580~1053
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 1 day, 1 hour, 29 minutes

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      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: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 0FFXD31242JL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307312254
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-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: 1.31.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.7
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

}}}
"	defect	closed	normal		Core		can't reproduce		Tom Goddard				all	ChimeraX