Opened 17 months ago

Closed 17 months ago

#15311 closed defect (can't reproduce)

Crash deleting part of structure

Reported by: tmckeith@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here. 
I was trying to delete several amino acids when it crashed. The pdf, generated by ChimeraX previously, had inconsistencies between the actual atoms and positions and the putative sequence.
Fatal Python error: Segmentation fault

Current thread 0x0000000205278240 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 107 in _make_ribbon_graphics
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600 in compute_ribbons
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1891 in _update_graphics_if_needed
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 55)


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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  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tmckeithan/Downloads/Chimera/PDB/4ZG4 Myo5c PPS.pdb" format pdb

4ZG4 Myo5c PPS.pdb title:  
Myosin VC pre-powerstroke [more info...]  
  
Chain information for 4ZG4 Myo5c PPS.pdb #1  
---  
Chain | Description | UniProt  
B E | myosin-VC | MYO5C_HUMAN 1-755  
  
Non-standard residues in 4ZG4 Myo5c PPS.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
EDO — 1,2-ethanediol (ethylene glycol)  
MG — magnesium ion  
VO4 — vanadate ion  
  

> select /E

10904 atoms, 10774 bonds, 14 pseudobonds, 952 residues, 3 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:571

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select /B:571-593

382 atoms, 386 bonds, 23 residues, 1 model selected  

> select sel @ select clear

> select /B:351

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select /B:351-375

388 atoms, 391 bonds, 25 residues, 1 model selected  

> select /B:570-571

37 atoms, 37 bonds, 2 residues, 1 model selected  

> select /B:571-593

382 atoms, 386 bonds, 23 residues, 1 model selected  

> close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/1MMD.pdb

1MMD.pdb title:  
Truncated head of myosin from dictyostelium discoideum complexed with mgadp-
BEF3 [more info...]  
  
Chain information for 1MMD.pdb #1  
---  
Chain | Description | UniProt  
A | myosin | MYS2_DICDI 1-759  
  
Non-standard residues in 1MMD.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select ::name="ADP"::name="BEF"::name="HOH"::name="MG"

407 atoms, 32 bonds, 5 pseudobonds, 378 residues, 2 models selected  

> select subtract ::name="HOH"

32 atoms, 32 bonds, 3 pseudobonds, 3 residues, 2 models selected  

> select sel @ select /A:237

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:233-237

36 atoms, 35 bonds, 5 residues, 1 model selected  

> select sel @ close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/6FSA.pdb

6FSA.pdb title:  
Beta-cardiac myosin post-rigor [more info...]  
  
Chain information for 6FSA.pdb #1  
---  
Chain | Description | UniProt  
A B | myosin-7 | MYH7_BOVIN 1-1935  
D H | myosin light chain 3 | MYL3_BOVIN 1-199  
  
Non-standard residues in 6FSA.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
EDO — 1,2-ethanediol (ethylene glycol)  
FMT — formic acid  
MG — magnesium ion  
  

> select /B

6336 atoms, 6139 bonds, 8 pseudobonds, 1076 residues, 3 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 43 residues  

> select up

521 atoms, 530 bonds, 64 residues, 1 model selected  

> select up

1178 atoms, 1197 bonds, 150 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /D

Alignment identifier is 1/D  

> select ::name="ADP"

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add ::name="MG"

28 atoms, 29 bonds, 2 residues, 1 model selected  

> select add sel @ select /A:242

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:238-242

36 atoms, 35 bonds, 5 residues, 1 model selected  

> select /A:242

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:241-242

12 atoms, 11 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 12 atom styles  

> hide sel cartoons

> show sel atoms

> select add ::name="ADP"

39 atoms, 40 bonds, 3 residues, 1 model selected  

> select add ::name="MG"

40 atoms, 40 bonds, 4 residues, 1 model selected  

> select add sel @ select clear

> select add ::name="ADP"

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add ::name="MG"

28 atoms, 29 bonds, 2 residues, 1 model selected  

> select add sel @ select clear

> select add ::name="ADP"

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add sel @ select /A:34

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:2-34

257 atoms, 261 bonds, 33 residues, 1 model selected  

> hide sel cartoons

> select add
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MLY"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

7425 atoms, 7572 bonds, 2 pseudobonds, 937 residues, 2 models selected  

> hide sel atoms

> select add ::name="ADP"

7452 atoms, 7601 bonds, 2 pseudobonds, 938 residues, 2 models selected  

> style sel sphere

Changed 7452 atom styles  

> select add ::name="MG"

7453 atoms, 7601 bonds, 2 pseudobonds, 939 residues, 2 models selected  

> style sel sphere

Changed 7453 atom styles  

> select clear

> select add ::name="HOH"

460 atoms, 460 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 460 atom styles  

> hide sel target a

> select add ::name="ADP"

487 atoms, 29 bonds, 461 residues, 1 model selected  

> select add ::name="MG"

488 atoms, 29 bonds, 462 residues, 1 model selected  

> select add sel @ select clear

> select add ::name="ADP"

27 atoms, 29 bonds, 1 residue, 1 model selected  

> select add ::name="MG"

28 atoms, 29 bonds, 2 residues, 1 model selected  

> select add sel @ select intersect ::name="ADP"::name="EDO"::name="FMT"::name="HOH"::name="MG"

39 atoms, 29 bonds, 1 pseudobond, 13 residues, 2 models selected  

> show sel atoms

> select intersect sel @ select sel @ select /A:461

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:461

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select sel @ close session

> open 8P94 fromDatabase pdb format mmcif

Summary of feedback from opening 8P94 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:1  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /E:1  
Atom H1 is not in the residue template for MET /V:1  
note | Fetching compressed mmCIF 8p94 from
http://files.rcsb.org/download/8p94.cif  
  
8p94 title:  
Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin
branches [more info...]  
  
Chain information for 8p94 #1  
---  
Chain | Description | UniProt  
A | Actin-related protein 3 | ARP3_HUMAN 1-418  
B | Actin-related protein 2 | ARP2_HUMAN 1-394  
C | Actin-related protein 2/3 complex subunit 1B | ARC1B_HUMAN 1-372  
D | Actin-related protein 2/3 complex subunit 2 | ARPC2_HUMAN 1-300  
E | Actin-related protein 2/3 complex subunit 3 | ARPC3_HUMAN 1-178  
F | Actin-related protein 2/3 complex subunit 4 | ARPC4_HUMAN 1-168  
G | Actin-related protein 2/3 complex subunit 5-like protein | ARP5L_HUMAN
1-153  
H J K N O P Q R S W | Actin, cytoplasmic 1 | ACTB_PIG 1-375  
I | Src substrate cortactin | SRC8_MOUSE 1-546  
U | F-actin-capping protein subunit alpha-1 | CAZA1_MOUSE 1-286  
V | Isoform 2 of F-actin-capping protein subunit beta | CAPZB_MOUSE 1-272  
a b c d h i j k l m | Phalloidin |  
  
Non-standard residues in 8p94 #1  
---  
ADP — adenosine-5'-diphosphate  
DTH — D-threonine  
EEP — (2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid  
MG — magnesium ion  
  

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain /I

Alignment identifier is 1/I  
Drag select of 1483 atoms, 95 bonds  

> select up

1488 atoms, 1348 bonds, 174 residues, 1 model selected  

> select up

2844 atoms, 2830 bonds, 174 residues, 1 model selected  

> select up

6129 atoms, 6176 bonds, 382 residues, 1 model selected  

> select up

24421 atoms, 24704 bonds, 1551 residues, 1 model selected  
Drag select of 376 atoms, 3 bonds  

> select up

378 atoms, 223 bonds, 88 residues, 1 model selected  

> select up

1492 atoms, 1467 bonds, 88 residues, 1 model selected  

> select up

4866 atoms, 4911 bonds, 304 residues, 1 model selected  

> select up

30144 atoms, 30488 bonds, 1922 residues, 1 model selected  

> select up

30304 atoms, 30652 bonds, 1930 residues, 1 model selected  

> select sel @ color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF cat-Ras 1a.pdb" format pdb

Chain information for RacGEF cat-Ras 1a.pdb #1  
---  
Chain | Description  
A | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
Q | No description available  
  

> select /Q

2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models selected  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select clear

> hide atoms

> show cartoons

> graphics silhouettes true

> select clear

Drag select of 1 residues  

> show sel atoms

> hide sel cartoons

> select /G:992@OXT

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /F:993

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /F:993@n

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> view sel

> show sel atoms

> hide sel cartoons

> ui tool show "Side View"

> select add /G:992@C

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel

Created 0 bonds  

> bond sel reasonable false

Created 1 bond  

> select clear

> select /G:992@C

1 atom, 1 residue, 1 model selected  

> select add /G:993@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Selection Inspector"

> style sel stick

Changed 2 atom styles  
Drag select of 29 atoms, 69 residues, 5 bonds  

> hide sel atoms

> show sel cartoons

> select /G:781

16 atoms, 16 bonds, 1 residue, 1 model selected  

> select add /E:780

34 atoms, 34 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select intersect sideonly

20 atoms, 19 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 20 atom styles  

> select clear

> select /G:781@N

1 atom, 1 residue, 1 model selected  

> select add /E:780@C

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /E:781@N

1 atom, 1 residue, 1 model selected  

> select add /E:780@C

2 atoms, 2 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select /E:781@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /Q:80

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

103 atoms, 104 bonds, 7 residues, 1 model selected  

> select up

2683 atoms, 2704 bonds, 169 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> combine #1 name 2xHP

> select clear

> select add #2

13714 atoms, 13864 bonds, 4 pseudobonds, 863 residues, 2 models selected  

> select subtract #2/D

13390 atoms, 13534 bonds, 4 pseudobonds, 822 residues, 2 models selected  

> select subtract #2/H

13275 atoms, 13418 bonds, 4 pseudobonds, 808 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #1/D

324 atoms, 330 bonds, 41 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/H

115 atoms, 116 bonds, 14 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/H

115 atoms, 116 bonds, 14 residues, 1 model selected  

> show sel atoms

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.73597,-0.35836,0.57439,52.128,0.18313,0.92217,0.3407,-143.26,-0.65178,-0.14555,0.74431,371.23

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.73597,-0.35836,0.57439,47.934,0.18313,0.92217,0.3407,-136.7,-0.65178,-0.14555,0.74431,368.43

> view matrix models
> #2,0.73597,-0.35836,0.57439,47.573,0.18313,0.92217,0.3407,-135.73,-0.65178,-0.14555,0.74431,367.43

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.79768,-0.4219,0.43093,95.347,0.1561,0.83465,0.5282,-151.34,-0.58253,-0.35407,0.73164,427.36

> view matrix models
> #2,0.65989,-0.63653,0.39922,238.05,0.34627,0.72917,0.59026,-198.35,-0.66682,-0.25127,0.70158,427.28

> view matrix models
> #2,0.83012,-0.55167,0.080973,244.6,0.49727,0.79818,0.34003,-200.25,-0.25222,-0.242,0.93692,200.47

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.83012,-0.55167,0.080973,244.27,0.49727,0.79818,0.34003,-197.77,-0.25222,-0.242,0.93692,203.02

> view matrix models
> #2,0.83012,-0.55167,0.080973,243.63,0.49727,0.79818,0.34003,-195.55,-0.25222,-0.242,0.93692,201.05

> view matrix models
> #2,0.83012,-0.55167,0.080973,244.26,0.49727,0.79818,0.34003,-195.19,-0.25222,-0.242,0.93692,201.56

> view matrix models
> #2,0.83012,-0.55167,0.080973,244.33,0.49727,0.79818,0.34003,-194.97,-0.25222,-0.242,0.93692,201.72

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.81482,-0.5794,-0.019352,292.3,0.56927,0.79337,0.21563,-179.61,-0.10958,-0.18672,0.97628,116.64

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.81482,-0.5794,-0.019352,291.26,0.56927,0.79337,0.21563,-180.8,-0.10958,-0.18672,0.97628,117.2

> view matrix models
> #2,0.81482,-0.5794,-0.019352,291.34,0.56927,0.79337,0.21563,-180.47,-0.10958,-0.18672,0.97628,116.94

> undo

> view matrix models
> #2,0.81482,-0.5794,-0.019352,292.41,0.56927,0.79337,0.21563,-179.76,-0.10958,-0.18672,0.97628,116.54

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.88642,-0.44755,-0.11812,246.84,0.44409,0.75032,0.48971,-204.78,-0.13054,-0.48654,0.86385,275.8

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.88642,-0.44755,-0.11812,251.34,0.44409,0.75032,0.48971,-211.99,-0.13054,-0.48654,0.86385,273.56

> view matrix models
> #2,0.88642,-0.44755,-0.11812,251.2,0.44409,0.75032,0.48971,-211.86,-0.13054,-0.48654,0.86385,273.76

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.80787,-0.50591,-0.30233,360.3,0.58872,0.66879,0.45401,-221.01,-0.027491,-0.54477,0.83813,267.38

> view matrix models
> #2,0.87968,-0.32084,-0.35103,278.2,0.47171,0.49494,0.72974,-198.8,-0.060393,-0.80752,0.58673,460.47

> view matrix models
> #2,0.99935,0.018066,-0.03135,2.8191,0.0091345,0.7124,0.70171,-107.83,0.035011,-0.70154,0.71177,345.58

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/E

Alignment identifier is 1/E  

> sequence chain #1/Q

Alignment identifier is 1/Q  

> sequence chain #2/D

Alignment identifier is 2/D  

> sequence chain #2/H

Alignment identifier is 2/H  

> select #2/H:950@CD

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> ui tool show Rotamers

> swapaa interactive sel ARG rotLib Dunbrack

2xHP #2/H ARG 950: phi -138.2, psi 130.4 trans  
Changed 600 bond radii  

> style sel sphere

Changed 11 atom styles  

> view matrix models
> #2,0.91937,0.35995,-0.15874,-60.64,-0.24004,0.83297,0.49854,-0.78149,0.31167,-0.42024,0.85221,92.76

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.91937,0.35995,-0.15874,-62.343,-0.24004,0.83297,0.49854,-1.7767,0.31167,-0.42024,0.85221,92.321

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93098,0.28121,-0.2328,-12.611,-0.14745,0.87301,0.46489,-39.942,0.33397,-0.39847,0.85421,75.236

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.93098,0.28121,-0.2328,-13.593,-0.14745,0.87301,0.46489,-39.833,0.33397,-0.39847,0.85421,75.454

> select add #2

439 atoms, 446 bonds, 55 residues, 1 model selected  

> show sel atoms

> select #1/E:813

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 63 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #2/H:949@CD

1 atom, 1 residue, 1 model selected  

> select add #2

439 atoms, 446 bonds, 55 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #1/Q

2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models selected  

> select sel @ select clear

> select #1/E:815@CG

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> sequence chain #1/E

Destroying pre-existing alignment with identifier 1/E  
Alignment identifier is 1/E  

> sequence chain #1/Q

Destroying pre-existing alignment with identifier 1/Q  
Alignment identifier is 1/Q  

> sequence chain #2/D

Destroying pre-existing alignment with identifier 2/D  
Alignment identifier is 2/D  

> sequence chain #2/H

Destroying pre-existing alignment with identifier 2/H  
Alignment identifier is 2/H  

> select #1/Q

2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models selected  

> select sel @ ui tool show "Show Sequence Viewer"

> sequence chain #1/E

Destroying pre-existing alignment with identifier 1/E  
Alignment identifier is 1/E  

> select #1/E:642

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

211 atoms, 212 bonds, 12 residues, 1 model selected  

> select up

8022 atoms, 8121 bonds, 483 residues, 1 model selected  

> select down

211 atoms, 212 bonds, 12 residues, 1 model selected  

> show sel atoms

> select #1/E:628

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

169 atoms, 171 bonds, 10 residues, 1 model selected  

> show sel atoms

> select clear

> select #1/E:607

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

153 atoms, 152 bonds, 8 residues, 1 model selected  

> show sel atoms

> select #2/H

115 atoms, 116 bonds, 14 residues, 1 model selected  

> show sel atoms

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9922,0.1076,-0.063023,-21.995,-0.049226,0.80234,0.59483,-88.839,0.11457,-0.58709,0.80138,244.11

> view matrix models
> #2,0.99911,0.0033059,0.041952,-17.249,-0.031526,0.71915,0.69414,-94.348,-0.027875,-0.69484,0.71862,363.18

Drag select of 129 atoms, 161 residues  

> select up

2448 atoms, 2219 bonds, 163 residues, 2 models selected  

> select up

3552 atoms, 3578 bonds, 234 residues, 2 models selected  

> select up

10986 atoms, 11114 bonds, 692 residues, 2 models selected  

> select down

3552 atoms, 3578 bonds, 234 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/H:951@CA

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select up

115 atoms, 116 bonds, 14 residues, 1 model selected  

> show sel atoms

> select #2/D:605

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/D:580-605

198 atoms, 201 bonds, 26 residues, 1 model selected  

> show sel atoms

> select #1/E:939

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

188 atoms, 189 bonds, 11 residues, 1 model selected  

> show sel atoms

> select #1/E:942

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

37 atoms, 36 bonds, 3 residues, 1 model selected  

> show sel atoms

> select clear

> hide atoms

> show cartoons

> select #1/E:944

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/E:944-956

223 atoms, 224 bonds, 13 residues, 1 model selected  

> select #1/E:957

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/E:944-957

237 atoms, 238 bonds, 14 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/H:957

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> select clear

> select #1/E:958

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2/H:957

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> hide sel cartoons

> select add #1/E:958

28 atoms, 27 bonds, 2 residues, 2 models selected  

> hide sel cartoons

> show sel atoms

> select intersect sideonly

18 atoms, 17 bonds, 2 residues, 2 models selected  

> style sel stick

Changed 18 atom styles  

> select #2/H:957@C

1 atom, 1 residue, 1 model selected  

> select add #1/E:958@N

2 atoms, 2 residues, 2 models selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Cannot bond atoms in different molecules  

> combine #1,2 close true name RacGEF

> ui tool show "Build Structure"

> bond sel reasonable false

Must specify two or more atoms  

> select /E:958@N

1 atom, 1 residue, 1 model selected  

> select add /H:957@C

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> hide sel atoms

> show sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /D

Alignment identifier is 1/D  

> sequence chain /H

Alignment identifier is 1/H  

> sequence chain /Q

Alignment identifier is 1/Q  

> select add /H:944

10 atoms, 7 bonds, 3 residues, 1 model selected  

> select add /H:945

17 atoms, 14 bonds, 4 residues, 1 model selected  

> select add /H:947

24 atoms, 20 bonds, 5 residues, 1 model selected  

> select subtract /H:947

17 atoms, 14 bonds, 4 residues, 1 model selected  

> select /H:946

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:944

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /H:945

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /H:944

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> hide sel cartoons

> select /H:945

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> hide sel cartoons

> select /H:945@CG

1 atom, 1 residue, 1 model selected  

> select add /H:944@CA

2 atoms, 2 residues, 1 model selected  

> select up

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select intersect sideonly

7 atoms, 5 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 7 atom styles  

> select /H:944@C

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /H:944@C

1 atom, 1 residue, 1 model selected  

> select add /H:945@N

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 0 bonds  

> select up

15 atoms, 15 bonds, 2 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select /H:944

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /H:944

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /H:943

15 atoms, 13 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> select /H:943@C

1 atom, 1 residue, 1 model selected  

> select add /H:944@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select up

15 atoms, 14 bonds, 2 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> sequence chain /D

Destroying pre-existing alignment with identifier 1/D  
Alignment identifier is 1/D  

> sequence chain /H

Destroying pre-existing alignment with identifier 1/H  
Alignment identifier is 1/H  

> sequence chain /Q

Destroying pre-existing alignment with identifier 1/Q  
Alignment identifier is 1/Q  

> select clear

> select /H:607

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

153 atoms, 152 bonds, 8 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /D

Alignment identifier is 1/D  

> sequence chain /H

Alignment identifier is 1/H  

> sequence chain /Q

Alignment identifier is 1/Q  

> select /H:587

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

58 atoms, 58 bonds, 3 residues, 1 model selected  

> delete atoms sel

> delete bonds sel


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 33 days, 29 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash deleting part of structure

comment:2 by Eric Pettersen, 17 months ago

Resolution: → can't reproduce
Status: accepted → closed

Hi Tim,

Thanks for reporting this problem, though without access to the particular PDB files you were working I don't think I have any shot to reproduce it. Also, there have been a lot of changes to the structure-editing code since the 1.7.1 release, so there's a good chance that the problem may be fixed in the 1.8 release candidate.
If you provided the files you were working on, I could look into it further, or you could try the 1.8 candidate...

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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