Crash in chem_group on Windows

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000079b8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001fe4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3213 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 536 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 593 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 339 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 420 in run_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 402 in try_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1386 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb format pdb

Summary of feedback from opening C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 15 15 THR A 528 GLU A 531 1 4  
End residue of secondary structure not found: HELIX 42 42 THR B 528 GLU B 531
1 4  
Start residue of secondary structure not found: SHEET 12 1212 ALA B 64 ARG B
67 0  
Cannot find LINK/SSBOND residue LIG (802 )  
  
Chain information for ABCH-WT-ceramide.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "C:\Users\olawu\Downloads\PE 38.pdb" format pdb

> select add #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> close

> source compare_PE_ceramide.cmd

Unknown command: source compare_PE_ceramide.cmd  

> open ABCH-WT-ceramide.pdb

No such file/path: ABCH-WT-ceramide.pdb  

> open ABCH-WT-ceramide

'ABCH-WT-ceramide' has no suffix  

> ABCH-WT-ceramide

Unknown command: ABCH-WT-ceramide  

> open ABCH-WT-ceramide.pdb

No such file/path: ABCH-WT-ceramide.pdb  

> open PE_38.pdb

No such file/path: PE_38.pdb  

> open PE 38.pdb

'PE' has no suffix  

> open "C:\Users\olawu\Downloads\PE 38.pdb" format pdb

> open C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb format pdb

Summary of feedback from opening C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 15 15 THR A 528 GLU A 531 1 4  
End residue of secondary structure not found: HELIX 42 42 THR B 528 GLU B 531
1 4  
Start residue of secondary structure not found: SHEET 12 1212 ALA B 64 ARG B
67 0  
Cannot find LINK/SSBOND residue LIG (802 )  
  
Chain information for ABCH-WT-ceramide.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> hide #1 models

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> show #1 models

> hide #1 models

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> show #1 models

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> hide #!2 models

> select subtract #2

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

> show #!2 models

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> matchmaker #1 #0

Missing required "to" argument  

> findhbond selRestrict any reveal true intraMol false interMol true saveFile
> hbonds.txt

Unknown command: findhbond selRestrict any reveal true intraMol false interMol
true saveFile hbonds.txt  

> findclash #0 test #1 overlapCutoff -0.4 hbondAllowance 0.0 saveFile
> hydrophobic_interactions.txt

Unknown command: findclash #0 test #1 overlapCutoff -0.4 hbondAllowance 0.0
saveFile hydrophobic_interactions.txt  

> distance #0:608 #1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 17 atoms and 0
measurable objects  

> distance #0:704 #1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 17 atoms and 0
measurable objects  

> distance #0:708 #1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 17 atoms and 0
measurable objects  

> save session.chimerax

No known data format for file suffix '.chimerax'  

> matchmaker #1 #0

Missing required "to" argument  

> hide #!2 models

> select subtract #2

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

> show #!2 models

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> hide #!2 models

> select subtract #2

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> show #!2 models

> ui tool show Matchmaker

> matchmaker #1 to #2

No matrix compatible with both reference structure and all match structures  

> matchmaker #1 to #2

No matrix compatible with both reference structure and all match structures  

> matchmaker #1 to #2/A pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> hide #!2 models

> select subtract #2

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> show #!2 models

> select subtract #2

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> hide #1 models

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> show #1 models

> hide #1 models

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> show #1 models

> select subtract #2

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

> ui mousemode right "translate selected models"

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> select subtract #2

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

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,211.73,0,1,0,84.866,0,0,1,102.14

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> view matrix models
> #1,1,0,0,307.85,0,1,0,146.58,0,0,1,127.83,#2,1,0,0,96.122,0,1,0,61.717,0,0,1,25.694

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #1

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

> view matrix models #1,1,0,0,305.84,0,1,0,144.58,0,0,1,127.93

> style sel stick

Changed 17 atom styles  

> undo

> hide #!2 models

> style sel stick

Changed 17 atom styles  

> style sel sphere

Changed 17 atom styles  

> style sel ball

Changed 17 atom styles  

> style sel stick

Changed 17 atom styles  

> show #!2 models

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> select subtract #2

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> hide #1 models

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> select ::name="UNL"

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

> select ::name="UNL"

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

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,93.025,0,1,0,57.968,0,0,1,26.437

> view matrix models #2,1,0,0,94.843,0,1,0,58.577,0,0,1,27.809

> show #1 target m

> hide #1 target m

> style sel sphere

Changed 144 atom styles  

> select protein

10068 atoms, 10292 bonds, 2 pseudobonds, 1284 residues, 2 models selected  

> hide #1 target m

> hide sel cartoons

> view matrix models #2,1,0,0,94.563,0,1,0,57.456,0,0,1,30.42

> view matrix models #2,1,0,0,97.421,0,1,0,58.622,0,0,1,31.084

> style sel sphere

Changed 10068 atom styles  

> style sel sphere

Changed 10068 atom styles  

> style sel stick

Changed 10068 atom styles  

> view matrix models #2,1,0,0,95.837,0,1,0,58.164,0,0,1,30.216

> close #1

> close

> open "C:\Users\olawu\Downloads\PE 38.pdb" format pdb

> open C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb format pdb

Summary of feedback from opening C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 15 15 THR A 528 GLU A 531 1 4  
End residue of secondary structure not found: HELIX 42 42 THR B 528 GLU B 531
1 4  
Start residue of secondary structure not found: SHEET 12 1212 ALA B 64 ARG B
67 0  
Cannot find LINK/SSBOND residue LIG (802 )  
  
Chain information for ABCH-WT-ceramide.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-134.3,0,1,0,-143.36,0,0,1,0

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> view matrix models
> #1,1,0,0,31.732,0,1,0,26.39,0,0,1,61.466,#2,1,0,0,-102.57,0,1,0,-116.97,0,0,1,61.466

> hide #!2 models

> select subtract #2

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> show #!2 models

> select subtract #2

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

> view matrix models #1,1,0,0,24.184,0,1,0,87.081,0,0,1,268.82

> view matrix models #1,1,0,0,38.101,0,1,0,89.793,0,0,1,266.41

> view matrix models #1,1,0,0,33.302,0,1,0,88.001,0,0,1,269.26

> view matrix models #1,1,0,0,29.888,0,1,0,86.625,0,0,1,264.43

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> view matrix models
> #1,1,0,0,20.995,0,1,0,84.7,0,0,1,215.59,#2,1,0,0,-111.46,0,1,0,-118.89,0,0,1,12.63

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> hide #1 models

> select subtract #2

Nothing selected  

> select main

10085 atoms, 10308 bonds, 2 pseudobonds, 1285 residues, 3 models selected  

> view matrix models
> #1,1,0,0,29.833,0,1,0,88.724,0,0,1,218,#2,1,0,0,-102.62,0,1,0,-114.87,0,0,1,15.042

> hide target m

> show target m

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> select subtract #2

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

> select protein

10068 atoms, 10292 bonds, 2 pseudobonds, 1284 residues, 2 models selected  

> hide target m

> show target m

> view matrix models #2,1,0,0,-104.56,0,1,0,-107.16,0,0,1,23.515

> cartoon hide (#!2 & sel)

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> show sel cartoons

> show sel surfaces

> view matrix models #2,1,0,0,-110.29,0,1,0,-83.575,0,0,1,20.823

> select add #1

161 atoms, 157 bonds, 4 residues, 3 models selected  

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 4 models selected  

> hide #!2 models

> show #!2 models

> select subtract #2

17 atoms, 16 bonds, 1 residue, 2 models selected  

> show sel surfaces

> view matrix models #1,1,0,0,30.057,0,1,0,87.797,0,0,1,218.26

> style sel stick

Changed 17 atom styles  

> show sel atoms

> style sel stick

Changed 17 atom styles  

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 4 models selected  

> select subtract #2

17 atoms, 16 bonds, 1 residue, 3 models selected  

> select subtract #1

1 model selected  

> select add #1

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

> style sel ball

Changed 17 atom styles  

> view matrix models #1,1,0,0,32.131,0,1,0,91.768,0,0,1,217.26

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 4 models selected  

> hide sel atoms

> view matrix models
> #1,1,0,0,31.851,0,1,0,86.511,0,0,1,217.53,#2,1,0,0,-110.57,0,1,0,-88.832,0,0,1,21.095

> view matrix models
> #1,1,0,0,39.575,0,1,0,86.747,0,0,1,212.96,#2,1,0,0,-102.85,0,1,0,-88.596,0,0,1,16.519

> style sel stick

Changed 10229 atom styles  

> select subtract #2

17 atoms, 16 bonds, 1 residue, 3 models selected  

> hide #!2 models

> style sel stick

Changed 17 atom styles  

> show sel cartoons

> view matrix models #1,1,0,0,43.383,0,1,0,86.197,0,0,1,218.22

> view matrix models #1,1,0,0,45.58,0,1,0,86.196,0,0,1,217.67

> show target m

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 4 models selected  

> select subtract #2

17 atoms, 16 bonds, 1 residue, 3 models selected  

> show sel atoms

> view matrix models #1,1,0,0,45.627,0,1,0,86.309,0,0,1,217.7

> hide #!1 models

> select subtract #1

1 model selected  

> save C:/ProgramData/ChimeraX/CERAMIDE.pdb

Computing secondary structure  

> show #!2 cartoons

> style #!2 sphere

Changed 10212 atom styles  

> hide #!2 surfaces

> save "C:/ProgramData/ChimeraX/TcABCH WT.pdb"

> show #!2 surfaces

> show #!2 cartoons

> show #!2 surfaces

> hide #!2 surfaces

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> style sel sphere

Changed 10212 atom styles  

> show sel surfaces

> view matrix models #2,1,0,0,-100.72,0,1,0,-86.707,0,0,1,24.27

> hide sel surfaces

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 3 models selected  

> style sel sphere

Changed 10212 atom styles  

> style sel ball

Changed 10212 atom styles  

> style sel sphere

Changed 10212 atom styles  

> show sel surfaces

> hide sel surfaces

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> view matrix models #2,1,0,0,-100.88,0,1,0,-89.535,0,0,1,22.571

> view matrix models #2,1,0,0,-101.51,0,1,0,-87.884,0,0,1,23.252

> view matrix models #2,1,0,0,-96.774,0,1,0,-100.36,0,0,1,17.365

> view matrix models #2,1,0,0,-97.329,0,1,0,-98.575,0,0,1,17.57

> view matrix models #2,1,0,0,-98.082,0,1,0,-94.563,0,0,1,21.348

> view matrix models #2,1,0,0,-98.765,0,1,0,-91.9,0,0,1,26.122

> show #!1 models

> select add #1

161 atoms, 157 bonds, 4 residues, 3 models selected  

> view matrix models
> #1,1,0,0,44.846,0,1,0,90.039,0,0,1,222.22,#2,1,0,0,-99.547,0,1,0,-88.169,0,0,1,30.643

> select subtract #1

144 atoms, 141 bonds, 3 residues, 3 models selected  

> hide #!1 models

> hide sel cartoons

> show sel surfaces

> view matrix models #2,1,0,0,-98.412,0,1,0,-98.15,0,0,1,30.31

> hide sel cartoons

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> select subtract #2

3 models selected  

> hide #!2 cartoons

> show #!1 models

> select add #1

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

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 4 models selected  

> ui tool show Matchmaker

> matchmaker #!1 to #2/A pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> style sel stick

Changed 10229 atom styles  

> show sel atoms

> hide sel atoms

> select subtract #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 6 models selected  

> hide #!1 models

> show sel atoms

> hide sel atoms

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 144 atom styles  

> style sel stick

Changed 144 atom styles  

> style sel stick

Changed 144 atom styles  

> style sel stick

Changed 144 atom styles  

> style sel stick

Changed 144 atom styles  

> view matrix models #2,1,0,0,-80.839,0,1,0,-85.629,0,0,1,28.047

> show sel atoms

> select add #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> hide sel cartoons

> show sel atoms

> hide sel atoms

> style sel sphere

Changed 10212 atom styles  

> show sel atoms

> hide sel atoms

> open C:/ProgramData/ChimeraX/CERAMIDE.pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
3.2/A 3.2/B | No description available  
  
Computing secondary structure  

> view matrix models #2,1,0,0,-25.938,0,1,0,-48.732,0,0,1,39.255

> undo

> hide #!3.2 models

> hide #!2 models

> show #!2 models

> close session

> open C:\ProgramData\ChimeraX\CERAMIDE.pdb format pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
  
Computing secondary structure  

> hide cartoons

> hide #!1.2 models

> open C:\ProgramData\ChimeraX\CERAMIDE.pdb format pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
2.2/A 2.2/B | No description available  
  
Computing secondary structure  

> close

> open C:\ProgramData\ChimeraX\CERAMIDE.pdb format pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
  
Computing secondary structure  

> close

> open C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb format pdb

Summary of feedback from opening C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 15 15 THR A 528 GLU A 531 1 4  
End residue of secondary structure not found: HELIX 42 42 THR B 528 GLU B 531
1 4  
Start residue of secondary structure not found: SHEET 12 1212 ALA B 64 ARG B
67 0  
Cannot find LINK/SSBOND residue LIG (802 )  
  
Chain information for ABCH-WT-ceramide.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> select protein

10068 atoms, 10292 bonds, 2 pseudobonds, 1284 residues, 2 models selected  

> select ::name="LIG"

144 atoms, 141 bonds, 3 residues, 1 model selected  

> show target m

> view matrix models #1,1,0,0,-0.41179,0,1,0,16.032,0,0,1,-20.219

> hide sel cartoons

> select add #1

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> hide sel cartoons

> view matrix models #1,1,0,0,-1.9704,0,1,0,5.2067,0,0,1,-0.25228

> select subtract #1

Nothing selected  

> open "C:\Users\olawu\Downloads\PE 38.pdb" format pdb

> hide #!1 models

> select add #2

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

> show #!1 models

> ui mousemode right "translate selected models"

> hide #!1 models

> show #!1 models

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> select subtract #1

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

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,192.96,0,1,0,102.76,0,0,1,182.96

> view matrix models #2,1,0,0,223,0,1,0,106.86,0,0,1,139.08

> select add #1

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> view matrix models
> #1,1,0,0,26.504,0,1,0,12.164,0,0,1,-23.151,#2,1,0,0,251.48,0,1,0,113.81,0,0,1,116.18

> select subtract #2

10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected  

> view matrix models #1,1,0,0,64.302,0,1,0,18.193,0,0,1,-73.037

> view matrix models #1,1,0,0,60.377,0,1,0,15.317,0,0,1,-81.54

> select add #2

10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected  

> view matrix models
> #1,1,0,0,31.338,0,1,0,9.0598,0,0,1,-53.092,#2,1,0,0,222.44,0,1,0,107.55,0,0,1,144.63

> select subtract #1

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

> select subtract #2

Nothing selected  

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> matchmaker #2 to #1/A pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> open C:\ProgramData\ChimeraX\CERAMIDE.pdb format pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
3.2/A 3.2/B | No description available  
  
Computing secondary structure  

> close

> open C:\ProgramData\ChimeraX\CERAMIDE.pdb format pdb

Chain information for CERAMIDE.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
  
Computing secondary structure  

> close

> open C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb format pdb

Summary of feedback from opening C:\Users\olawu\Downloads\ABCH-WT-ceramide.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 15 15 THR A 528 GLU A 531 1 4  
End residue of secondary structure not found: HELIX 42 42 THR B 528 GLU B 531
1 4  
Start residue of secondary structure not found: SHEET 12 1212 ALA B 64 ARG B
67 0  
Cannot find LINK/SSBOND residue LIG (802 )  
  
Chain information for ABCH-WT-ceramide.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> hide cartoons

> style ball

Changed 10212 atom styles  

> style ball

Changed 10212 atom styles  

> style sphere

Changed 10212 atom styles  

> style stick

Changed 10212 atom styles  

> show surfaces

> hide surfaces

> coulombic


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 31.0.101.5333
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 15 3511
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 8,311,836,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.12.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501142332
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.11
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.0
    PyQt6-Qt6: 6.8.1
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.1
    PyQt6_sip: 13.9.1
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1