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 0x000081ec (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 0x00003d04 (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\E224Q-LMNG-Cer.pdb format pdb
Summary of feedback from opening C:\Users\olawu\Downloads\E224Q-LMNG-Cer.pdb
---
warning | End residue of secondary structure not found: HELIX 39 39 THR B 528 GLU B 531 1 4
Chain information for E224Q-LMNG-Cer.pdb #1
---
Chain | Description
A | No description available
B | No description available
> distance #1:105.A@CA #1:205.B@CA
Missing or invalid "objects" argument: only initial part "#1:105" of atom
specifier valid
> distance 105:205
Missing or invalid "objects" argument: invalid objects specifier
> distance #1:105 #1:205
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 30 atoms and 0
measurable objects
> distance #105 #205
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 0 atoms and 0
measurable objects
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> select /B:103
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:103-110
53 atoms, 52 bonds, 8 residues, 1 model selected
> select /A:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> color sel red
> select /B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> color sel red
> select /B:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:220-224
41 atoms, 40 bonds, 5 residues, 1 model selected
> color sel lime
> select /A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:220-224
41 atoms, 40 bonds, 5 residues, 1 model selected
> color sel lime
> select /A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select
> /B:103-114,158-168,173-187,196-198,201-213,231-245,260-264,282-288,391-406,409-429,472-474,488-495,510-520,546-567,572-575,594-622,626-631,639-663,675-699,703-720,727-729,734-740,745-755,763-786
2467 atoms, 2496 bonds, 314 residues, 1 model selected
> undo
> select subtract /A:223
Nothing selected
> select add /B:223
8 atoms, 7 bonds, 1 residue, 1 model selected
Exactly two atoms must be selected!
> style sel stick
Changed 8 atom styles
> select protein
10068 atoms, 10292 bonds, 2 pseudobonds, 1284 residues, 2 models selected
> style (#!1 & sel) stick
Changed 10068 atom styles
> show (#!1 & sel) target ab
> cartoon hide (#!1 & sel)
> select subtract /A:223@O
10067 atoms, 10291 bonds, 2 pseudobonds, 1284 residues, 2 models selected
> select subtract /B:223@OD2
10066 atoms, 10290 bonds, 2 pseudobonds, 1284 residues, 2 models selected
> ui tool show Distances
Exactly two atoms must be selected!
> select /A:224@O
1 atom, 1 residue, 1 model selected
> select /B:224@NE2
1 atom, 1 residue, 1 model selected
> select subtract /B:224@NE2
Nothing selected
> select /B:224@NE2
1 atom, 1 residue, 1 model selected
> select /A:224@OE1
1 atom, 1 residue, 1 model selected
> select /B:224@NE2
1 atom, 1 residue, 1 model selected
> select add /A:224@OE1
2 atoms, 2 residues, 1 model selected
> distance /B:224@NE2 /A:224@OE1
Distance between /B GLN 224 NE2 and /A GLN 224 OE1: 12.561Å
> hide target m
> open C:\Users\olawu\Downloads\E224Q-ATP.pdb format pdb
Chain information for E224Q-ATP.pdb #3
---
Chain | Description
A B | No description available
> select #1/B:103-104
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/B:103-108
37 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> color #3 red
> undo
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select subtract #1
Nothing selected
> show target m
> hide target m
> show target m
> undo
> hide #!2 models
> hide #!1 models
> hide #2.1 models
> select add #3
10004 atoms, 10230 bonds, 2 pseudobonds, 1272 residues, 2 models selected
> select subtract #3
Nothing selected
> select #1/B:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:220-224
41 atoms, 40 bonds, 5 residues, 1 model selected
> color #3 red
> undo
> hide #!3 models
> show #!3 models
> select add #3
10045 atoms, 10270 bonds, 2 pseudobonds, 1277 residues, 3 models selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> hide #!3 models
> show #!3 models
> view clip false
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select subtract #1
Nothing selected
> select #1/B:85-100
115 atoms, 115 bonds, 16 residues, 1 model selected
> select #1/B:85-100
115 atoms, 115 bonds, 16 residues, 1 model selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> hide #3.1 models
> show #3.1 models
> select add #3
10056 atoms, 10281 bonds, 2 pseudobonds, 1281 residues, 3 models selected
> select #1/B:100
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:100-108
52 atoms, 51 bonds, 9 residues, 1 model selected
> show target m
> hide target m
> show target m
> undo
> show #!3 models
> show #!2 target m
> hide #!3 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> select add #2
52 atoms, 51 bonds, 1 pseudobond, 9 residues, 3 models selected
> hide #!2 models
> select subtract #2
52 atoms, 51 bonds, 9 residues, 1 model selected
> show #!3 target m
> select add #3/B:224
61 atoms, 59 bonds, 10 residues, 2 models selected
> select add #3/A:224
70 atoms, 67 bonds, 11 residues, 2 models selected
Exactly two atoms must be selected!
> color (#!3 & sel) red
> select protein
20008 atoms, 20456 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> style (#!3 & sel) stick
Changed 9940 atom styles
> cartoon hide (#!3 & sel)
> select subtract #3/B:224@OE1
20007 atoms, 20455 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/B:224@OE1
20008 atoms, 20455 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select subtract #3/A:224@OE1
20007 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/A:224@OE1
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
Exactly two atoms must be selected!
> select subtract #3/B:224@OE1
20007 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/B:224@OE1
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select subtract #3/A:224@OE1
20007 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/A:224@OE1
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
Exactly two atoms must be selected!
> select subtract #3/B:224@OE1
20007 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/B:224@OE1
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select subtract #3/A:224@OE1
20007 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
> select add #3/A:224@OE1
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 5 models selected
Exactly two atoms must be selected!
> select add #2
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 6 models selected
> select subtract #2
20008 atoms, 20454 bonds, 4 pseudobonds, 2552 residues, 4 models selected
> select add #2
20008 atoms, 20454 bonds, 5 pseudobonds, 2552 residues, 6 models selected
> select add #3
20072 atoms, 20522 bonds, 5 pseudobonds, 2556 residues, 6 models selected
> select subtract #3
10068 atoms, 10292 bonds, 3 pseudobonds, 1284 residues, 4 models selected
> select add #3
20072 atoms, 20522 bonds, 5 pseudobonds, 2556 residues, 6 models selected
> select subtract #3
10068 atoms, 10292 bonds, 3 pseudobonds, 1284 residues, 4 models selected
> select add #3/B:224@OE1
10069 atoms, 10292 bonds, 3 pseudobonds, 1285 residues, 5 models selected
> select add #3/A:224@OE1
10070 atoms, 10292 bonds, 3 pseudobonds, 1286 residues, 5 models selected
Exactly two atoms must be selected!
> select subtract #3/B:224@OE1
10069 atoms, 10292 bonds, 3 pseudobonds, 1285 residues, 5 models selected
> select add #3/B:224@OE1
10070 atoms, 10292 bonds, 3 pseudobonds, 1286 residues, 5 models selected
> select subtract #3/A:224@OE1
10069 atoms, 10292 bonds, 3 pseudobonds, 1285 residues, 5 models selected
> select add #3/A:224@OE1
10070 atoms, 10292 bonds, 3 pseudobonds, 1286 residues, 5 models selected
Exactly two atoms must be selected!
> ui tool show Distances
Exactly two atoms must be selected!
> show #!3 target m
> select add #3
20072 atoms, 20522 bonds, 5 pseudobonds, 2556 residues, 6 models selected
> select subtract #2
20072 atoms, 20522 bonds, 4 pseudobonds, 2556 residues, 4 models selected
> select subtract #1.1
20072 atoms, 20522 bonds, 2 pseudobonds, 2556 residues, 3 models selected
> select add #1
20354 atoms, 20807 bonds, 5 pseudobonds, 2561 residues, 5 models selected
> select subtract #1
10004 atoms, 10230 bonds, 2 pseudobonds, 1272 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3/B:224@OE1
1 atom, 1 residue, 1 model selected
> select add #3/A:224@OE1
2 atoms, 2 residues, 1 model selected
> distance #3/B:224@OE1 #3/A:224@OE1
Distance between E224Q-ATP.pdb #3/B GLN 224 OE1 and /A GLN 224 OE1: 11.454Å
> show #!1 target m
> cartoon sel
> hide sel target a
> cartoon sel
> hide #!1 models
> open C:\Users\olawu\Downloads\E224Q-ATP.pdb format pdb
Chain information for E224Q-ATP.pdb #4
---
Chain | Description
A B | No description available
> hide #!3 models
> select add #3
10004 atoms, 10230 bonds, 3 pseudobonds, 1272 residues, 3 models selected
> select subtract #3
Nothing selected
> hide #!4 models
> show #!1 models
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select subtract #1
Nothing selected
> cartoon #!1
> hide #!1 target a
> undo
> redo
> show #!1 cartoons
> hide #!1 target a
> select add #1
10350 atoms, 10577 bonds, 3 pseudobonds, 1289 residues, 3 models selected
> select add #3
20354 atoms, 20807 bonds, 6 pseudobonds, 2561 residues, 5 models selected
> select add #4
30358 atoms, 31037 bonds, 8 pseudobonds, 3833 residues, 7 models selected
> close #1
> close
> open C:\Users\olawu\Downloads\E224Q-LMNG-Cer.pdb format pdb
Summary of feedback from opening C:\Users\olawu\Downloads\E224Q-LMNG-Cer.pdb
---
warning | End residue of secondary structure not found: HELIX 39 39 THR B 528 GLU B 531 1 4
Chain information for E224Q-LMNG-Cer.pdb #1
---
Chain | Description
A | No description available
B | No description available
> cartoon hide
> select ::name="AV0"
138 atoms, 144 bonds, 2 residues, 1 model selected
> select ::name="AV0"
138 atoms, 144 bonds, 2 residues, 1 model selected
> hide target m
> show target m
> hide sel atoms
> show sel atoms
> open C:\Users\olawu\Downloads\E224Q-ATP.pdb format pdb
Chain information for E224Q-ATP.pdb #2
---
Chain | Description
A B | No description available
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!2 target m
> select add #1
10350 atoms, 10577 bonds, 2 pseudobonds, 1289 residues, 2 models selected
> hide #!1 models
> select subtract #1
Nothing selected
> show #!2 models
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="AV0"
138 atoms, 144 bonds, 2 residues, 1 model selected
> select ::name="LIG"
144 atoms, 141 bonds, 3 residues, 1 model selected
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel cartoons
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> close #2
> undo
> show #!1 models
> undo
> close
> open C:\Users\olawu\Downloads\E224Q-ATP.pdb format pdb
Chain information for E224Q-ATP.pdb #1
---
Chain | Description
A B | No description available
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> hide target m
> undo
> hide sel cartoons
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> hide sel atoms
> open C:\Users\olawu\Downloads\E224Q-LMNG-Cer.pdb format pdb
Summary of feedback from opening C:\Users\olawu\Downloads\E224Q-LMNG-Cer.pdb
---
warning | End residue of secondary structure not found: HELIX 39 39 THR B 528 GLU B 531 1 4
Chain information for E224Q-LMNG-Cer.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 atoms
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker E224Q-ATP.pdb, chain A (#1) with E224Q-LMNG-Cer.pdb, chain B (#2),
sequence alignment score = 2853.3
RMSD between 257 pruned atom pairs is 0.992 angstroms; (across all 634 pairs:
4.227)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!2 atoms
> hide #!2 atoms
> show #!1 models
> open
> "C:/Users/olawu/Downloads/PubChem_compound_text_Phosphatidylethanolamine
> (PE)_records.sdf"
PubChem entry 25203060
PubChem entry 14238554
PubChem entry 6437392
PubChem entry 46891780
PubChem entry 53479704
PubChem entry 5289133
PubChem entry 445468
PubChem entry 53479734
PubChem entry 52924920
PubChem entry 53479611
PubChem entry 53479639
PubChem entry 136212473
PubChem entry 102515363
PubChem entry 52925127
PubChem entry 9546812
PubChem entry 52924901
PubChem entry 52924890
PubChem entry 5326793
PubChem entry 134763077
PubChem entry 52925126
PubChem entry 102515246
PubChem entry 447078
PubChem entry 131822086
PubChem entry 130586
PubChem entry 52924917
PubChem entry 52924229
PubChem entry 123850
PubChem entry 124842
PubChem entry 75228680
PubChem entry 102514920
PubChem entry 52924479
PubChem entry 6443215
PubChem entry 3037809
PubChem entry 127398
PubChem entry 139291744
PubChem entry 15061529
PubChem entry 53480857
PubChem entry 53480880
PubChem entry 52924897
PubChem entry 9547031
PubChem entry 21668201
PubChem entry 46891781
PubChem entry 9546747
PubChem entry 46891779
PubChem entry 59834030
PubChem entry 9546798
PubChem entry 9546749
PubChem entry 46891778
PubChem entry 123133557
PubChem entry 9546755
PubChem entry 9546799
PubChem entry 52924944
PubChem entry 52924900
PubChem entry 71306340
PubChem entry 9546802
PubChem entry 52924899
PubChem entry 90657244
PubChem entry 91746202
PubChem entry 5283496
PubChem entry 9547069
PubChem entry 52924130
PubChem entry 65109
PubChem entry 52924121
PubChem entry 52925128
PubChem entry 44251425
PubChem entry 71728379
PubChem entry 9546801
PubChem entry 108390
PubChem entry 76972714
PubChem entry 9546757
PubChem entry 9546807
PubChem entry 46907846
PubChem entry 52924864
PubChem entry 9547071
PubChem entry 46891690
PubChem entry 6454188
PubChem entry 52924721
PubChem entry 9546836
PubChem entry 9546809
PubChem entry 58177709
PubChem entry 102515396
PubChem entry 102515010
PubChem entry 102514977
PubChem entry 46891875
PubChem entry 70698985
PubChem entry 102515283
PubChem entry 102515439
PubChem entry 5282290
PubChem entry 9852308
PubChem entry 102515412
PubChem entry 102515444
PubChem entry 102515063
PubChem entry 9546744
PubChem entry 53480667
PubChem entry 102515099
PubChem entry 102515259
PubChem entry 102515110
PubChem entry 102515334
PubChem entry 102514909
PubChem entry 102514973
PubChem entry 9546742
PubChem entry 11802774
PubChem entry 102515405
PubChem entry 102515168
PubChem entry 102514896
PubChem entry 102515152
PubChem entry 76957626
PubChem entry 52924172
PubChem entry 102547
PubChem entry 90657571
PubChem entry 9547068
PubChem entry 9546806
PubChem entry 10476720
PubChem entry 15061530
PubChem entry 53480922
PubChem entry 6426727
PubChem entry 52924075
PubChem entry 24178114
PubChem entry 46891874
PubChem entry 52924937
PubChem entry 52924930
PubChem entry 52924227
PubChem entry 446872
PubChem entry 9547000
PubChem entry 52924933
PubChem entry 52924718
PubChem entry 129626772
PubChem entry 129626771
PubChem entry 135563762
PubChem entry 135563763
PubChem entry 52924925
PubChem entry 114944
PubChem entry 9546969
PubChem entry 86583449
> hide #!1 models
> hide #!2 models
> open
> "C:/Users/olawu/Downloads/PubChem_compound_text_Phosphatidylethanolamine
> (PE)_records.sdf"
PubChem entry 25203060
PubChem entry 14238554
PubChem entry 6437392
PubChem entry 46891780
PubChem entry 53479704
PubChem entry 5289133
PubChem entry 445468
PubChem entry 53479734
PubChem entry 52924920
PubChem entry 53479611
PubChem entry 53479639
PubChem entry 136212473
PubChem entry 102515363
PubChem entry 52925127
PubChem entry 9546812
PubChem entry 52924901
PubChem entry 52924890
PubChem entry 5326793
PubChem entry 134763077
PubChem entry 52925126
PubChem entry 102515246
PubChem entry 447078
PubChem entry 131822086
PubChem entry 130586
PubChem entry 52924917
PubChem entry 52924229
PubChem entry 123850
PubChem entry 124842
PubChem entry 75228680
PubChem entry 102514920
PubChem entry 52924479
PubChem entry 6443215
PubChem entry 3037809
PubChem entry 127398
PubChem entry 139291744
PubChem entry 15061529
PubChem entry 53480857
PubChem entry 53480880
PubChem entry 52924897
PubChem entry 9547031
PubChem entry 21668201
PubChem entry 46891781
PubChem entry 9546747
PubChem entry 46891779
PubChem entry 59834030
PubChem entry 9546798
PubChem entry 9546749
PubChem entry 46891778
PubChem entry 123133557
PubChem entry 9546755
PubChem entry 9546799
PubChem entry 52924944
PubChem entry 52924900
PubChem entry 71306340
PubChem entry 9546802
PubChem entry 52924899
PubChem entry 90657244
PubChem entry 91746202
PubChem entry 5283496
PubChem entry 9547069
PubChem entry 52924130
PubChem entry 65109
PubChem entry 52924121
PubChem entry 52925128
PubChem entry 44251425
PubChem entry 71728379
PubChem entry 9546801
PubChem entry 108390
PubChem entry 76972714
PubChem entry 9546757
PubChem entry 9546807
PubChem entry 46907846
PubChem entry 52924864
PubChem entry 9547071
PubChem entry 46891690
PubChem entry 6454188
PubChem entry 52924721
PubChem entry 9546836
PubChem entry 9546809
PubChem entry 58177709
PubChem entry 102515396
PubChem entry 102515010
PubChem entry 102514977
PubChem entry 46891875
PubChem entry 70698985
PubChem entry 102515283
PubChem entry 102515439
PubChem entry 5282290
PubChem entry 9852308
PubChem entry 102515412
PubChem entry 102515444
PubChem entry 102515063
PubChem entry 9546744
PubChem entry 53480667
PubChem entry 102515099
PubChem entry 102515259
PubChem entry 102515110
PubChem entry 102515334
PubChem entry 102514909
PubChem entry 102514973
PubChem entry 9546742
PubChem entry 11802774
PubChem entry 102515405
PubChem entry 102515168
PubChem entry 102514896
PubChem entry 102515152
PubChem entry 76957626
PubChem entry 52924172
PubChem entry 102547
PubChem entry 90657571
PubChem entry 9547068
PubChem entry 9546806
PubChem entry 10476720
PubChem entry 15061530
PubChem entry 53480922
PubChem entry 6426727
PubChem entry 52924075
PubChem entry 24178114
PubChem entry 46891874
PubChem entry 52924937
PubChem entry 52924930
PubChem entry 52924227
PubChem entry 446872
PubChem entry 9547000
PubChem entry 52924933
PubChem entry 52924718
PubChem entry 129626772
PubChem entry 129626771
PubChem entry 135563762
PubChem entry 135563763
PubChem entry 52924925
PubChem entry 114944
PubChem entry 9546969
PubChem entry 86583449
> view #3 clip false
> save C:/Users/olawu/Downloads/PE.pdb models #1-2#3.1
> open C:/Users/olawu/Downloads/PE.pdb
Summary of feedback from opening C:/Users/olawu/Downloads/PE.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 110 ILE A 113 1 4
Start residue of secondary structure not found: HELIX 2 2 ILE A 158 TYR A 164
1 7
Start residue of secondary structure not found: HELIX 3 3 ILE A 176 PHE A 186
1 11
Start residue of secondary structure not found: HELIX 4 4 VAL A 196 ASN A 198
1 3
Start residue of secondary structure not found: HELIX 5 5 PRO A 231 ILE A 237
1 7
64 messages similar to the above omitted
Chain information for PE.pdb
---
Chain | Description
5.1/A 5.1/B | No description available
5.2/A | No description available
5.2/B | No description available
> hide #!3 models
> hide #!4 models
> hide #!5.1 models
> hide #!5.2 models
> hide #5.3 models
> show #5.3 models
> show #!5.2 models
> show #!5.1 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!5 models
> show #!5 models
> hide #5.3 models
> show #5.3 models
> close #4
> close
> open C:/Users/olawu/Downloads/ABCH-WT-ceramide.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.pdb format pdb
Summary of feedback from opening C:\Users\olawu\Downloads\PE.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 110 ILE A 113 1 4
Start residue of secondary structure not found: HELIX 2 2 ILE A 158 TYR A 164
1 7
Start residue of secondary structure not found: HELIX 3 3 ILE A 176 PHE A 186
1 11
Start residue of secondary structure not found: HELIX 4 4 VAL A 196 ASN A 198
1 3
Start residue of secondary structure not found: HELIX 5 5 PRO A 231 ILE A 237
1 7
64 messages similar to the above omitted
Chain information for PE.pdb
---
Chain | Description
2.1/A 2.1/B | No description available
2.2/A | No description available
2.2/B | No description available
> hide #!1 models
> hide #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #2.3 models
> hide #!2 models
> show #!2 models
> hide #2.3 models
> hide #!2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #2.3 models
> hide #2.3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2.1 models
> show #!1 models
> close
> open C:\Users\olawu\Downloads\PE.pdb format pdb
Summary of feedback from opening C:\Users\olawu\Downloads\PE.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 110 ILE A 113 1 4
Start residue of secondary structure not found: HELIX 2 2 ILE A 158 TYR A 164
1 7
Start residue of secondary structure not found: HELIX 3 3 ILE A 176 PHE A 186
1 11
Start residue of secondary structure not found: HELIX 4 4 VAL A 196 ASN A 198
1 3
Start residue of secondary structure not found: HELIX 5 5 PRO A 231 ILE A 237
1 7
64 messages similar to the above omitted
Chain information for PE.pdb
---
Chain | Description
1.1/A 1.1/B | No description available
1.2/A | No description available
1.2/B | No description available
> hide #!1 models
> close
> open
> C:/Users/olawu/Downloads/DepositedStructure_SUBSTANCE_SID_160713653_Version_4.sdf
> save "C:/Users/olawu/Downloads/PE 38:1.pdb" relModel #1
> save "C:/Users/olawu/Downloads/PE 38.pdb" relModel #1
> close
> open "C:/Users/olawu/Downloads/PE 38.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
> hide #1 models
> select add #2
10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected
> hide #!2 models
> select subtract #2
Nothing selected
> show #!2 models
> select add #2
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
> close #2
> 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
> open C:/Users/olawu/Downloads/ABCH-WT-ceramide.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
> hide #!1 models
> select add #2
10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected
> 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
> open "C:/Users/olawu/Downloads/PE 38.pdb"
> hide #!1 models
> hide #2 models
> show #!1 models
> show #2 models
> hide #!1 models
> show target m
> hide #!1 models
> select add #2
17 atoms, 16 bonds, 1 residue, 1 model selected
> show target m
> 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
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> close
> open "C:\Users\olawu\Downloads\PE 38:1.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
> hide #!2 models
> hide #1 models
> show #!2 models
> 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, 3 models selected
> ui tool show "Render/Select by Attribute"
No attribute chosen for rendering
> close #1
> 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
> open C:\Users\olawu\Downloads\E224Q-ATP.pdb format pdb
Chain information for E224Q-ATP.pdb #2
---
Chain | Description
A B | No description available
> close
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> 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
> close
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> style stick
Changed 17 atom styles
> style sphere
Changed 17 atom styles
> style ball
Changed 17 atom styles
> style sphere
Changed 17 atom styles
> 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
> select add #1
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
> hide #!2 models
> select subtract #2
Nothing selected
> open
> C:\Users\olawu\Downloads\DepositedStructure_SUBSTANCE_SID_160713653_Version_4.sdf
> format sdf
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> hide #4 models
> hide #3 models
> show #4 models
> show #3 models
> hide #4 models
> select add #3
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #4
34 atoms, 32 bonds, 2 residues, 2 models selected
> show #4 models
> show #!2 models
> hide #3 models
> select subtract #3
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide #4 models
> select subtract #4
Nothing selected
> select add #2
10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected
> show target m
> hide #3 models
> show #3 models
> select add #3
10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected
> select subtract #2
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide #!2 models
> select subtract #3
Nothing selected
> hide #1 models
> select add #4
17 atoms, 16 bonds, 1 residue, 1 model selected
> 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
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show AlphaFold
> alphafold match #1/A
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold A0A139WBU4 from
https://alphafold.ebi.ac.uk/files/AF-A0A139WBU4-F1-model_v4.cif
Collection has bfactors
1 AlphaFold model found using sequence similarity searches: A0A139WBU4 (chain
A)
AlphaFold prediction matching ABCH-WT-ceramide.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A139WBU4 | A0A139WBU4_TRICA | 6.51 | 727 | 642 | 100
Opened 1 AlphaFold model
> alphafold match #1/A
Collection has bfactors
1 AlphaFold model found using sequence similarity searches: A0A139WBU4 (chain
A)
AlphaFold prediction matching ABCH-WT-ceramide.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A139WBU4 | A0A139WBU4_TRICA | 6.51 | 727 | 642 | 100
Opened 1 AlphaFold model
> undo
Undo failed, probably because structures have been modified.
> hide #!1 models
> hide #!3 models
> show #!3 models
> close #2
> show #!1 models
> 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
> open "C:\Users\olawu\Downloads\PE 38:1.pdb" format pdb
> ui mousemode right "translate selected models"
> hide #!1 models
> ui mousemode right "translate selected models"
> show #!1 models
> hide #!1 models
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> show #!1 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> hide #!1 models
> show #!1 models
> select add #1
10212 atoms, 10433 bonds, 2 pseudobonds, 1287 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
17 atoms, 16 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,175.93,0,1,0,178.76,0,0,1,0
> select add #1
10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected
> view matrix models
> #1,1,0,0,-135.69,0,1,0,-145.7,0,0,1,0,#2,1,0,0,40.245,0,1,0,33.063,0,0,1,0
> select subtract #1
17 atoms, 16 bonds, 1 residue, 1 model selected
> select subtract #2
Nothing selected
> select add #2
17 atoms, 16 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,15.814,0,1,0,45.612,0,0,1,114.21
> select add #1
10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected
> view matrix models
> #1,1,0,0,-123.79,0,1,0,-154.11,0,0,1,-52.992,#2,1,0,0,27.712,0,1,0,37.196,0,0,1,61.221
> select subtract #1
17 atoms, 16 bonds, 1 residue, 1 model selected
> select subtract #2
Nothing selected
> select add #2
17 atoms, 16 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,27.814,0,1,0,40.434,0,0,1,56.99
> hide #!1 models
> view matrix models #2,1,0,0,30.151,0,1,0,37.145,0,0,1,48.652
> 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
> view matrix models #2,1,0,0,27.166,0,1,0,39.042,0,0,1,61.992
> select add #1
10229 atoms, 10449 bonds, 2 pseudobonds, 1288 residues, 3 models selected
> view matrix models
> #1,1,0,0,-117.64,0,1,0,-163.48,0,0,1,-74.118,#2,1,0,0,33.319,0,1,0,29.673,0,0,1,40.866
> view matrix models
> #1,1,0,0,-113.68,0,1,0,-156.67,0,0,1,-102.7,#2,1,0,0,37.279,0,1,0,36.481,0,0,1,12.287
> select subtract #1
17 atoms, 16 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,39.511,0,1,0,37.922,0,0,1,-1.0221
> view matrix models #2,1,0,0,35.939,0,1,0,38.537,0,0,1,16.87
> select subtract #2
Nothing selected
> hide #2 models
> show #2 models
> select ::name="UNL"
17 atoms, 16 bonds, 1 residue, 1 model selected
> undo
No Surface models open
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B
Alignment identifier is 1
> select #1/A-B:62-76
242 atoms, 248 bonds, 30 residues, 1 model selected
> select #1/A-B:62-553
6408 atoms, 6542 bonds, 2 pseudobonds, 810 residues, 2 models selected
> select #1/A-B:553
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A-B:554-568
232 atoms, 234 bonds, 30 residues, 1 model selected
> select #1/A-B:790
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:404-790
6080 atoms, 6224 bonds, 774 residues, 1 model selected
> coulombic sel
===== 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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
