![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16937 closed defect (can't reproduce)
Crash in chem_group on Windows
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202502220014 (2025-02-22 00:14:16 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Windows fatal exception: access violation
Windows fatal exception: Windows fatal exception: access violationaccess violation
Thread 0x00002d6cWindows fatal exception: access violation (most recent call first):
Windows fatal exception: access violation
File Windows fatal exception: access violation
"D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in Windows fatal exception: call_c_plus_plusaccess violation
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\hbonds\cmd.py", line 94 in cmd_hbonds
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\hbonds\tool.py", line 53 in run_hbonds
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
File "D:\software\ChimeraX 1.10.dev202502220014\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open F:/上海交大/交大-生物合成/IAAS/S58-ChimeraX.pdb
Summary of feedback from opening F:/上海交大/交大-生物合成/IAAS/S58-ChimeraX.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 16 ASN A 37 1 22
Start residue of secondary structure not found: HELIX 2 2 GLN A 41 GLN A 45 1
5
Start residue of secondary structure not found: HELIX 3 3 SER A 47 HIS A 59 1
13
Start residue of secondary structure not found: HELIX 4 4 ASP A 64 PHE A 74 1
11
End residue of secondary structure not found: HELIX 5 5 TYR A 80 PHE A 90 1 11
Start residue of secondary structure not found: HELIX 6 6 GLU A 97 LEU A 100 1
4
Start residue of secondary structure not found: HELIX 7 7 TYR A 146 TRP A 148
1 3
Start residue of secondary structure not found: HELIX 8 8 VAL A 183 PHE A 192
1 10
Start residue of secondary structure not found: HELIX 9 9 ASP A 199 ARG A 202
1 4
Start residue of secondary structure not found: HELIX 10 10 TRP A 214 MET A
218 1 5
6 messages similar to the above omitted
End residue of secondary structure not found: HELIX 17 17 TRP A 312 VAL A 316
1 5
Start residue of secondary structure not found: HELIX 18 18 GLY A 329 LEU A
342 1 14
Start residue of secondary structure not found: HELIX 19 19 GLU A 391 CYS A
393 1 3
Start residue of secondary structure not found: HELIX 20 20 ALA A 397 GLU A
399 1 3
Start residue of secondary structure not found: HELIX 21 21 LYS A 445 LEU A
447 1 3
Start residue of secondary structure not found: HELIX 22 22 ASP A 458 ILE A
468 1 11
11 messages similar to the above omitted
End residue of secondary structure not found: SHEET 8 8 1 MET A 322 ILE A 326
0
Start residue of secondary structure not found: SHEET 9 9 1 ASN A 347 ILE A
349 0
Start residue of secondary structure not found: SHEET 10 10 1 TYR A 353 GLY A
354 0
Start residue of secondary structure not found: SHEET 11 11 1 ASN A 359 ASP A
365 0
Start residue of secondary structure not found: SHEET 12 12 1 ASP A 368 ILE A
374 0
Start residue of secondary structure not found: SHEET 13 13 1 VAL A 379 ASP A
384 0
10 messages similar to the above omitted
S58-ChimeraX.pdb title:
Unplaced genomic scaffold scaffold_58, whole Ge... [more info...]
Chain information for S58-ChimeraX.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
Computing secondary structure
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #1.2 models
> show #1.1 models
> show #1.2 models
> close
> open F:\上海交大\交大-生物合成\IAAS\A0A0C9V216_icn3d-S58.pdb format pdb
Summary of feedback from opening F:\上海交大\交大-生物合成\IAAS\A0A0C9V216_icn3d-S58.pdb
---
warning | Ignored bad PDB record found on line 52
A0A0C9V216_icn3d-S58.pdb title:
Unplaced genomic scaffold scaffold_58, whole Ge... [more info...]
Chain information for A0A0C9V216_icn3d-S58.pdb #1
---
Chain | Description
A | No description available
> color #55ffffff
> color #55ff7fff
> color #aaff7fff
> color #acff7fff
> color #abfe7fff
> color #a8fa7dff
> color #a5f57aff
> color #a4f379ff
> color #9fec76ff
> color #9ce773ff
> color #99e371ff
> color #98e170ff
> color #8fd46aff
> color #8bcf67ff
> color #8bce67ff
> color #89cc66ff
> color #87c864ff
> color #81bf5fff
> color #7bb65bff
> color #79b45aff
> color #7ab55aff
> color #f6f6f6ff
> color #f3f3f3ff
> color #b2f3f3ff
> color #f3f3f3ff
> color #d39045ff
> color #f3f3f3ff
> color #b3b3b3ff
> color #f3f3f3ff
> color #b3b3b3ff
> color #c5c5c5ff
> color #f4f4f4ff
> color #fbfbfbff
> color #fefefeff
> color #fbfbfbff
> color #d7d7d7ff
> color #3d3d3dff
> color #a3452dff
> color #c94e2eff
> color #d1d1d1ff
> color #e2e2e2ff
> color #464646ff
> color #e6e6e6ff
> color #403032ff
> color #785d54ff
> color #715e56ff
> color #59656eff
> color #5d737fff
> color #636f7bff
> color #636568ff
> color #4c4b36ff
> color #806e33ff
> color #1a1e1bff
> color #3d3d3dff
> color #ffffffff
> color #e6e6e6ff
> color #f1f1f1ff
> color #ffffffff
> color #f9f9f9ff
> color #85835eff
> color #e6e6e6ff
> color #ffffffff
> color #f6f6f6ff
> color #f3f3f3ff
> color #fbfbfbff
> color #f3f3f3ff
> color #b54629ff
> color #a92b1aff
> color #b6462aff
> color #efefefff
> color #e9e9e9ff
> color #efefefff
> color #f3f3f3ff
> color #fbfbfbff
> color #f3f3f3ff
> color #efefefff
> color #eaeaeaff
> color #e9e9e9ff
> color #f3f3f3ff
> color #f6b46dff
> color #f3f3f3ff
> color #f2f2f2ff
> color #f3f3f3ff
> color #ffffffff
> color #7eb35bff
> color #ffffffff
> color #e8eae9ff
> color #97d76dff
> color #1a1812ff
> color #673c47ff
> color #6f9f50ff
> color #88c262ff
> color #79ad57ff
> color #75a754ff
> color #79ad57ff
> color #91ce68ff
> save F:/上海交大/交大-生物合成/IAAS/S58.cxs
> show target ab
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide #* target a
> show target ab
> hide target a
> ui tool show "Show Sequence Viewer"
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> ui dockable false "Show Sequence Viewer"
> show target ab
> hide target a
> show target m
> view clip false
> log metadata #1
Metadata for A0A0C9V216_icn3d-S58.pdb #1
---
Title | Unplaced genomic scaffold scaffold_58, whole Ge...
> log chains #1
Chain information for A0A0C9V216_icn3d-S58.pdb #1
---
Chain | Description
A | No description available
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> show #1 models
> ui tool show "Model Loops"
> show atoms
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> color sel magenta
> color sel cornflower blue
> color sel yellow
> color sel orange
> color sel #f6f6f6ff
> color sel #f3f3f3ff
> color sel #000000ff
> color sel #67924aff
> color sel #d9d9d9ff
> color sel #fefefeff
> color sel #212929ff
> color sel #222a2aff
> color sel #25302fff
> color sel #2b3837ff
> color sel #22302fff
> color sel #e23a2eff
> color sel #e33b2eff
> color sel #f6f6f6ff
> color sel #9d9dacff
> color sel #f3f3f3ff
> color sel #c88588ff
> color sel #f3f3f3ff
> color sel #fbfbfbff
> color sel #e8e8e8ff
> color sel #edededff
> color sel #f3f3f3ff
> color sel #f2f2f2ff
> color sel #f7630cff
> color sel #f3f3f3ff
> color sel #c8ab08ff
> color sel #c8af24ff
> color sel #c89c34ff
> color sel #c85d42ff
> color sel #c84f44ff
> color sel #f3f3f3ff
> color sel #af4428ff
> color sel #ac4327ff
> color sel #b6472aff
> color sel #b7472aff
> surface sel
> surface hidePatches (#!1 & sel)
> ui tool show "Show Sequence Viewer"
> chain/A
Unknown command: sequence chain/A
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select /A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 80
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-201
1631 atoms, 1678 bonds, 201 residues, 1 model selected
> select /A:202
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:202-240
307 atoms, 315 bonds, 39 residues, 1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:316-447
1019 atoms, 1040 bonds, 132 residues, 1 model selected
> select /A:315
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:211-315
846 atoms, 865 bonds, 105 residues, 1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:211-447
1865 atoms, 1906 bonds, 237 residues, 1 model selected
> surface (#!1 & sel)
> select /A:210
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:106-210
854 atoms, 884 bonds, 105 residues, 1 model selected
> surface (#!1 & sel)
> select /A:316-447
1019 atoms, 1040 bonds, 132 residues, 1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-447
3562 atoms, 3653 bonds, 447 residues, 1 model selected
> surface (#!1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select
> /A:95-96,111-114,125-128,153-156,161-170,173-181,241-246,322-326,347-349,353-354,359-365,368-374,379-384,394-395,405-411,419-430,437-444,449-451,454-456,476-484,491-498,537-541,583-586
1063 atoms, 1063 bonds, 130 residues, 1 model selected
> select /A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> sequence chain /A
Alignment identifier is 1/A
> select
> /A:16-37,41-45,47-59,64-74,80-90,97-100,146-148,183-192,199-202,214-218,222-235,247-259,261-270,280-289,294-303,306-308,312-316,329-342,391-393,397-399,445-447,458-468,506-520,523-529,545-556,573-580
1878 atoms, 1899 bonds, 229 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:444-447
34 atoms, 33 bonds, 4 residues, 1 model selected
> transparency (#!1 & sel) 60
> select /A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 60
> transparency (#!1 & sel) 70
> transparency (#!1 & sel) 80
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:281-447
1298 atoms, 1326 bonds, 167 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-447
3562 atoms, 3653 bonds, 447 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 60
> transparency (#!1 & sel) 10
> select /A:586-587
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> select /A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:443-446
30 atoms, 29 bonds, 4 residues, 1 model selected
> select /A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> /A:95-96,111-114,125-128,153-156,161-170,173-181,241-246,322-326,347-349,353-354,359-365,368-374,379-384,394-395,405-411,419-430,437-444,449-451,454-456,476-484,491-498,537-541,583-586
1063 atoms, 1063 bonds, 130 residues, 1 model selected
> select /A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-121
45 atoms, 44 bonds, 7 residues, 1 model selected
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-118
26 atoms, 25 bonds, 4 residues, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> select /A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-118
26 atoms, 25 bonds, 4 residues, 1 model selected
> style (#!1 & sel) ball
Changed 26 atom styles
> select /A:119
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:119
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style (#!1 & sel) ball
Changed 9 atom styles
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-118
26 atoms, 25 bonds, 4 residues, 1 model selected
> surface (#!1 & sel)
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> undo
> surface hidePatches (#!1 & sel)
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select subtract #1
1 model selected
> sequence chain /A
Alignment identifier is 1/A
> select /A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select
> /A:16-37,41-45,47-59,64-74,80-90,97-100,146-148,183-192,199-202,214-218,222-235,247-259,261-270,280-289,294-303,306-308,312-316,329-342,391-393,397-399,445-447,458-468,506-520,523-529,545-556,573-580
1878 atoms, 1899 bonds, 229 residues, 1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-121
45 atoms, 44 bonds, 7 residues, 1 model selected
> style (#!1 & sel) ball
Changed 45 atom styles
> color (#!1 & sel) magenta
> select /A:353
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:353-357
38 atoms, 38 bonds, 5 residues, 1 model selected
> style (#!1 & sel) ball
Changed 38 atom styles
> select /A:353
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:353-357
38 atoms, 38 bonds, 5 residues, 1 model selected
> surface (#!1 & sel)
> undo
> surface hidePatches (#!1 & sel)
> select /A:353
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:353-357
38 atoms, 38 bonds, 5 residues, 1 model selected
> color (#!1 & sel) magenta
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) ball
Changed 38 atom styles
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select
> /A:95-96,111-114,125-128,153-156,161-170,173-181,241-246,322-326,347-349,353-354,359-365,368-374,379-384,394-395,405-411,419-430,437-444,449-451,454-456,476-484,491-498,537-541,583-586
1063 atoms, 1063 bonds, 130 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select
> /A:95-96,111-114,125-128,153-156,161-170,173-181,241-246,322-326,347-349,353-354,359-365,368-374,379-384,394-395,405-411,419-430,437-444,449-451,454-456,476-484,491-498,537-541,583-586
1063 atoms, 1063 bonds, 130 residues, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:422-423
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) ball
Changed 8 atom styles
> color (#!1 & sel) magenta
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> select subtract #1
1 model selected
> select /A:587
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 30
> select
> /A:16-37,41-45,47-59,64-74,80-90,97-100,146-148,183-192,199-202,214-218,222-235,247-259,261-270,280-289,294-303,306-308,312-316,329-342,391-393,397-399,445-447,458-468,506-520,523-529,545-556,573-580
1878 atoms, 1899 bonds, 229 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:281-447
1298 atoms, 1326 bonds, 167 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-447
3562 atoms, 3653 bonds, 447 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 30
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> surface
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> select subtract #1
1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> select subtract #1
1 model selected
> select /A:42
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:42-45
32 atoms, 32 bonds, 4 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> transparency (#!1 & sel) 0
> select subtract #1
1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-423
37 atoms, 37 bonds, 5 residues, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) ball
Changed 37 atom styles
> color (#!1 & sel) magenta
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-422
29 atoms, 29 bonds, 4 residues, 1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-420
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:421-423
20 atoms, 19 bonds, 3 residues, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:421-423
20 atoms, 19 bonds, 3 residues, 1 model selected
> select
> /A:95-96,111-114,125-128,153-156,161-170,173-181,241-246,322-326,347-349,353-354,359-365,368-374,379-384,394-395,405-411,419-430,437-444,449-451,454-456,476-484,491-498,537-541,583-586
1063 atoms, 1063 bonds, 130 residues, 1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-420
17 atoms, 17 bonds, 2 residues, 1 model selected
> color (#!1 & sel) #f6f6f6ff
> color (#!1 & sel) #f6d9bcff
> color (#!1 & sel) #f6f6f6ff
> color (#!1 & sel) #f3f3f3ff
> color (#!1 & sel) #f800f8ff
> color (#!1 & sel) #aac062ff
> color (#!1 & sel) #c1da70ff
> color (#!1 & sel) #90a353ff
> color (#!1 & sel) #69773dff
> color (#!1 & sel) #616e38ff
> color (#!1 & sel) #5f6b37ff
> color (#!1 & sel) #4f592dff
> color (#!1 & sel) #545f30ff
> color (#!1 & sel) #535e30ff
> color (#!1 & sel) #5c6835ff
> color (#!1 & sel) #8c9e51ff
> color (#!1 & sel) #f3f3f3ff
> color (#!1 & sel) #586433ff
> color (#!1 & sel) #b6cd69ff
> color (#!1 & sel) #586433ff
> color (#!1 & sel) #7a8a47ff
> color (#!1 & sel) #abc163ff
> color (#!1 & sel) #f3f3f3ff
> color (#!1 & sel) #6cb2f3ff
> color (#!1 & sel) #f3f3f3ff
> color (#!1 & sel) #7f904aff
> color (#!1 & sel) #c0d96fff
> color (#!1 & sel) #748343ff
> color (#!1 & sel) #000000ff
> color (#!1 & sel) #80904aff
> color (#!1 & sel) #9eb25bff
> color (#!1 & sel) #99ad59ff
> color (#!1 & sel) #5d6936ff
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-420
17 atoms, 17 bonds, 2 residues, 1 model selected
> color (#!1 & sel) magenta
> surface hidePatches (#!1 & sel)
> undo
> redo
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select subtract #1
1 model selected
> select /A:419
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:419-423
37 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:416-418
33 atoms, 34 bonds, 3 residues, 1 model selected
> select /A:415
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:415-416
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:415
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:415-423
74 atoms, 76 bonds, 9 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:415-423
74 atoms, 76 bonds, 9 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:420
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:420
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) ball
Changed 9 atom styles
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:115
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:115-121
45 atoms, 44 bonds, 7 residues, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> select /A:353
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:353-357
38 atoms, 38 bonds, 5 residues, 1 model selected
> select /A:415
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:415-426
98 atoms, 100 bonds, 12 residues, 1 model selected
> select /A:423
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:415-423
74 atoms, 76 bonds, 9 residues, 1 model selected
> select /A:525
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:525
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> select subtract #1
1 model selected
> save F:/上海交大/交大-生物合成/IAAS/S58蛋白结构细节图.tif width 603 height 439 supersample 3
> select add #1
4657 atoms, 4771 bonds, 587 residues, 1 model selected
> surface (#!1 & sel)
> select subtract #1
1 model selected
> save F:/上海交大/交大-生物合成/IAAS/S58蛋白结构表面图.tif width 603 height 439 supersample 3
> open F:/上海交大/交大-生物合成/IAAS/4EPL_icn3d.pdb
Summary of feedback from opening F:/上海交大/交大-生物合成/IAAS/4EPL_icn3d.pdb
---
warning | Ignored bad PDB record found on line 44
4EPL_icn3d.pdb title:
Crystal Structure Of Arabidopsis Thaliana Gh3.1... [more info...]
Chain information for 4EPL_icn3d.pdb #2
---
Chain | Description
A | No description available
> hide #!1 models
> sequence chain /A
Chains must have same sequence
> surface #2
> surface hidePatches #2
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:100-105
38 atoms, 37 bonds, 6 residues, 1 model selected
> select add #2
4367 atoms, 4465 bonds, 3 pseudobonds, 552 residues, 3 models selected
> select subtract #2
1 model selected
> hide #!2 models
> open F:/上海交大/交大-生物合成/IAAS/4EPL.PDB
4EPL.PDB title:
Crystal structure of arabidopsis thaliana GH3.11 (JAR1) In complex with ja-ile
[more info...]
Chain information for 4EPL.PDB #3
---
Chain | Description | UniProt
A | jasmonic acid-amido synthetase JAR1 | JAR1_ARATH 1-575
Non-standard residues in 4EPL.PDB #3
---
JAI —
N-({(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine
> color #3 cornflower blue
> undo
> color #3 cornflower blue
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select
> #3/A:9-39,42-47,57-65,69-82,114-136,164-171,174-183,189-194,197-212,224-248,256-265,270-284,289-295,306-321,380-382,437-454,486-501,503-512,526-537,555-564
2129 atoms, 2148 bonds, 265 residues, 1 model selected
> select #3/A:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-106
42 atoms, 41 bonds, 7 residues, 1 model selected
> select #3/A:150
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:150-157
63 atoms, 63 bonds, 8 residues, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-109
69 atoms, 69 bonds, 10 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 69 atom styles
> color sel magenta
> select #3/A:330
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:330-334
37 atoms, 37 bonds, 5 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 37 atom styles
> color sel magenta
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-101
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:397
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:397-405
78 atoms, 79 bonds, 9 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel ball
Changed 78 atom styles
> color sel magenta
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/A:400
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:400
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select
> #3/A:96-104,107-113,143-147,154-155,161-163,216-223,301-304,325-327,330-332,335-339,352-354,360-365,377-378,387-393,401-413,416-424,459-467,474-481,519-523,566-571
956 atoms, 970 bonds, 117 residues, 1 model selected
> select #3/A:401
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:401
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:399
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:399
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel target a
> select #3/A:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #3/A:96-104,107-113,143-147,154-155,161-163,216-223,301-304,325-327,330-332,335-339,352-354,360-365,377-378,387-393,401-413,416-424,459-467,474-481,519-523,566-571
956 atoms, 970 bonds, 117 residues, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:102
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:102
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:102
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel target a
> select #3/A:106
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:106
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:107-108
18 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel target a
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:421
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:421
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:421-422
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/A:426
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:426
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:427-572
1099 atoms, 1114 bonds, 1 pseudobond, 140 residues, 2 models selected
> select #3/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:427-575
1123 atoms, 1139 bonds, 1 pseudobond, 143 residues, 2 models selected
> show #!1 models
> hide #!3 models
> surface hidePatches #1
> show #!3 models
> color (#!3 & sel) #f6f6f6ff
> color (#!3 & sel) #f3f3f3ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #3d180eff
> color (#!3 & sel) #f3603aff
> color (#!3 & sel) #fe633bff
> color (#!3 & sel) #e65935ff
> color (#!3 & sel) #ca4e2eff
> color (#!3 & sel) #b34629ff
> color (#!3 & sel) #ea5b36ff
> color (#!3 & sel) #f4623cff
> color (#!3 & sel) #fb6741ff
> color (#!3 & sel) #9c3c24ff
> color (#!3 & sel) #6b984dff
> color (#!3 & sel) #6a2918ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #a23f25ff
> color (#!3 & sel) #f35e38ff
> color (#!3 & sel) #e75a35ff
> color (#!3 & sel) #de5633ff
> color (#!3 & sel) #e75a35ff
> color (#!3 & sel) #ff673fff
> color (#!3 & sel) #f2603aff
> color (#!3 & sel) #903821ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #628c47ff
> color (#!3 & sel) #b04428ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #522013ff
> color (#!3 & sel) #3b170dff
> color (#!3 & sel) #f55f38ff
> color (#!3 & sel) #81321eff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ff673fff
> color (#!3 & sel) #ff643cff
> color (#!3 & sel) #ff6d44ff
> color (#!3 & sel) #ff6d45ff
> color (#!3 & sel) #c54c2dff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #a3e875ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #577c3eff
> color (#!3 & sel) #bcff87ff
> color (#!3 & sel) #8ac463ff
> color (#!3 & sel) #90cd67ff
> color (#!3 & sel) #a4e975ff
> color (#!3 & sel) #6c9a4eff
> color (#!3 & sel) #9fe272ff
> color (#!3 & sel) #8ac563ff
> color (#!3 & sel) #9fe272ff
> color (#!3 & sel) #446030ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #702b1aff
> color (#!3 & sel) #ff744dff
> color (#!3 & sel) #ffa079ff
> color (#!3 & sel) #ff9d75ff
> color (#!3 & sel) #ffa47cff
> color (#!3 & sel) #f9653eff
> color (#!3 & sel) #ff6b44ff
> color (#!3 & sel) #c84d2eff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #d15130ff
> color (#!3 & sel) #d05130ff
> color (#!3 & sel) #c44c2dff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #c74d2eff
> color (#!3 & sel) #b7472aff
> color (#!3 & sel) #b9482aff
> color (#!3 & sel) #bd492bff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #beff89ff
> color (#!3 & sel) #a0e473ff
> color (#!3 & sel) #b5ff82ff
> color (#!3 & sel) #c64d2eff
> color (#!3 & sel) #cc4f2fff
> color (#!3 & sel) #ce502fff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #638d47ff
> color (#!3 & sel) #5c2315ff
> color (#!3 & sel) #6b2a19ff
> color (#!3 & sel) #652717ff
> color (#!3 & sel) #712c1aff
> color (#!3 & sel) #6f2b19ff
> color (#!3 & sel) #324724ff
> color (#!3 & sel) #87341fff
> color (#!3 & sel) #cf502fff
> color (#!3 & sel) #4d6d37ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ff7048ff
> color (#!3 & sel) #ff6941ff
> color (#!3 & sel) #ff6c45ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #9fe272ff
> color (#!3 & sel) #a0e473ff
> color (#!3 & sel) #b7472aff
> color (#!3 & sel) #c64d2dff
> color (#!3 & sel) #bd492bff
> color (#!3 & sel) #e75a35ff
> color (#!3 & sel) #ce502fff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #ef5d37ff
> color (#!3 & sel) #ff6941ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ff734cff
> color (#!3 & sel) #ff714aff
> color (#!3 & sel) #f05f39ff
> color (#!3 & sel) #df5733ff
> color (#!3 & sel) #da5532ff
> color (#!3 & sel) #cd502fff
> color (#!3 & sel) #bd492bff
> color (#!3 & sel) #7a2f1cff
> color (#!3 & sel) #ff00ffff
> color (#!3 & sel) #7aae58ff
> color (#!3 & sel) #d65331ff
> color (#!3 & sel) #bc492bff
> color (#!3 & sel) #b3fe80ff
> color (#!3 & sel) #5e8543ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #b6472aff
> color (#!3 & sel) #cd4f2fff
> color (#!3 & sel) #d65331ff
> color (#!3 & sel) #cd4f2fff
> color (#!3 & sel) #b5462aff
> color (#!3 & sel) #7f311dff
> color (#!3 & sel) #c2ff8bff
> color (#!3 & sel) #8fcc67ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ec5b36ff
> color (#!3 & sel) #ee5c37ff
> color (#!3 & sel) #ef5d37ff
> color (#!3 & sel) #ee5c37ff
> color (#!3 & sel) #ec5c36ff
> color (#!3 & sel) #4f7139ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #8b3620ff
> color (#!3 & sel) #8c3620ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #c24b2cff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #af4428ff
> color (#!3 & sel) #983b23ff
> color (#!3 & sel) #6f2b19ff
> color (#!3 & sel) #943922ff
> color (#!3 & sel) #762e1bff
> color (#!3 & sel) #7a2f1cff
> color (#!3 & sel) #9fe272ff
> color (#!3 & sel) #fafafaff
> color (#!3 & sel) #e3e3e3ff
> color (#!3 & sel) #ff55ffff
> color (#!3 & sel) #f3f3f3ff
> color (#!3 & sel) #55007fff
> color (#!3 & sel) #efefefff
> color (#!3 & sel) #fafafaff
> color (#!3 & sel) #f1f1f1ff
> color (#!3 & sel) #fefefeff
> color (#!3 & sel) #476aa9ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #f3f3f3ff
> color (#!3 & sel) #979797ff
> color (#!3 & sel) #c88e9dff
> color (#!3 & sel) #c88c9eff
> color (#!3 & sel) #c897a8ff
> color (#!3 & sel) #c8a1adff
> color (#!3 & sel) #c8a2a9ff
> color (#!3 & sel) #f3f3f3ff
> color (#!3 & sel) #f6f6f6ff
> color (#!3 & sel) #42629cff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #85c6ffff
> color (#!3 & sel) #20304cff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #bf4a2cff
> color (#!3 & sel) #953a22ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #511f12ff
> color (#!3 & sel) #983b23ff
> color (#!3 & sel) #aa4227ff
> color (#!3 & sel) #b14529ff
> color (#!3 & sel) #b5462aff
> color (#!3 & sel) #bc492bff
> color (#!3 & sel) #bf4a2cff
> color (#!3 & sel) #b34529ff
> color (#!3 & sel) #632617ff
> color (#!3 & sel) #5f2516ff
> color (#!3 & sel) #542113ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #df5633ff
> color (#!3 & sel) #cf5030ff
> color (#!3 & sel) #d35230ff
> color (#!3 & sel) #d45231ff
> color (#!3 & sel) #ea5b36ff
> color (#!3 & sel) #fc623aff
> color (#!3 & sel) #f76039ff
> color (#!3 & sel) #e45934ff
> color (#!3 & sel) #88c161ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #c1ff8aff
> color (#!3 & sel) #cbff93ff
> color (#!3 & sel) #963a22ff
> color (#!3 & sel) #792f1cff
> color (#!3 & sel) #582214ff
> color (#!3 & sel) #592214ff
> color (#!3 & sel) #762e1bff
> color (#!3 & sel) #993c23ff
> color (#!3 & sel) #762e1bff
> color (#!3 & sel) #993c23ff
> color (#!3 & sel) #9c3d24ff
> color (#!3 & sel) #d95432ff
> color (#!3 & sel) #622617ff
> color (#!3 & sel) #9c3d24ff
> color (#!3 & sel) #f05d37ff
> color (#!3 & sel) #ea5b36ff
> color (#!3 & sel) #e75a35ff
> color (#!3 & sel) #d05130ff
> color (#!3 & sel) #db5532ff
> color (#!3 & sel) #b34629ff
> color (#!3 & sel) #5d2415ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #bbff86ff
> color (#!3 & sel) #702b1aff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #e45934ff
> color (#!3 & sel) #88351fff
> color (#!3 & sel) #7a301cff
> color (#!3 & sel) #8c3620ff
> color (#!3 & sel) #933922ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #b34629ff
> color (#!3 & sel) #4b6b36ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #d35230ff
> color (#!3 & sel) #f35f39ff
> color (#!3 & sel) #ee5c37ff
> color (#!3 & sel) #f45f38ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #ff00ffff
> color (#!3 & sel) #e500e5ff
> color (#!3 & sel) #622616ff
> color (#!3 & sel) #cf5030ff
> color (#!3 & sel) #000000ff
> color (#!3 & sel) #9c3d24ff
> color (#!3 & sel) #983b23ff
> hide #!1 models
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
Nothing selected
> surface #3
> surface hidePatches #3
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select clear
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
1 model selected
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
1 model selected
> select #3/A:149-150
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-109
69 atoms, 69 bonds, 10 residues, 1 model selected
> surface (#!3 & sel)
> color (#!3 & sel) magenta
> select #3/A:397
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:397-405
78 atoms, 79 bonds, 9 residues, 1 model selected
> surface (#!3 & sel)
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> select subtract #3
1 model selected
> surface hidePatches #3
> select #3/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> select #3/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:427-575
1123 atoms, 1139 bonds, 1 pseudobond, 143 residues, 2 models selected
> surface (#!3 & sel)
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> surface (#!3 & sel)
> volume planes z style image imageMode "full region"
No volumes specified
> select subtract #3
1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!1 models
> surface #1,3
> ui tool show Matchmaker
> hide #!3 models
> hide #!1 models
> show #!2 models
> close #2
> show #!1 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 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 A0A0C9V216_icn3d-S58.pdb, chain A (#1) with 4EPL.PDB, chain A (#3),
sequence alignment score = 647.3
RMSD between 188 pruned atom pairs is 1.121 angstroms; (across all 532 pairs:
16.109)
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> save F:/上海交大/交大-生物合成/IAAS/S58蛋白结构表面图.tif width 554 height 439 supersample 3
> show #!3 models
> hide #!1 models
> ~label #3 residues
> undo
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select clear
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-109
69 atoms, 69 bonds, 10 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> select #3/A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:100-109
69 atoms, 69 bonds, 10 residues, 1 model selected
> select #3/A:102
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:102-108
48 atoms, 48 bonds, 7 residues, 1 model selected
> color (#!3 & sel) cornflower blue
> surface (#!3 & sel)
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> surface (#!3 & sel)
> select subtract #3
1 model selected
> select add #3
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #3
1 model selected
> surface hidePatches #3
> close #3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> open F:/上海交大/交大-生物合成/IAAS/4EPL.PDB
4EPL.PDB title:
Crystal structure of arabidopsis thaliana GH3.11 (JAR1) In complex with ja-ile
[more info...]
Chain information for 4EPL.PDB #2
---
Chain | Description | UniProt
A | jasmonic acid-amido synthetase JAR1 | JAR1_ARATH 1-575
Non-standard residues in 4EPL.PDB #2
---
JAI —
N-({(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine
> hide #!1 models
> surface #2
> surface hidePatches #2
> hide #!2 models
> show #!1 models
> surface hidePatches #1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:448
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:448-587
1095 atoms, 1117 bonds, 140 residues, 1 model selected
> surface (#!1 & sel)
> color (#!1 & sel) #f6f6f6ff
> color (#!1 & sel) #f2f2f2ff
> color (#!1 & sel) #fbfbfbff
> color (#!1 & sel) #fefefeff
> color (#!1 & sel) #fbfbfbff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #fefefeff
> color (#!1 & sel) #e05307ff
> color (#!1 & sel) #fefefeff
> color (#!1 & sel) #efefefff
> color (#!1 & sel) #fefefeff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #e05307ff
> color (#!1 & sel) #e35407ff
> color (#!1 & sel) #e15307ff
> color (#!1 & sel) #d85007ff
> color (#!1 & sel) #ce4c06ff
> color (#!1 & sel) #bc4606ff
> color (#!1 & sel) #b04106ff
> color (#!1 & sel) #a23c05ff
> color (#!1 & sel) #953705ff
> color (#!1 & sel) #883204ff
> color (#!1 & sel) #873204ff
> color (#!1 & sel) #792d04ff
> color (#!1 & sel) #7a2d04ff
> color (#!1 & sel) #7e2f04ff
> color (#!1 & sel) #7f2f04ff
> color (#!1 & sel) #8a3304ff
> color (#!1 & sel) #8f3504ff
> color (#!1 & sel) #933605ff
> color (#!1 & sel) #993905ff
> color (#!1 & sel) #9c3a05ff
> color (#!1 & sel) #9e3b05ff
> color (#!1 & sel) #9f3b05ff
> color (#!1 & sel) #a23c05ff
> select add #1
4657 atoms, 4771 bonds, 587 residues, 2 models selected
> surface (#!1 & sel)
> select subtract #1
1 model selected
> save F:/上海交大/交大-生物合成/IAAS/S58蛋白结构表面图.tif width 554 height 439 supersample 3
> show #!2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> color (#!2 & sel) #a63d05ff
> color (#!2 & sel) #a53d05ff
> color (#!2 & sel) #a33c05ff
> color (#!2 & sel) #a13c05ff
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> select subtract #2
1 model selected
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #2
1 model selected
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> surface (#!2 & sel)
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> surface (#!2 & sel)
> select subtract #2
1 model selected
> show #!1 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 A0A0C9V216_icn3d-S58.pdb, chain A (#1) with 4EPL.PDB, chain A (#2),
sequence alignment score = 647.3
RMSD between 188 pruned atom pairs is 1.121 angstroms; (across all 532 pairs:
16.109)
> undo
> show #!1 models
> hide #!1 models
> select #2/A:427-428
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:427-481
445 atoms, 452 bonds, 55 residues, 1 model selected
> select #2/A:428-429
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> color (#!2 & sel) orange red
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> select subtract #2
1 model selected
> show #!1 models
> hide #!1 models
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> color (#!2 & sel) orange
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> show #!1 models
> select subtract #2
1 model selected
> hide #!1 models
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> color (#!2 & sel) purple
> color (#!2 & sel) hot pink
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> show #!1 models
> select subtract #2
1 model selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 3 models selected
> select subtract #2
1 model selected
> select #2/A:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:428-575
1115 atoms, 1131 bonds, 1 pseudobond, 142 residues, 2 models selected
> color (#!2 & sel) #ffaaffff
> color (#!2 & sel) #ff55ffff
> color (#!2 & sel) #ff5500ff
> color (#!2 & sel) #ffaa00ff
> color (#!2 & sel) #00ffffff
> color (#!2 & sel) #00ff7fff
> color (#!2 & sel) #ffff00ff
> color (#!2 & sel) #ffff7fff
> color (#!2 & sel) #ffff00ff
> color (#!2 & sel) #ff00ffff
> color (#!2 & sel) #ff007fff
> color (#!2 & sel) #ff55ffff
> color (#!2 & sel) #ffaaffff
> color (#!2 & sel) #55ffffff
> color (#!2 & sel) #ffffffff
> color (#!2 & sel) #ffff7fff
> color (#!2 & sel) #ffff00ff
> color (#!2 & sel) #aaffffff
> color (#!2 & sel) #ffff00ff
> color (#!2 & sel) #fefe00ff
> color (#!2 & sel) #f4f400ff
> color (#!2 & sel) #e6e600ff
> color (#!2 & sel) #d9d900ff
> color (#!2 & sel) #cccc00ff
> color (#!2 & sel) #c2c200ff
> color (#!2 & sel) #b8b800ff
> color (#!2 & sel) #adad00ff
> color (#!2 & sel) #afaf00ff
> color (#!2 & sel) #b5b500ff
> color (#!2 & sel) #baba00ff
> color (#!2 & sel) #bcbc00ff
> color (#!2 & sel) #bdbd00ff
> color (#!2 & sel) #ffaa00ff
> color (#!2 & sel) #fda900ff
> color (#!2 & sel) #f3a200ff
> color (#!2 & sel) #e89b00ff
> color (#!2 & sel) #e39700ff
> color (#!2 & sel) #e29700ff
> color (#!2 & sel) #e28c01ff
> color (#!2 & sel) #e28f01ff
> color (#!2 & sel) #e2c806ff
> color (#!2 & sel) #3ce216ff
> color (#!2 & sel) #2b99e2ff
> color (#!2 & sel) #b33be2ff
> color (#!2 & sel) #e242dfff
> color (#!2 & sel) #e24dbaff
> color (#!2 & sel) #e2589fff
> color (#!2 & sel) #e2589bff
> color (#!2 & sel) #e25896ff
> color (#!2 & sel) #e25695ff
> color (#!2 & sel) #e25394ff
> color (#!2 & sel) #e24a8cff
> color (#!2 & sel) #e24181ff
> color (#!2 & sel) #e23b7eff
> color (#!2 & sel) #e23a7dff
> color (#!2 & sel) #e22b74ff
> color (#!2 & sel) #e22b7bff
> color (#!2 & sel) #e235baff
> color (#!2 & sel) #4439e2ff
> color (#!2 & sel) #39e260ff
> color (#!2 & sel) #e2bd36ff
> color (#!2 & sel) #e29933ff
> color (#!2 & sel) #e2772fff
> color (#!2 & sel) #e2602dff
> color (#!2 & sel) #e2662dff
> color (#!2 & sel) #e2832fff
> color (#!2 & sel) #e29f33ff
> color (#!2 & sel) #e2a835ff
> color (#!2 & sel) #e2a936ff
> color (#!2 & sel) #e2ae36ff
> color (#!2 & sel) #e2ae35ff
> color (#!2 & sel) #e2a732ff
> color (#!2 & sel) #e2a52bff
> color (#!2 & sel) #e2a325ff
> color (#!2 & sel) #e2901cff
> color (#!2 & sel) #e28f1bff
> color (#!2 & sel) #e28719ff
> color (#!2 & sel) #e28419ff
> color (#!2 & sel) #e27d19ff
> color (#!2 & sel) #e28419ff
> color (#!2 & sel) #e28e19ff
> color (#!2 & sel) #e29519ff
> color (#!2 & sel) #e29417ff
> color (#!2 & sel) #e29314ff
> color (#!2 & sel) #e29212ff
> color (#!2 & sel) #e29211ff
> color (#!2 & sel) #e2910fff
> color (#!2 & sel) #e2900dff
> color (#!2 & sel) #e2900cff
> color (#!2 & sel) #e2880bff
> color (#!2 & sel) #e2810aff
> color (#!2 & sel) #e27d0aff
> color (#!2 & sel) #e27509ff
> color (#!2 & sel) #e26e09ff
> color (#!2 & sel) #e27509ff
> color (#!2 & sel) #e2810bff
> color (#!2 & sel) #e2820cff
> color (#!2 & sel) #e29612ff
> color (#!2 & sel) #e29d13ff
> color (#!2 & sel) #e2a516ff
> color (#!2 & sel) #e2a91aff
> color (#!2 & sel) #e2aa1bff
> color (#!2 & sel) #e2aa1cff
> color (#!2 & sel) #e2a71cff
> color (#!2 & sel) #e29f1aff
> color (#!2 & sel) #e29714ff
> color (#!2 & sel) #e29212ff
> color (#!2 & sel) #e28b11ff
> color (#!2 & sel) #e28a0fff
> color (#!2 & sel) #e2830fff
> select add #2
4765 atoms, 4488 bonds, 3 pseudobonds, 928 residues, 4 models selected
> select subtract #2
1 model selected
> show #!1 models
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> undo
> redo
> surface #2.1#!1-2
> ui mousemode right "delete markers"
> undo
> volume projectionMode rays
No volumes specified
> ui tool show H-Bonds
> hbonds makePseudobonds false relax false
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202502220014 (2025-02-22)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 388.73
OpenGL renderer: GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Timi
Model: TM1703
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 8,494,747,648
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.1.1
build: 1.2.1
certifi: 2025.1.31
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: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.0.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
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.dev202502220014
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: 2.1.7
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: 1.14.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
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: 2.5.2
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: 1.44
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: 7.6.12
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.17.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.13.0
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: 4.2.0
lxml: 5.2.2
lz4: 4.4.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.1.0
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: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pywin32: 306
pyzmq: 26.2.1
qtconsole: 5.5.2
QtPy: 2.4.3
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: 8.1.3
sphinx-autodoc-typehints: 3.0.1
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: 0.7.1
tables: 3.10.2
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: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in chem_group on Windows |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
