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Opened 3 years ago
Closed 3 years ago
#6904 closed defect (duplicate)
Long atom spec crashes ChimeraX
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow
Current thread 0x0000a6dc (most recent call first):
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 138 in _safekey
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 71 in set
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 106 in __setitem__
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 61 in upairs
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 67 in update
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 19 in __init__
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\ast.py", line 90 in copy
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 642 in _try
File "E:\Program Files\ChimeraX 1.3\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 679 in _choice
File "E:\Program Files\ChimeraX 1.3\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 688 in _optional
File "E:\Program Files\ChimeraX 1.3\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 427 in _part_range_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 409 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.3\bin\lib\site-packages\grako\contexts.py", line 458 in _call
...
===== Log before crash start =====
> open E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/acidic_APO_fig.cxs
opened ChimeraX session
> hide #!1 models
> select #2
30679 atoms, 31351 bonds, 3949 residues, 1 model selected
> surface sel probeRadius 1.2 gridSpacing 0.3
> hide #2.9 models
> show #2.9 models
> color #2.9 #ffff7f transparency 0
> color #2.9 yellow transparency 0
> hide #2.10 models
> select clear
> color #2.10 #3f65d9 transparency 0
> color #2.10 #3f65d905
> color #2.10 #3f65d9 transparency 0
> show #2.10 models
> hide #2.11 models
> color #2.11 #969696 transparency 0
> show #2.11 models
> hide #2.12 models
> color #2.12 #a80000 transparency 0
> show #2.12 models
> hide #2.13 models
> color #2.13 #ed799f transparency 0
> color #2.13 #e8779c transparency 0
> show #2.13 models
> hide #2.14 models
> color #2.14 #005500 transparency 0
> show #2.14 models
> hide #2.15 models
> color #2.15 #00dbf8 transparency 0
> show #2.15 models
> hide #2.16 models
> color #2.16 #c6961d transparency 0
> show #2.16 models
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> color #2.9 #e3e300 transparency 0
> color #2.9 #b4b400 transparency 0
> color #2.9 #b3b300 transparency 0
> color #2.16 #ffaa00 transparency 0
> color #2.16 #d48d00 transparency 0
> color #2.16 #c68400 transparency 0
> lighting soft
> lighting simple
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> ui tool show "Side View"
> view name surface1
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1A.png supersample 8
> transparentBackground true
> color #2.15 #00c1da transparency 0
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1A.png supersample 8
> transparentBackground true
> turn x 90
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1B.png supersample 8
> transparentBackground true
> view name surface2
> hide #2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.5 models
> hide #!2.6 models
> hide #2.4 models
> hide #2.7 models
> hide #!2.8 models
> hide #!2.9 models
> hide #2.10 models
> hide #!2.11 models
> hide #!2.12 models
> hide #!2.13 models
> hide #2.14 models
> hide #!2.15 models
> hide #!2.16 models
> lighting full
> lighting shadows false
> lighting shadows true
> select ::name="CA"
16 atoms, 16 residues, 2 models selected
> select ions
32 atoms, 32 residues, 2 models selected
> style (#!2 & sel) sphere
Changed 16 atom styles
> show (#!2 & sel) target ab
> select clear
> select ::name="CA"
16 atoms, 16 residues, 2 models selected
> ui tool show "Color Actions"
> color sel purple
> select clear
> select ::name="MG"
16 atoms, 16 residues, 2 models selected
> color sel lawn green
> color sel chartreuse
> select clear
> select ::name="ZN"
32 atoms, 32 residues, 2 models selected
> color sel black
> style (#!2 & sel) sphere
Changed 16 atom styles
> show (#!2 & sel) target ab
> select clear
> select ions
32 atoms, 32 residues, 2 models selected
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1D.png supersample 8
> transparentBackground true
> turn x -90
> turn y 5
> turn y -2
> turn x -2
> turn x 1
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1C.png supersample 8
> transparentBackground true
> show #!2.9 models
> show #2.10 models
> show #!2.11 models
> show #!2.13 models
> show #2.14 models
> show #!2.15 models
> show #!2.16 models
> show #!2.12 models
> show #!2.8 models
> show #2.7 models
> show #!2.6 models
> show #!2.5 models
> show #2.4 models
> show #!2.3 models
> show #!2.2 models
> show #2.1 models
> lighting soft
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig1A.png supersample 8
> transparentBackground true
> view name surface1
> turn y 90
> transparency #2.1-16 0
> transparency #2.1-16 50
> transparency #2.1-16 0
> transparency #2.1-16 50
> transparency #2.1-16 0
> turn y -90
> view list
Named views: surface1, surface2
> view surface1
> select #2.1-2.8
Nothing selected
> select #2.1-8
672 atoms, 48 residues, 10 models selected
> transparency sel 50
> select clear
> save E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/acidic_APO_fig.cxs
> includeMaps true
> surface hidePatches #2
> select #2/D:499
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:282
15 atoms, 14 bonds, 2 residues, 2 models selected
> select clear
> ui tool show Contacts
> contacts resSeparation 5 interModel false intraMol false radius 0.155
5322 contacts
> close session
> open E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/acidic_APO_fig.cxs
opened ChimeraX session
> close #1
> close #2.1,7#2.2-6,8-16
> save
> E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/acidic_APO_fig_contact.cxs
> select #2/B:22,35,31,79,281,80,78,370
72 atoms, 69 bonds, 8 residues, 1 model selected
> lighting shadows true intensity 0.5
> lighting simple
> show sel target ab
> select ::name="NAG"
672 atoms, 688 bonds, 48 residues, 1 model selected
> hide sel target a
> select #2/B:22,35,31,79,281,80,78,370
72 atoms, 69 bonds, 8 residues, 1 model selected
> select clear
> hide target a
> select #2/B:22,35,31,79,281,80,78,370
72 atoms, 69 bonds, 8 residues, 1 model selected
> show sel target ab
> select #2/D:22,35,31,79,281,80,78,370,49,321
91 atoms, 86 bonds, 10 residues, 1 model selected
> select #2/B,D:22,35,31,79,281,80,78,370,49,321
182 atoms, 172 bonds, 20 residues, 1 model selected
> show sel target ab
Drag select of 9 residues
> select up
280 atoms, 277 bonds, 40 residues, 1 model selected
> select up
7674 atoms, 7842 bonds, 988 residues, 1 model selected
Drag select of 13 residues
> select up
8062 atoms, 8227 bonds, 1044 residues, 1 model selected
> select up
15348 atoms, 15684 bonds, 1976 residues, 1 model selected
> transparency 50
> transparency sel 50 target c
> transparency sel 100 target c
> select clear
> select #2/B,D:22,35,31,79,281,80,78,370,49,321,213,156
220 atoms, 206 bonds, 24 residues, 1 model selected
> show sel target ab
> select clear
> select #2/F: 213,156
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel target ab
> select /B:144
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select clear
> select /H:213
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/B,D: 264
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/G,H: 264
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2: 264
72 atoms, 64 bonds, 8 residues, 1 model selected
> hide sel target a
> open E:/writing/ALPL/models/YDQ/WT/0928/round2/alp_Oct25_refine_7-coot-0.pdb
Chain information for alp_Oct25_refine_7-coot-0.pdb #1
---
Chain | Description
A | No description available
B C E F | No description available
D G H | No description available
> close #2
> close
> open
> E:\writing\ALPL\models\YDQ\prefigure\acidic_APO\acidic_APO_fig_contact.cxs
> format session
opened ChimeraX session
> select #2/B,D:22,35,31,79,281,80,78,370,49,321,213,156
220 atoms, 206 bonds, 24 residues, 1 model selected
> select clear
> hide target a
Drag select of 26 residues
Drag select of 9 residues
> select up
502 atoms, 504 bonds, 68 residues, 1 model selected
> select up
15348 atoms, 15684 bonds, 1976 residues, 1 model selected
> transparency sel 100 target c
> select clear
> select #2/B,D:22,35,31,79,281,80,78,370,49,321,213,156
220 atoms, 206 bonds, 24 residues, 1 model selected
> show sel target ab
> select #2/F: 213,156
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel target ab
> open E:/writing/ALPL/models/YDQ/basic_inhibito/newOCT_ALPL.pdb
Chain information for newOCT_ALPL.pdb #1
---
Chain | Description
A G | No description available
B C D E F H | No description available
> ui tool show Matchmaker
> matchmaker #1 to #2
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 APO_OCT_cartoon, chain D (#2) with newOCT_ALPL.pdb, chain G (#1),
sequence alignment score = 2487.2
RMSD between 478 pruned atom pairs is 0.298 angstroms; (across all 482 pairs:
0.614)
> select #1
30712 atoms, 31438 bonds, 3941 residues, 1 model selected
> rename #2 acidic
> rename #1 basic
> style sel stick
Changed 30712 atom styles
> size sel stickRadius 0.4
Changed 31438 bond radii
> color sel byelement
> hide sel target a
> show sel target ab
> hide sel target a
> cartoon sel
> select clear
> ui mousemode right pivot
> ui tool show "Side View"
> select #1/H,G:22,35,31,79,281,80,78,370,49,321,213,156
220 atoms, 206 bonds, 24 residues, 1 model selected
> show sel target ab
> select #1/H,G:264
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1:264
72 atoms, 64 bonds, 8 residues, 1 model selected
> show sel target ab
> hide #2 models
> select #1/C:282
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> undo
> select #1:167
56 atoms, 48 bonds, 8 residues, 1 model selected
> save E:/writing/ALPL/models/YDQ/prefigure/basic/basic_vs_acidic.cxs
> close session
> open D:/EM/YYT/ALPL_Em/ALPL_Ab1/200/cryosparc_P18_J143_map_locres.mrc
Opened cryosparc_P18_J143_map_locres.mrc as #1, grid size 240,240,240, pixel
1.2, shown at level 5.03, step 1, values float32
> open
> D:/EM/YYT/ALPL_Em/ALPL_Ab1/200/cryosparc_P18_J138_006_volume_map_sharp_local.mrc
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc as #2, grid size
240,240,240, pixel 1.2, shown at level 0.138, step 1, values float32
> close #1
> volume #2 level 0.2385
> volume #2 level 0.7827
> volume #2 level 0.6906
> open
> E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/Dimer_alp_Yuyat_refine_2_edited.pdb
Chain information for Dimer_alp_Yuyat_refine_2_edited.pdb #1
---
Chain | Description
A F | No description available
> ui mousemode right "translate selected models"
> close session
> open E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/alp_Yuyat_refine_2.pdb
Chain information for alp_Yuyat_refine_2.pdb #1
---
Chain | Description
A C D E F G | No description available
B | No description available
H | No description available
> open
> D:/EM/YYT/ALPL_Em/ALPL_Ab1/200/cryosparc_P18_J138_006_volume_map_sharp_local.mrc
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc as #2, grid size
240,240,240, pixel 1.2, shown at level 0.138, step 1, values float32
> ui mousemode right "translate selected models"
> select #1
30679 atoms, 31399 bonds, 23 pseudobonds, 3949 residues, 2 models selected
> view matrix models #1,1,0,0,121.19,0,1,0,26.2,0,0,1,-7.8458
> view matrix models #1,1,0,0,140.74,0,1,0,7.3602,0,0,1,78.6
> view matrix models #1,1,0,0,127.62,0,1,0,12.126,0,0,1,19.861
> surface dust #2 size 4
> view matrix models #1,1,0,0,127.82,0,1,0,12.457,0,0,1,19.805
> ui mousemode right pivot
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> close #1
> open
> E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/Dimer_alp_Yuyat_refine_2_edited.pdb
Chain information for Dimer_alp_Yuyat_refine_2_edited.pdb #1
---
Chain | Description
A F | No description available
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,74.534,0,1,0,29.202,0,0,1,41.984
> close session
> open
> E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/Dimer_alp_Yuyat_refine_2_edited.pdb
Chain information for Dimer_alp_Yuyat_refine_2_edited.pdb #1
---
Chain | Description
A F | No description available
> open
> D:/EM/YYT/ALPL_Em/ALPL_Ab1/200/cryosparc_P18_J138_006_volume_map_sharp_local.mrc
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc as #2, grid size
240,240,240, pixel 1.2, shown at level 0.138, step 1, values float32
> surface dust #2 size 4
> volume #2 level 0.1966
> ui mousemode right pivot
> select #1
7674 atoms, 7842 bonds, 988 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,80.476,0,1,0,14.02,0,0,1,15.417
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.017877,0.59379,0.80442,-58.601,0.92002,-0.30524,0.24576,113.53,0.39147,0.74447,-0.54084,100.84
> view matrix models
> #1,0.0049035,0.60679,0.79485,-60.233,0.64784,-0.60742,0.45971,139.91,0.76176,0.51268,-0.39608,95.028
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.0049035,0.60679,0.79485,-42.948,0.64784,-0.60742,0.45971,141.59,0.76176,0.51268,-0.39608,104.9
> volume #2 level 0.8246
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.0049035,0.60679,0.79485,-46.751,0.64784,-0.60742,0.45971,140.73,0.76176,0.51268,-0.39608,76.592
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.11374,0.59337,0.79686,-39.364,0.98542,-0.034745,0.16653,84.627,0.1265,0.80418,-0.58076,92.294
> ui tool show "Fit in Map"
Fit molecule Dimer_alp_Yuyat_refine_2_edited.pdb (#1) to map
cryosparc_P18_J138_006_volume_map_sharp_local.mrc (#2) using 7674 atoms
average map value = 0.2334, steps = 72
shifted from previous position = 2.72
rotated from previous position = 7.36 degrees
atoms outside contour = 6565, contour level = 0.82455
Position of Dimer_alp_Yuyat_refine_2_edited.pdb (#1) relative to
cryosparc_P18_J138_006_volume_map_sharp_local.mrc (#2) coordinates:
Matrix rotation and translation
-0.21480515 0.64257178 0.73550001 -32.75485489
0.96591052 0.02836319 0.25731769 67.76329130
0.14448396 0.76570036 -0.62675940 103.48791923
Axis 0.60236399 0.70027326 0.38311223
Axis point -33.24634379 0.00000000 44.79709727
Rotation angle (degrees) 155.03973755
Shift along axis 67.36996326
> volume flip #2
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip as #3, grid
size 240,240,240, pixel 1.2, shown at step 1, values float32
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.21481,0.64257,0.7355,-33.371,0.96591,0.028363,0.25732,72.676,0.14448,0.7657,-0.62676,125.42
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.098925,0.70551,0.70176,-43.162,0.64937,-0.48859,0.58275,115.77,0.75401,0.51335,-0.40981,101.56
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.098925,0.70551,0.70176,-37.25,0.64937,-0.48859,0.58275,110.14,0.75401,0.51335,-0.40981,107.29
Fit molecule Dimer_alp_Yuyat_refine_2_edited.pdb (#1) to map
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) using 7674 atoms
average map value = 0.2707, steps = 240
shifted from previous position = 2.38
rotated from previous position = 14.2 degrees
atoms outside contour = 6467, contour level = 0.82455
Position of Dimer_alp_Yuyat_refine_2_edited.pdb (#1) relative to
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.14629533 0.84015061 0.52224959 -31.40492713
0.69430580 -0.28885007 0.65917001 71.46636074
0.70465391 0.45903441 -0.54106402 132.07484406
Axis -0.65070966 -0.59305921 -0.47419165
Axis point 0.00000000 55.51075220 76.21386397
Rotation angle (degrees) 171.15380439
Shift along axis -84.57708186
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.1463,0.84015,0.52225,-32.226,0.69431,-0.28885,0.65917,72.093,0.70465,0.45903,-0.54106,127.52
Fit molecule Dimer_alp_Yuyat_refine_2_edited.pdb (#1) to map
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) using 7674 atoms
average map value = 0.7472, steps = 72
shifted from previous position = 0.779
rotated from previous position = 4.24 degrees
atoms outside contour = 4450, contour level = 0.82455
Position of Dimer_alp_Yuyat_refine_2_edited.pdb (#1) relative to
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.20623116 0.85019960 0.48438553 -26.52566650
0.66881598 -0.23886319 0.70400963 60.53935493
0.71425058 0.46915351 -0.51936605 122.56599674
Axis -0.62568184 -0.61238508 -0.48322537
Axis point 0.00000000 49.61017168 70.63860597
Rotation angle (degrees) 169.18256858
Shift along axis -79.70376921
> open 4x0k
Summary of feedback from opening 4x0k fetched from pdb
---
note | Fetching compressed mmCIF 4x0k from
http://files.rcsb.org/download/4x0k.cif
4x0k title:
Engineered Fab fragment specific for EYMPME (EE) peptide [more info...]
Chain information for 4x0k #4
---
Chain | Description
A H | Fab fragment heavy chain
B L | Fab fragment light chain
4x0k mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #4
> open 3LS5
Summary of feedback from opening 3LS5 fetched from pdb
---
note | Fetching compressed mmCIF 3ls5 from
http://files.rcsb.org/download/3ls5.cif
3ls5 title:
Anti-tetrahydrocannabinol Fab Fragment, Free Form [more info...]
Chain information for 3ls5 #4
---
Chain | Description
H | Heavy chain of antibody Fab fragment
L | Light chain of antibody Fab fragment
> select #4
3538 atoms, 3358 bonds, 694 residues, 1 model selected
> view matrix models #4,1,0,0,99.227,0,1,0,29.763,0,0,1,126.43
> view matrix models #4,1,0,0,140.93,0,1,0,100.66,0,0,1,123.43
> view matrix models #4,1,0,0,130.9,0,1,0,154.88,0,0,1,96.957
> view matrix models #4,1,0,0,120.31,0,1,0,145.23,0,0,1,101.59
> open 2A9M
Summary of feedback from opening 2A9M fetched from pdb
---
note | Fetching compressed mmCIF 2a9m from
http://files.rcsb.org/download/2a9m.cif
2a9m title:
Structural Analysis of a Tight-binding Fluorescein-scFv; apo form [more
info...]
Chain information for 2a9m #5
---
Chain | Description
H I | fluorescein-scfv heavy chain
L M | fluorescein-scfv light chain
2a9m mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #5
> open 6PIL9M
'6PIL9M' has no suffix
> open 6PIL9M
'6PIL9M' has no suffix
> open 6PIL
Summary of feedback from opening 6PIL fetched from pdb
---
note | Fetching compressed mmCIF 6pil from
http://files.rcsb.org/download/6pil.cif
6pil title:
Antibody scFv-M204 monomeric state [more info...]
Chain information for 6pil #5
---
Chain | Description
A | scFv-M204 antibody
Non-standard residues in 6pil #5
---
CL — chloride ion
> close #4
> select #5
1814 atoms, 1750 bonds, 1 pseudobond, 333 residues, 2 models selected
> view matrix models #5,1,0,0,145.09,0,1,0,105.88,0,0,1,73.916
> view matrix models #5,1,0,0,124.47,0,1,0,136.44,0,0,1,76.788
> view matrix models #5,1,0,0,130.32,0,1,0,127.97,0,0,1,62.957
> volume #3 level 0.2623
> volume #3 level 0.1601
> surface dust #3 size 6
> view matrix models #5,1,0,0,135.13,0,1,0,121.01,0,0,1,63.378
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.43817,-0.7393,-0.51132,156.1,-0.71623,0.056578,-0.69557,148.92,0.54316,0.671,-0.50471,96.852
> view matrix models
> #5,0.28791,-0.70362,-0.64963,159.73,-0.62137,0.37892,-0.6858,145.72,0.72871,0.60111,-0.32811,92.435
> view matrix models
> #5,0.32412,-0.86526,-0.38246,153.94,-0.35762,0.26222,-0.8963,151.91,0.87582,0.42728,-0.22445,90.928
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.32412,-0.86526,-0.38246,161.5,-0.35762,0.26222,-0.8963,151.46,0.87582,0.42728,-0.22445,89.823
Fit molecule 6pil (#5) to map
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) using 1814 atoms
average map value = 0.4318, steps = 128
shifted from previous position = 7.38
rotated from previous position = 28.5 degrees
atoms outside contour = 457, contour level = 0.16011
Position of 6pil (#5) relative to
cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.20750922 -0.79429710 -0.57099216 167.36897509
-0.00346255 0.58309742 -0.81239486 149.40632208
0.97822693 0.17055652 0.11824780 85.90876001
Axis 0.49198685 -0.77541519 0.39582853
Axis point 78.27757327 0.00000000 184.04881110
Rotation angle (degrees) 92.61203272
Shift along axis 0.49654289
> transparency #3.1 50
> select clear
> hide #!5 models
> hide #!3 models
> show #!5 models
> select clear
Drag select of 1 residues
> select up
126 atoms, 133 bonds, 13 residues, 1 model selected
> select clear
> hide #!5 models
Drag select of 5 residues
> show sel target ab
> show #!5 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> select clear
> show #!3 models
> show #!5 models
> color #3 #82828280 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> show #!3 models
> select #3
2 models selected
> ~select #3
Nothing selected
> select #5
1814 atoms, 1750 bonds, 1 pseudobond, 333 residues, 2 models selected
> select #1
7674 atoms, 7842 bonds, 988 residues, 1 model selected
> select #5
1814 atoms, 1750 bonds, 1 pseudobond, 333 residues, 2 models selected
> transparency #3.1 0
> transparency #3.1 50
> transparency #3.1 75
> select clear
> color #5 #55ff00 transparency 0
> hide #!3 models
Drag select of 50 atoms, 52 residues, 48 bonds
Drag select of 20 residues
> select up
301 atoms, 303 bonds, 38 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> color sel cornflower blue
> select clear
Drag select of 9 atoms, 18 residues, 8 bonds
> select up
406 atoms, 415 bonds, 48 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> color sel red
> select clear
> show #!3 models
> select #1/F:262@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!3 models
> select add #1/F:263@CB
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
16 atoms, 12 bonds, 4 residues, 1 model selected
> select up
39 atoms, 40 bonds, 4 residues, 1 model selected
> color sel byelement
> select clear
> show #!3 models
> hide #!3 models
Drag select of 63 atoms, 241 residues, 60 bonds
> select up
1898 atoms, 1922 bonds, 244 residues, 1 model selected
> select up
1901 atoms, 1925 bonds, 244 residues, 1 model selected
> show #!3 models
> volume zone #2 nearAtoms #1 newMap true
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc zone as #4, grid size
240,240,240, pixel 1.2, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 3840x2298+0+34 (frame:
3862x2354-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY2".
Resulting geometry: 3840x2054+0+34 (frame: 3862x2110-11-11) margins: 11, 45,
11, 11 minimum size: 542x1149 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1106,2354 maxtrack=0,0)
> hide #!3 models
> volume #4 level 0.4227
> hide #!4 models
> close #4
> volume zone #3 nearAtoms #1 newMap true
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip zone as #4,
grid size 240,240,240, pixel 1.2, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 3840x2298+0+34 (frame:
3862x2354-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY2".
Resulting geometry: 3840x2054+0+34 (frame: 3862x2110-11-11) margins: 11, 45,
11, 11 minimum size: 542x1149 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1106,2354 maxtrack=0,0)
> color #4 blue models transparency 0
> color #4 black models transparency 0
> color #4 #ff557f models transparency 0
> color #4 #ffaaff models transparency 0
> show #!3 models
> volume zone #3 nearAtoms #1 newMap true inverted 1
Expected a keyword
> volume zone #3 nearAtoms #1 newMap true invert true
Opened cryosparc_P18_J138_006_volume_map_sharp_local.mrc z flip zone as #6,
grid size 240,240,240, pixel 1.2, shown at step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 3840x2448+0+34 (frame:
3862x2504-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY2".
Resulting geometry: 3840x2054+0+34 (frame: 3862x2110-11-11) margins: 11, 45,
11, 11 minimum size: 542x1224 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1106,2504 maxtrack=0,0)
> surface dust #6 size 6
> color #6 #55aaff models transparency 0
> volume #6 level 0.06654
> volume #6 level 0.1133
> surface dust #6 size 20
> save D:/EM/YYT/ALPL_Em/ALPL_Ab1/200/analysis_ALPL_ab1.cxs
> surface dust #6 size 60
> surface dust #6 size 40
> color #4 #ffaaff78 models
> color #4 #96969678 models
> select clear
> color #6 #55ff7f models transparency 0
> color #6 #00aa00 models transparency 0
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close session
> open E:\writing\ALPL\models\YDQ\prefigure\basic\basic_vs_acidic.cxs format
> session
opened ChimeraX session
> show #2 models
> hide #1 models
> select #2/B,D:22,35,31,79,281,80,78,370,49,321,213,156
220 atoms, 206 bonds, 24 residues, 1 model selected
> select subtract #2/B:156
212 atoms, 199 bonds, 23 residues, 1 model selected
> select add #2/F:156
220 atoms, 206 bonds, 24 residues, 1 model selected
> select subtract #2/D:156
212 atoms, 199 bonds, 23 residues, 1 model selected
> select subtract #2/D:213
201 atoms, 189 bonds, 22 residues, 1 model selected
> select up
950 atoms, 955 bonds, 114 residues, 1 model selected
> select ~sel
60441 atoms, 61834 bonds, 7776 residues, 2 models selected
> transparency sel 100 target c
> transparency sel 75 target c
> transparency sel 80 target c
> transparency sel 95 target c
> select clear
> lighting full
> lighting flat
> lighting soft
> lighting full
> graphics silhouettes false
> lighting flat
> undo
> transparency sel 0 target c
> color (#2 & sel) light gray
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Side View"
> cartoon style thickness 0.1
> select clear
> camera fieldOfView 60
> camera fieldOfView 80
> ui mousemode right pivot
> select #2/B:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> camera fieldOfView 300
> camera fieldOfView 30
> select #2/B:486
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
61 atoms, 63 bonds, 8 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> surface sel probeRadius 1.2 gridSpacing 0.3
> color #2 #55aaff transparency 0
> undo
> color #2.1 #55aaff transparency 0
> color #2.1 #55aaff37
> select clear
> select #2/D:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/F:282
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
65 atoms, 66 bonds, 8 residues, 1 model selected
> select up
7657 atoms, 7825 bonds, 985 residues, 1 model selected
> surface sel probeRadius 1.2 gridSpacing 0.3
> color #2.2 #aa0000 transparency 0
> color #2.2 #aa000037
> color #2.3 #005500 transparency 0
> color #2.3 #00550037
> select clear
> select #2/G:28
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
142 atoms, 146 bonds, 16 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select clear
> select #2/H:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> surface sel probeRadius 1.2 gridSpacing 0.3
> color #2.4 #ffaa00 transparency 0
> color #2.4 #ffaa0037
> select clear
> hide #2.3 models
> select #2/F:213@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> hide (#!2 & sel) target a
> select clear
> show #2.3 models
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
Drag select of acidic_B SES surface, 17020 of 989422 triangles, acidic_D SES
surface, 20 of 977352 triangles, acidic_F SES surface, 1951 of 998472
triangles, acidic_H SES surface, 9594 of 982326 triangles, 8 residues
> select add #2/D:499@CD
57 atoms, 9 residues, 3 models selected
> select up
63 atoms, 63 bonds, 9 residues, 4 models selected
> select up
302 atoms, 311 bonds, 41 residues, 4 models selected
> select up
11500 atoms, 11752 bonds, 1480 residues, 4 models selected
> select add #2/F:237@CB
11501 atoms, 11752 bonds, 1481 residues, 4 models selected
> select up
11509 atoms, 11760 bonds, 1481 residues, 5 models selected
> select up
11751 atoms, 12006 bonds, 1511 residues, 5 models selected
> select up
15331 atoms, 15667 bonds, 1973 residues, 5 models selected
> transparency sel 50
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting soft
> lighting simple
> transparency sel 75
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> undo
> transparency sel 100
> select clear
> undo
> select ~sel
46060 atoms, 47122 bonds, 5917 residues, 2 models selected
> transparency sel 100 target c
> select clear
Drag select of acidic_B SES surface, 23727 of 989422 triangles, acidic_F SES
surface, 5073 of 998472 triangles, acidic_H SES surface, 6230 of 982326
triangles, 10 residues
> select up
250 atoms, 259 bonds, 33 residues, 3 models selected
> select up
7668 atoms, 7836 bonds, 987 residues, 3 models selected
> select add #2/D:278@CG
7669 atoms, 7836 bonds, 988 residues, 3 models selected
> select add #2/H:494@CD1
7670 atoms, 7836 bonds, 989 residues, 4 models selected
> select up
7684 atoms, 7850 bonds, 989 residues, 5 models selected
> select up
7766 atoms, 7934 bonds, 1002 residues, 5 models selected
> select up
15331 atoms, 15667 bonds, 1973 residues, 5 models selected
> transparency sel 75
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2B.png supersample 8
> transparentBackground true
> transparency sel 25
> transparency sel 50
> lighting full
> select clear
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2B.png supersample 8
> transparentBackground true
> hide #!2.4 models
> hide #!2.3 models
> hide #2.2 models
> hide #2.1 models
> lighting full
> save E:/writing/ALPL/models/YDQ/prefigure/AI/CXS/OCTfig_interactions.cxs
> includeMaps true
> open
> E:/writing/ALPL/models/YDQ/prefigure/acidic_APO/Dimer_alp_Yuyat_refine_2_edited.pdb
Chain information for Dimer_alp_Yuyat_refine_2_edited.pdb #3
---
Chain | Description
A F | No description available
> hide #!2 models
> select #3/A:28
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
142 atoms, 146 bonds, 16 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select clear
> select #3/F:485
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
61 atoms, 63 bonds, 8 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> color sel royal blue
> color sel byelement
> select clear
> select #3/F:703@CA
1 atom, 1 residue, 1 model selected
> select #3/A:360
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
138 atoms, 138 bonds, 19 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> color sel gold
> color sel yellow
> color sel gold
> select clear
> select #3/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
82 atoms, 81 bonds, 11 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> color sel byelement
> select clear
> select #3/A:703@CA
1 atom, 1 residue, 1 model selected
> ui mousemode right pivot
> select add #3/F:703@CA
2 atoms, 2 residues, 1 model selected
> color sel dark violet
> select clear
Drag select of 3 residues
> setattr sel res ss_type 1
Assigning ss_type attribute to 3 items
> select #3/A:494
8 atoms, 7 bonds, 1 residue, 1 model selected
> setattr sel res ss_type 1
Assigning ss_type attribute to 1 item
> undo
> select #3/A:494
8 atoms, 7 bonds, 1 residue, 1 model selected
> setattr sel res ss_type 0
Assigning ss_type attribute to 1 item
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
Drag select of 13 residues
> select up
296 atoms, 303 bonds, 36 residues, 1 model selected
> select up
7674 atoms, 7842 bonds, 988 residues, 1 model selected
> select intersect
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SEP"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
7498 atoms, 7670 bonds, 968 residues, 1 model selected
> hide sel target a
> select clear
Drag select of 176 atoms, 968 residues, 172 bonds
> select intersect ::name="NAG"
168 atoms, 172 bonds, 12 residues, 1 model selected
> size sel stickRadius 0.4
Changed 172 bond radii
> select clear
> undo
> color sel magenta
> color sel hot pink
> select sel @ show (#3 & sel) target ab
> size sel stickRadius 0.4
Changed 560 bond radii
> select clear
Drag select of 200 atoms, 968 residues, 187 bonds
> select intersect ions
8 atoms, 8 residues, 1 model selected
> size sel atomRadius 2
Changed 8 atom radii
> size sel atomRadius 1.5
Changed 8 atom radii
> size sel atomRadius 1.2
Changed 8 atom radii
> size sel atomRadius 1
Changed 8 atom radii
> select clear
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
Drag select of 15 residues
> select up
227 atoms, 227 bonds, 31 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select sel : select intersect #3/F
923 atoms, 908 bonds, 116 residues, 1 model selected
> show sel target ab
> undo
> select sel : select clear
Drag select of 27 residues
> select up
483 atoms, 494 bonds, 58 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select sel : select intersect #3/F
752 atoms, 730 bonds, 94 residues, 1 model selected
> show sel target ab
> name frozen inter_B sel
registering illegal selector name "inter_B"
> name frozen interB sel
> ui tool show Contacts
Restriction atom specifier must not be blank
> contacts resSeparation 5 intraModel false intraMol false radius 0.155
483791 contacts
> select #4
483791 pseudobonds, 1 model selected
> hide #3 models
> show #3 models
> ~select #4
Nothing selected
> select #4
483791 pseudobonds, 1 model selected
> ~select #4
Nothing selected
> show #3-4 target ab
> undo
> close #4
> contacts #3/A restrict #3/F
460 contacts
> contacts #3/A restrict #3/F select true
460 contacts
> show sel target ab
> hide #!3 models
> show #!3 models
> hide #3.1 models
> select clear
> show #3.1 models
> contacts #3/A restrict #3/F select true
460 contacts
> select intersect #3/A
236 atoms, 87 residues, 1 model selected
> show sel target ab
> select up
696 atoms, 673 bonds, 87 residues, 1 model selected
> show sel target ab
> hide #3.1 models
> select clear
> show #3.1 models
> ui tool show Contacts
> hide #3.1 models
> select #3
7674 atoms, 7842 bonds, 460 pseudobonds, 988 residues, 2 models selected
> select subtract ::name="NAG"
7506 atoms, 7670 bonds, 460 pseudobonds, 976 residues, 2 models selected
> select subtract ions
7498 atoms, 7670 bonds, 460 pseudobonds, 968 residues, 2 models selected
> hide (#!3 & sel) target a
> select clear
> select ::name="NAG"
1526 atoms, 1563 bonds, 109 residues, 3 models selected
> select sel : select sel : select subtract #3/A:432
2846 atoms, 2831 bonds, 262 residues, 7 models selected
> select subtract #3/F:432
2840 atoms, 2826 bonds, 261 residues, 7 models selected
> select subtract #3/F:274
2831 atoms, 2818 bonds, 260 residues, 7 models selected
> select subtract #3/A:301
2820 atoms, 2808 bonds, 259 residues, 7 models selected
> select subtract #3/A:270
2806 atoms, 2793 bonds, 258 residues, 7 models selected
> select subtract #3/F:199
2797 atoms, 2785 bonds, 257 residues, 7 models selected
> show (#!3 & sel) target ab
> select intersect #3
254 atoms, 254 bonds, 22 residues, 1 model selected
> show sel target ab
> select subtract #3/A:302
246 atoms, 247 bonds, 21 residues, 1 model selected
> select subtract #3/F:270
232 atoms, 232 bonds, 20 residues, 1 model selected
> show sel target ab
> undo
> select subtract #3/A:303
224 atoms, 225 bonds, 19 residues, 1 model selected
> select add #3/A:302
232 atoms, 232 bonds, 20 residues, 1 model selected
> show sel target ab
> undo
> select subtract #3/A:302
224 atoms, 225 bonds, 19 residues, 1 model selected
> select add #3/A:303
232 atoms, 232 bonds, 20 residues, 1 model selected
> show sel target ab
> size sel stickRadius 0.4
Changed 232 bond radii
> select ::name="NAG"
1526 atoms, 1563 bonds, 109 residues, 3 models selected
> select intersect #3
168 atoms, 172 bonds, 12 residues, 1 model selected
> surface sel probeRadius 1 gridSpacing 0.2
> color #3.2 #ffaaff transparency 0
> color #3.3 #ffaaff transparency 0
> color #3.3 #ffaaff37
> color #3.2 #ffaaff37
> select clear
> select #3.2
84 atoms, 6 residues, 1 model selected
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> surface style #3.2 mesh
> hide #3.2 models
> show #3.2 models
> undo
> redo
> surface style #3 mesh
> surface style #3 solid
> select clear
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting full
> lighting simple
> lighting flat
> lighting full
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2B.png supersample 8
> transparentBackground true
> turn x -90
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2A.png supersample 8
> transparentBackground true
> hide #3.2 models
> hide #!3.3 models
> hide #!3 target a
> contacts #3/A restrict #3/F select true
460 contacts
> show sel target ab
> select up
1373 atoms, 1326 bonds, 172 residues, 1 model selected
> show sel target ab
> size sel stickRadius 0.4
Changed 1326 bond radii
> select clear
> contacts #3/A restrict #3/F select true
460 contacts
> select up
1373 atoms, 1326 bonds, 172 residues, 1 model selected
> name frozen interAF sel
> select clear
> select #3/F:176
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
23 atoms, 23 bonds, 4 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> surface sel probeRadius 1 gridSpacing 0.2
> hide #!3.4 models
> select clear
> select #3/A:361
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
138 atoms, 138 bonds, 19 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> transparency sel 100 target c
> select clear
> select interAF
1373 atoms, 1326 bonds, 460 pseudobonds, 172 residues, 2 models selected
> select intersect #3/A
696 atoms, 673 bonds, 87 residues, 1 model selected
> transparency sel 50 target a
> transparency sel 0 target a
> select intersect sideonly
348 atoms, 559 bonds, 272 pseudobonds, 80 residues, 2 models selected
> select up
678 atoms, 559 bonds, 272 pseudobonds, 152 residues, 2 models selected
> select down
348 atoms, 559 bonds, 272 pseudobonds, 80 residues, 3 models selected
> select intersect C
267 atoms, 362 bonds, 167 pseudobonds, 80 residues, 2 models selected
> color (#!3 & sel) light sea green
> select up
503 atoms, 362 bonds, 167 pseudobonds, 148 residues, 2 models selected
> color (#!3 & sel) light sea green
> undo
> select clear
> select intersect interAF
Nothing selected
> select clear
> select interAF
1373 atoms, 1326 bonds, 460 pseudobonds, 172 residues, 2 models selected
> select intersect #3/A
696 atoms, 673 bonds, 87 residues, 1 model selected
> select sideonly
32655 atoms, 25890 bonds, 272 pseudobonds, 7949 residues, 4 models selected
> select intersect sideonly
348 atoms, 285 bonds, 80 residues, 1 model selected
> color sel green yellow
> color sel olive drab
> color sel white
> color sel gold
> color sel yellow
> color sel dark orange
> color sel medium aquamarine
> color sel dark green
> undo
> select intersect C
267 atoms, 185 bonds, 80 residues, 1 model selected
> color sel olive drab
> select clear
> select #3/A:360
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
138 atoms, 138 bonds, 19 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> transparency sel 80 target c
> select clear
> undo
> select clear
> undo
> select clear
> select #3/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
39 atoms, 38 bonds, 6 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> transparency sel 100 target c
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2C.png supersample 8
> transparentBackground true
> select #3/F:157
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> surface sel probeRadius 1 gridSpacing 0.2
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for Dimer_alp_Yuyat_refine_2_edited.pdb_F SES surface #3.4:
minimum, -37.86, mean -2.75, maximum 13.81
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #3/A:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 4 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> cartoon hide (#!3 & sel)
> select clear
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> select #3/F:199
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> cartoon hide (#!3 & sel)
> select clear
Drag select of 1373 atoms, 1326 bonds
> color (#!3 & sel) byelement
> select intersect #3/F
653 bonds, 1 model selected
> select intersect sideonly
274 bonds, 1 model selected
> select up
330 atoms, 274 bonds, 72 residues, 1 model selected
> select up
618 atoms, 592 bonds, 72 residues, 2 models selected
> select intersect sideonly
274 bonds, 1 model selected
> select intersect C
177 bonds, 1 model selected
> color sel cadet blue
> select up
236 atoms, 177 bonds, 68 residues, 1 model selected
> color sel olive drab
> select up
594 atoms, 569 bonds, 68 residues, 2 models selected
> select up
1793 atoms, 1831 bonds, 232 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> cartoon (#!3 & sel)
> undo
> color sel olive drab
> select up
594 atoms, 569 bonds, 68 residues, 2 models selected
> select up
1793 atoms, 1831 bonds, 232 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> cartoon (#!3 & sel)
> undo
> select clear
> select #3
7674 atoms, 7842 bonds, 460 pseudobonds, 988 residues, 5 models selected
> cartoon (#!3 & sel)
> select clear
> undo
> select #3
7674 atoms, 7842 bonds, 460 pseudobonds, 988 residues, 5 models selected
> cartoon (#!3 & sel)
> select clear
> select #3/F:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> select up
7674 atoms, 7842 bonds, 988 residues, 3 models selected
> select down
3837 atoms, 3921 bonds, 494 residues, 4 models selected
> color sel royal blue
> color (#!3 & sel) byelement
> select clear
> select interAF
1373 atoms, 1326 bonds, 460 pseudobonds, 172 residues, 2 models selected
> select intersect #3/F
653 bonds, 1 model selected
> select intersect C
341 bonds, 1 model selected
> color sel olive drab
> undo
> select intersect sideonly
177 bonds, 1 model selected
> color sel olive drab
> undo
> select intersect sideonly
177 bonds, 1 model selected
> color sel goldenrod
> undo
> color sel green yellow
> undo
> select down
177 bonds, 1 model selected
> color sel olive drab
> undo
> color sel olive drab
> undo
> select up
236 atoms, 177 bonds, 68 residues, 1 model selected
> select up
594 atoms, 569 bonds, 68 residues, 2 models selected
> select up
1793 atoms, 1831 bonds, 232 residues, 2 models selected
> select down
594 atoms, 569 bonds, 68 residues, 2 models selected
> select intersect sideonly
270 bonds, 1 model selected
> select intersect C
177 bonds, 1 model selected
> color sel olive drab
> undo
> select up
236 atoms, 177 bonds, 68 residues, 1 model selected
> select down
177 bonds, 2 models selected
> select down
236 atoms, 177 bonds, 68 residues, 1 model selected
> select up
594 atoms, 569 bonds, 68 residues, 2 models selected
> select up
1793 atoms, 1831 bonds, 232 residues, 2 models selected
> select down
594 atoms, 569 bonds, 68 residues, 2 models selected
> select down
236 atoms, 177 bonds, 68 residues, 2 models selected
> select down
177 bonds, 2 models selected
> color sel indian red
> undo
> color sel orange
> undo
> hide sel target b
> undo
> hide sel target b
> undo
> select intersect interAF
177 bonds, 1 model selected
> select #3/F:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> select intersect sideonly
1436 bonds, 1 model selected
> color sel goldenrod
> undo
> select intersect sidechain
1436 bonds, 1 model selected
> color sel hot pink
> undo
> select interAF
1373 atoms, 1326 bonds, 460 pseudobonds, 172 residues, 2 models selected
> select intersect #3/F
653 bonds, 1 model selected
> select subtract backbone
357 bonds, 1 model selected
> color sel yellow
> undo
> color sel cornflower blue
> undo
> select #3/A:310
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
82 atoms, 81 bonds, 11 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select interB
752 atoms, 730 bonds, 94 residues, 1 model selected
> select up
1793 atoms, 1831 bonds, 232 residues, 2 models selected
> select down
752 atoms, 730 bonds, 94 residues, 2 models selected
> color sel cornflower blue
> undo
> select subtract main
1 model selected
> undo
> select subtract backbone
376 atoms, 397 bonds, 86 residues, 2 models selected
> color sel magenta
> select intersect C
281 bonds, 1 model selected
> color sel olive drab
> undo
> select #3/F:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> select clear
> select interB
752 atoms, 730 bonds, 94 residues, 1 model selected
> select subtract backbone
376 atoms, 397 bonds, 86 residues, 2 models selected
> color sel yellow
> undo
> select subtract O
330 atoms, 397 bonds, 86 residues, 2 models selected
> select subtract N
285 atoms, 397 bonds, 86 residues, 2 models selected
> select subtract S
284 atoms, 397 bonds, 86 residues, 2 models selected
> color sel olive drab
> undo
> color sel olive drab
> undo
> select subtract backbone
284 atoms, 397 bonds, 86 residues, 2 models selected
> close #3.4
> select subtract backbone
284 atoms, 397 bonds, 86 residues, 1 model selected
> color sel goldenrod
> undo
> color sel goldenrod
> undo
> color sel goldenrod
> undo
> select intersect sideonly
284 atoms, 307 bonds, 86 residues, 1 model selected
> color sel olive drab
> undo
> select intersect sidechain
284 atoms, 307 bonds, 86 residues, 1 model selected
> select intersect sideonly
284 atoms, 307 bonds, 86 residues, 1 model selected
Drag select of 1 residues
> select up
326 atoms, 333 bonds, 43 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select intersect sideonly
1813 atoms, 1436 bonds, 442 residues, 1 model selected
> color sel orange
> undo
> select intersect C
1377 atoms, 916 bonds, 442 residues, 1 model selected
> color sel olive drab
> select #3/F:153
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
46 atoms, 47 bonds, 5 residues, 1 model selected
> select up
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> select intersect backbone
1936 atoms, 1935 bonds, 484 residues, 1 model selected
> color sel royal blue
> select clear
> save E:\writing\ALPL\models\YDQ\prefigure\temp\fig2C.png supersample 8
> transparentBackground true
> select #3
7674 atoms, 7842 bonds, 460 pseudobonds, 988 residues, 4 models selected
> cartoon hide (#!3 & sel)
> select clear
> show #!2 models
> select #2/B:255
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
59 atoms, 60 bonds, 7 residues, 2 models selected
> select up
3837 atoms, 3921 bonds, 494 residues, 2 models selected
> select up
30679 atoms, 31351 bonds, 3949 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide (#!2 & sel) target a
> select #2/B
3837 atoms, 3921 bonds, 494 residues, 1 model selected
> surface sel probeRadius 1 gridSpacing 0.2
> transparency sel 0
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for acidic_B SES surface #2.1: minimum, -37.90, mean -2.76,
maximum 13.81
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #2.1
3749 atoms, 484 residues, 2 models selected
> transparency sel 50
> transparency sel 25
> transparency sel 0
> select clear
> select #3/A:71,417,420
23 atoms, 20 bonds, 3 residues, 1 model selected
> select #3/A:71,417,420, 478
31 atoms, 27 bonds, 4 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
warning | Unable to enumerate family ' "WenYue XinQingNianTi (Authorization
Required)" '
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 8930
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 34,159,955,968
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Long atom spec crashes ChimeraX |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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duplicate of #4842