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Opened 2 years ago
Closed 2 years ago
#9189 closed defect (duplicate)
MemoryError saving map in session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.5rc202211240003 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5rc202211240003 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "D:\\\Peking University\\\Xiao Lab\\\Data\\\IgM & IgA project\\\IgM-AIM
> paper related\\\interaction\\\cxs\\\overall interactionL NEW.cxs"
Log from Thu Aug 4 13:49:17 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\wangyx\\\Desktop\\\final_local_Ca_real_space_refined-
> coot-2.pdb
Summary of feedback from opening
C:\\\Users\\\wangyx\\\Desktop\\\final_local_Ca_real_space_refined-coot-2.pdb
---
warning | Ignored bad PDB record found on line 6482
END
Chain information for final_local_Ca_real_space_refined-coot-2.pdb #1
---
Chain | Description
A L | No description available
J | No description available
M | No description available
> select /M
1671 atoms, 1718 bonds, 215 residues, 1 model selected
> color sel #f3ae47ff
> select clear
> select ::name="CA"
2 atoms, 2 residues, 1 model selected
> style sel ball
Changed 2 atom styles
> ui tool show "Color Actions"
> color sel lime green
> select /A
1812 atoms, 1861 bonds, 233 residues, 1 model selected
> surface sel
> color sel deep sky blue
> color sel pale turquoise
> select /J
1045 atoms, 1064 bonds, 1 pseudobond, 130 residues, 2 models selected
> surface (#!1 & sel)
> color sel light coral
> select /L
1812 atoms, 1861 bonds, 233 residues, 1 model selected
> surface sel
> color sel teal
> select clear
> select ::name="NAG"
56 atoms, 57 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of final_local_Ca_real_space_refined-coot-2.pdb_A SES surface,
final_local_Ca_real_space_refined-coot-2.pdb_J SES surface,
final_local_Ca_real_space_refined-coot-2.pdb_L SES surface, 78 atoms, 805
residues, 1 pseudobonds, 62 bonds
> color (#!1 & sel) byhetero
> undo
> select clear
> select /M:270
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /M:339
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add /M:311
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add /M:271
33 atoms, 29 bonds, 4 residues, 1 model selected
> select add /M:334@CA
34 atoms, 29 bonds, 5 residues, 1 model selected
> color sel byhetero
> select clear
> select clear
> select /M:334
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> ui tool show Distances
> select /M:601@CA
1 atom, 1 residue, 1 model selected
> select add /M:271@OD1
2 atoms, 2 residues, 1 model selected
> distance /M:601@CA /M:271@OD1
Distance between /M CA 601 CA and ASP 271 OD1: 3.0Å
> select clear
> select /M:601@CA
1 atom, 1 residue, 1 model selected
> select add /M:270@OD1
2 atoms, 2 residues, 1 model selected
> distance /M:601@CA /M:270@OD1
Distance between /M CA 601 CA and ASP 270 OD1: 2.1Å
> select clear
> select /M:601@CA
1 atom, 1 residue, 1 model selected
> select add /M:339@OE2
2 atoms, 2 residues, 1 model selected
> distance /M:601@CA /M:339@OE2
Distance between /M CA 601 CA and GLU 339 OE2: 1.4Å
> select clear
> ~distance /M:601@CA /M:339@OE2
> ~distance /M:601@CA /M:270@OD1
> ~distance /M:601@CA /M:271@OD1
> select clear
> save C:\Users\wangyx\Desktop\image1.png supersample 3
> save "E:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/AIMlocal new.cxs"
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> save C:\Users\wangyx\Desktop\image1.png supersample 3
> save "E:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/AIMlocal new.cxs"
> select /L
1812 atoms, 1861 bonds, 233 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select /J
1045 atoms, 1064 bonds, 1 pseudobond, 130 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> select /A
1812 atoms, 1861 bonds, 233 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> select clear
> select /A
1812 atoms, 1861 bonds, 233 residues, 1 model selected
> hide sel atoms
> select /J
1045 atoms, 1064 bonds, 1 pseudobond, 130 residues, 2 models selected
> hide sel atoms
> select /M:241-345
826 atoms, 849 bonds, 105 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select ::name="CA"
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select /L:445-576
1026 atoms, 1054 bonds, 132 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /L:408-417
70 atoms, 69 bonds, 10 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select /L:392-397
46 atoms, 46 bonds, 6 residues, 1 model selected
> select /L:390-396
56 atoms, 56 bonds, 7 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select clear
> select /L:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /M:189-194
53 atoms, 53 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /M:228-234
56 atoms, 56 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> transparency 70 cartoons
> transparency 80 cartoons
> transparency 70 cartoons
> select clear
> lighting full
> lighting shadows false
> select /L:346
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /L:346-374
222 atoms, 226 bonds, 29 residues, 1 model selected
> hide sel cartoons
> select /L:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /L:417
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select /M:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> select clear
> select /M:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select clear
> select /L:390
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /M:231@OD1
1 atom, 1 residue, 1 model selected
> select add /L:391@NZ
2 atoms, 2 residues, 1 model selected
> distance /M:231@OD1 /L:391@NZ
Distance between /M ASP 231 OD1 and /L LYS 391 NZ: 3.0Å
> ~distance /M:231@OD1 /L:391@NZ
> select clear
> select /M:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /M:234
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select /M:231@OD1
1 atom, 1 residue, 1 model selected
> select add /L:391@NZ
2 atoms, 2 residues, 1 model selected
> distance /M:231@OD1 /L:391@NZ
Distance between /M ASP 231 OD1 and /L LYS 391 NZ: 3.0Å
> select /L:412@OG
1 atom, 1 residue, 1 model selected
> select add /M:230@NE2
2 atoms, 2 residues, 2 models selected
> distance /L:412@OG /M:230@NE2
Distance between /L SER 412 OG and /M HIS 230 NE2: 1.9Å
> select clear
> select /M:229@OD1
1 atom, 1 residue, 1 model selected
> select add /L:395@ND2
2 atoms, 2 residues, 1 model selected
> distance /M:229@OD1 /L:395@ND2
Distance between /M ASN 229 OD1 and /L ASN 395 ND2: 6.2Å
> ~distance /M:229@OD1 /L:395@ND2
> select clear
> transparency 80 cartoons
> select clear
> select /M:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /M:228@CA
7 atoms, 5 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /M:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /L:408
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /M:229@OD1
1 atom, 1 residue, 1 model selected
> select add /L:393@NE2
2 atoms, 2 residues, 1 model selected
> distance /M:229@OD1 /L:393@NE2
Distance between /M ASN 229 OD1 and /L HIS 393 NE2: 5.3Å
> ~distance /M:229@OD1 /L:393@NE2
> select clear
> lighting full
> lighting shadows false
> select /L:392
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /L:393
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /L:410
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /L:394@CA
1 atom, 1 residue, 1 model selected
> select /L:395
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> select /M:229@OD1
1 atom, 1 residue, 1 model selected
> select add /L:395@ND2
2 atoms, 2 residues, 1 model selected
> distance /M:229@OD1 /L:395@ND2
Distance between /M ASN 229 OD1 and /L ASN 395 ND2: 6.2Å
> ~distance /M:229@OD1 /L:395@ND2
> select clear
> select /M:229@OD1
1 atom, 1 residue, 1 model selected
> select /L:393@NE2
1 atom, 1 residue, 1 model selected
> select add /M:229@OD1
2 atoms, 2 residues, 2 models selected
> distance /L:393@NE2 /M:229@OD1
Distance between /L HIS 393 NE2 and /M ASN 229 OD1: 5.3Å
> ~distance /L:393@NE2 /M:229@OD1
> select clear
> select /M:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /M:190
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add /M:192
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add /M:193
37 atoms, 33 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> select /M:229@CB
1 atom, 1 residue, 1 model selected
> select add /L:394@CA
2 atoms, 1 bond, 2 residues, 1 model selected
> select add /L:410
11 atoms, 9 bonds, 3 residues, 1 model selected
> select add /L:393
21 atoms, 19 bonds, 4 residues, 2 models selected
> select add /L:411
26 atoms, 23 bonds, 5 residues, 2 models selected
> select subtract /L:411
21 atoms, 19 bonds, 4 residues, 2 models selected
> select add /L:392
28 atoms, 25 bonds, 5 residues, 2 models selected
> hide sel atoms
> select clear
> select /L:395
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /L:409
12 atoms, 10 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select /L:394
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /M:229
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /L:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /M:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /M:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /M:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /M:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #2.1 models
> select /L:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /M:194
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add /L:413
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add /L:411
23 atoms, 21 bonds, 3 residues, 2 models selected
> hide sel atoms
> select clear
> select /M:232
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> select /L:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /M:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select clear
> select /M:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /M:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /M:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select /L:390
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /L:392
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select /L:393
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /L:410
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /L:393
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /L:394
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> transparency 70 cartoons
> select /L:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /L:408
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select /L:395
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select clear
> select /L:408
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> save "E:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/overall interactionL NEW.cxs"
> save C:\Users\wangyx\Desktop\image1.png supersample 3
> select /M:185
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /M:186
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add /M:187
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add /M:188
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add /M:189
40 atoms, 35 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select clear
> undo
> undo
> undo
> select clear
> save "E:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/overall interactionL NEW.cxs"
——— End of log from Thu Aug 4 13:49:17 2022 ———
opened ChimeraX session
> select /L:414
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /M:191
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add /M:232
21 atoms, 18 bonds, 3 residues, 2 models selected
> select add /M:194
31 atoms, 28 bonds, 4 residues, 2 models selected
> select add /M:231
39 atoms, 35 bonds, 5 residues, 2 models selected
> select add /M:230
49 atoms, 45 bonds, 6 residues, 2 models selected
> select add /L:412
55 atoms, 50 bonds, 7 residues, 2 models selected
> select add /L:413
63 atoms, 57 bonds, 8 residues, 2 models selected
> select add /L:411
68 atoms, 61 bonds, 9 residues, 2 models selected
> select add /L:410
77 atoms, 69 bonds, 10 residues, 2 models selected
> select add /L:391
86 atoms, 77 bonds, 11 residues, 2 models selected
> select add /L:393
96 atoms, 87 bonds, 12 residues, 2 models selected
> hide #!2 models
> show #!2 models
> select ~sel
6244 atoms, 6401 bonds, 1 pseudobond, 799 residues, 3 models selected
> color (#!1 & sel) dim gray
> color (#!1 & sel) white
> select ~sel
96 atoms, 94 bonds, 2 pseudobonds, 12 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> select clear
> select add /M:231
8 atoms, 11 bonds, 1 residue, 1 model selected
> select up
16 atoms, 11 bonds, 5 residues, 1 model selected
> select up
43 atoms, 42 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ff33aaff
> color sel #f3ae47ff
> select /L:414
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /L:413
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add /L:412
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add /L:411
25 atoms, 21 bonds, 4 residues, 2 models selected
> select add /L:410
34 atoms, 29 bonds, 5 residues, 2 models selected
> select add /L:391
43 atoms, 37 bonds, 6 residues, 2 models selected
> select add /L:393
53 atoms, 47 bonds, 7 residues, 2 models selected
> color sel teal
> select clear
> hide #!2 models
> select /M:191
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /L:414
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add /L:413
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add /L:412
26 atoms, 22 bonds, 4 residues, 2 models selected
> select add /L:411
31 atoms, 26 bonds, 5 residues, 2 models selected
> select add /L:410
40 atoms, 34 bonds, 6 residues, 2 models selected
> select add /L:391
49 atoms, 42 bonds, 7 residues, 2 models selected
> select add /L:393
59 atoms, 52 bonds, 8 residues, 2 models selected
> select add /M:232
68 atoms, 60 bonds, 9 residues, 2 models selected
> select add /M:231
76 atoms, 67 bonds, 10 residues, 2 models selected
> select add /M:194
86 atoms, 77 bonds, 11 residues, 2 models selected
> select add /M:230
96 atoms, 87 bonds, 12 residues, 2 models selected
> color (#!1 & sel) light gray
> ui tool show "Color Actions"
> color (#!1 & sel) #dd33ddff
> color (#!1 & sel) #d3d3d3ff
> open "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_localrefine_bin_filter.mrc"
Opened IgM-J-AIM_localrefine_bin_filter.mrc as #3, grid size 800,800,800,
pixel 0.415, shown at step 1, values float32
> volume #3 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #3 step 1
> volume #3 change image level -0.02029,0 level 0.1044,0.8 level 1.516,1
> volume #3 level 0.06478
> volume #3 level 0.1072
> ui tool show "Color Zone"
> color zone #3 near #1 distance 2.49
> color zone #3 near #1 distance 3.3
> color zone #3 near #1 distance 1
> color zone #3 near #1 distance 10
[Repeated 2 time(s)]
> volume splitbyzone #3
Opened IgM-J-AIM_localrefine_bin_filter.mrc 0 as #4.1, grid size 800,800,800,
pixel 0.415, shown at level 0.107, step 1, values float32
Opened IgM-J-AIM_localrefine_bin_filter.mrc 1 as #4.2, grid size 800,800,800,
pixel 0.415, shown at level 0.107, step 1, values float32
Opened IgM-J-AIM_localrefine_bin_filter.mrc 2 as #4.3, grid size 800,800,800,
pixel 0.415, shown at level 0.107, step 1, values float32
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> volume #4.3 level 0.1124
> close #4
> close #3
> open "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_localrefine_bin.mrc"
Opened IgM-J-AIM_localrefine_bin.mrc as #3, grid size 800,800,800, pixel
0.415, shown at step 1, values float32
> volume #3 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #3 step 1
> volume #3 change image level -0.02433,0 level 0.1076,0.8 level 1.764,1
> volume #3 level 0.1512
> volume #3 level 0.0932
> volume #3 level 0.109
> volume #3 level 0.09847
> volume #3 level 0.1196
> color zone #3 near #1 distance 10
> volume splitbyzone #3
Opened IgM-J-AIM_localrefine_bin.mrc 0 as #4.1, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 1 as #4.2, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 2 as #4.3, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
> volume splitbyzone #3
Opened IgM-J-AIM_localrefine_bin.mrc 0 as #5.1, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 1 as #5.2, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 2 as #5.3, grid size 800,800,800, pixel
0.415, shown at level 0.12, step 1, values float32
> close #5
> hide #!4.2 models
> volume #3 level 0.1899
> hide #!3 models
> volume #3 level 0.1412
> hide #!3 models
> volume #4.3 level 0.1235
> transparency (#!1 & sel) 70
> select clear
> transparency #1#4.1,3#!4 70
> hide #!4 models
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/colorzone L.cxs"
> undo
[Repeated 9 time(s)]
> close #4
> hide #!3 models
> select clear
> select /M:194
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add /L:413
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add /L:411
23 atoms, 21 bonds, 3 residues, 2 models selected
> select add /L:410
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add /L:391
41 atoms, 37 bonds, 5 residues, 2 models selected
> select add /L:393
51 atoms, 47 bonds, 6 residues, 2 models selected
> select add /M:231
59 atoms, 54 bonds, 7 residues, 2 models selected
> color (#!1 & sel) white
> select clear
> show #!3 models
> color zone #3 near #1 distance 10
[Repeated 1 time(s)]
> volume #3 level 0.06213
> volume splitbyzone #3
Opened IgM-J-AIM_localrefine_bin.mrc 0 as #4.1, grid size 800,800,800, pixel
0.415, shown at level 0.0621, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 1 as #4.2, grid size 800,800,800, pixel
0.415, shown at level 0.0621, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 2 as #4.3, grid size 800,800,800, pixel
0.415, shown at level 0.0621, step 1, values float32
> hide #!4.2 models
> volume #3 level 0.08378
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #4.3 level 0.07723
> hide #!4.1 models
> hide cartoons
> transparency #1#4.3#!4 70
> show cartoons
> select /L:528
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select /L:528
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select /M:231
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /M:194
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add /L:391
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add /L:410
36 atoms, 33 bonds, 4 residues, 2 models selected
> select add /L:411
41 atoms, 37 bonds, 5 residues, 2 models selected
> select add /L:413
49 atoms, 44 bonds, 6 residues, 2 models selected
> select add /L:393
59 atoms, 54 bonds, 7 residues, 2 models selected
> hide sel atoms
> select clear
> hide cartoons
> show #!4.1 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> volume #4.3 level 0.06208
> select #4.3
2 models selected
> select clear
> hide #!4 models
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
25 atoms, 23 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ff33aaff
> color sel #f3ae47ff
> color sel byelement
[Repeated 1 time(s)]
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
25 atoms, 23 bonds, 3 residues, 1 model selected
> color sel bychain
> color sel byhetero
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 2 models selected
> color sel teal
> color sel bychain
> color sel byelement
> color sel teal
> color sel byhetero
> select /M:230@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 2 bonds, 3 residues, 1 model selected
> select up
25 atoms, 23 bonds, 3 residues, 1 model selected
> select clear
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_local_colorzoneL.mrc" models #4.3
> open "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_Lfilter.mrc"
Opened IgM-J-AIM_Lfilter.mrc as #5, grid size 800,800,400, pixel 0.415, shown
at level 7.24e-07, step 4, values float32
> volume #5 step 1
> volume #5 level 0.02891
> volume #5 color #d3d33d
> volume #5 color lightgrey
> transparency #1,5 70
> select clear
> volume #5 level 0.07228
> select /L:411
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) light gray
> undo
[Repeated 1 time(s)]
> select /L:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /M:231
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add /L:414@CA
1 atom, 2 bonds, 1 residue, 1 model selected
> select up
13 atoms, 6 bonds, 7 residues, 2 models selected
> select up
53 atoms, 52 bonds, 7 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> show #!3 models
> color zone #3 near #1 distance 10
> volume #3 level 0.1869
> volume #3 level 0.328
> select add /M:232@CB
1 atom, 1 bond, 1 residue, 1 model selected
> select up
13 atoms, 6 bonds, 7 residues, 1 model selected
> select up
53 atoms, 52 bonds, 7 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #dd33ddff
> color (#!1 & sel) #d3d3d3ff
> select clear
> show #!3 models
> color zone #3 near #1 distance 10
> volume #3 level 0.6157
> volume #3 level 0.1163
> volume splitbyzone #3
Opened IgM-J-AIM_localrefine_bin.mrc 0 as #6.1, grid size 800,800,800, pixel
0.415, shown at level 0.116, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 1 as #6.2, grid size 800,800,800, pixel
0.415, shown at level 0.116, step 1, values float32
Opened IgM-J-AIM_localrefine_bin.mrc 2 as #6.3, grid size 800,800,800, pixel
0.415, shown at level 0.116, step 1, values float32
> hide #!6 models
> show #!6 models
> hide #!6.2 models
> hide #!6.1 models
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_local_colorzoneL1.mrc" models #6.3
> hide #!6 models
> hide #!6.3 models
> show cartoons
> select /L:414
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /M:232
15 atoms, 13 bonds, 2 residues, 2 models selected
> hide sel cartoons
> undo
[Repeated 2 time(s)]
> select clear
> hide cartoons
> select up
14 atoms, 7 bonds, 7 residues, 1 model selected
> select up
53 atoms, 52 bonds, 7 residues, 2 models selected
> color (#!1 & sel) light gray
> select ~sel
6287 atoms, 6449 bonds, 1 pseudobond, 804 residues, 22 models selected
> color (#!1 & sel) dim gray
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> open "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/IgM-J-AIM_L1filter.mrc"
Opened IgM-J-AIM_L1filter.mrc as #7, grid size 800,800,800, pixel 0.415, shown
at step 1, values float32
> volume #7 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #7 color lightgrey
> volume #7 step 1
> volume #7 level 0.01488
> transparency (#!1 & sel) 70
> select clear
[Repeated 1 time(s)]
> transparency #1#7.2#!7 70
> volume #7 level 0.1105
> volume #7 level 0.08744
> select #7
3 models selected
> select clear
> volume #7 level 0.0726
> volume #7 level 0.09569
> surface dust #7 size 4.15
> volume #7 level 0.09569
> close #4
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
25 atoms, 23 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ff33aaff
> color sel #f3ae47ff
> color sel byhetero
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel teal
> color sel byhetero
> select clear
> volume #7 level 0.1072
> volume #7 level 0.09733
> volume #7 level 0.09898
> volume #7 level 0.09569
> transparency #1#7.2#!7 70
> lighting full
> lighting shadows false
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/picture/colorzone_L.tif" width 1030 height 808
> supersample 3
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/colorzone L.cxs"
> save "D:/Peking University/Xiao Lab/Data/IgM & IgA project/IgM-AIM paper
> related/interaction/cxs/11111.cxs"
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\map\session.py",
line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\map\session.py",
line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000201FEFC8940> ->
<chimerax.map.volume.VolumeSurface object at 0x000002019FE3D3D0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000201AF3C6850> 'IgM-J-
AIM_localrefine_bin.mrc 0' -> <chimerax.map.session.GridDataState object at
0x00000201A1C61100>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save
mgr.discovery(self._state_containers)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000201FEFC8940> -> <chimerax.map.volume.VolumeSurface object at
0x000002019FE3D3D0> 'surface' -> <chimerax.map.volume.Volume object at
0x00000201AF3C6850> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x00000201A1C61100>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000201FEFC8940> -> <chimerax.map.volume.VolumeSurface object at
0x000002019FE3D3D0> 'surface' -> <chimerax.map.volume.Volume object at
0x00000201AF3C6850> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x00000201A1C61100>
ValueError: error processing: 'models' -> -> 'surface' -> 'IgM-J-
AIM_localrefine_bin.mrc 0' -> : Error while saving session data for 'models'
-> -> 'surface' -> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\map\session.py",
line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\map\session.py",
line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000201FEFC8940> ->
<chimerax.map.volume.VolumeSurface object at 0x000002019FE3D3D0> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000201AF3C6850> 'IgM-J-
AIM_localrefine_bin.mrc 0' -> <chimerax.map.session.GridDataState object at
0x00000201A1C61100>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\programs\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save
mgr.discovery(self._state_containers)
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000201FEFC8940> -> <chimerax.map.volume.VolumeSurface object at
0x000002019FE3D3D0> 'surface' -> <chimerax.map.volume.Volume object at
0x00000201AF3C6850> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x00000201A1C61100>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000201FEFC8940> -> <chimerax.map.volume.VolumeSurface object at
0x000002019FE3D3D0> 'surface' -> <chimerax.map.volume.Volume object at
0x00000201AF3C6850> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x00000201A1C61100>
ValueError: error processing: 'models' -> -> 'surface' -> 'IgM-J-
AIM_localrefine_bin.mrc 0' -> : Error while saving session data for 'models'
-> -> 'surface' -> 'IgM-J-AIM_localrefine_bin.mrc 0' ->
File "D:\programs\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ProArt Studiobook H7600ZM_H7600ZM
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,856,571,904
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202211240003
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.0.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.10.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving map in session |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Used volume split by zone on 800x800x800 maps producing many of them then ran out of memory saving session.
Added better error message a few weeks ago for ticket #9032.