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Opened 7 weeks ago
Closed 7 weeks ago
#18861 closed defect (duplicate)
MemoryError opening mmCIF files
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/state_1_bovine_head_central_c-ring-coot-ABCDEF.pdb"
Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/state_1_bovine_head_central_c-ring-coot-ABCDEF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 MET 8 1
LEU 8 4 1 4
Start residue of secondary structure not found: HELIX 2 2 ASP 8 5 PHE 8 21 1
17
Start residue of secondary structure not found: HELIX 3 3 ILE 8 22 LYS 8 30 1
9
Start residue of secondary structure not found: HELIX 126 126 THR G 2 ALA G 55
1 54
Start residue of secondary structure not found: HELIX 127 127 ILE G 81 ALA G
99 1 19
95 messages similar to the above omitted
Cannot find LINK/SSBOND residue LEU (69 )
Chain information for state_1_bovine_head_central_c-ring-coot-ABCDEF.pdb #1
---
Chain | Description
A B C | No description available
D E F | No description available
> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb"
Chain information for mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb #2
---
Chain | Description | UniProt
A | No description available | ATPA_MOUSE 1-553
B C | No description available |
D E F | No description available |
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> color #1 white
> color #1 #969696ff
> select add #2
71818 atoms, 72446 bonds, 32 pseudobonds, 5846 residues, 4 models selected
> select subtract #1
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> set bgColor white
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> select #2/A,B,C
13565 atoms, 13713 bonds, 1512 residues, 1 model selected
> color sel red
> select clear
> select #2/D,E,F
13631 atoms, 13801 bonds, 1420 residues, 1 model selected
> color sel yellow
> select clear
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> show sel surfaces
> select subtract #2
6 models selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel surfaces
> select clear
> select #2/B:137
10 atoms, 9 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select #2/B:136
10 atoms, 9 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> show sel atoms
> style sel stick
Changed 10 atom styles
> select #2/F:188
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3
9 atoms, 8 bonds, 1 pseudobond, 1 residue, 3 models selected
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> select add #1
44631 atoms, 44940 bonds, 33 pseudobonds, 2915 residues, 6 models selected
> hide sel atoms
> close #3
> select clear
> select #2/B:313@CB
1 atom, 1 residue, 1 model selected
> select add #2/B:313@ND2
2 atoms, 1 residue, 2 models selected
> select add #2/B:313@CG
3 atoms, 1 residue, 2 models selected
> select subtract #2/B:313@CB
2 atoms, 1 residue, 2 models selected
> select add #2/B:313@CB
3 atoms, 1 residue, 2 models selected
> select add #2/B:313@CA
4 atoms, 1 residue, 2 models selected
> select add #2/B:313@OD1
5 atoms, 1 residue, 2 models selected
> hide sel atoms
> show sel cartoons
> select #1/F:429
7 atoms, 6 bonds, 1 residue, 1 model selected
> select ::name="ILE"
6391 atoms, 5975 bonds, 446 residues, 2 models selected
> show sel atoms
> select clear
> hide #!2 models
> show #!2 models
> select #2/D:94@CD1
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select #1/D,E,F
21553 atoms, 21721 bonds, 12 pseudobonds, 1416 residues, 2 models selected
> color (#!1 & sel) black
> select clear
> select #1/D,E,F
21553 atoms, 21721 bonds, 12 pseudobonds, 1416 residues, 2 models selected
> color (#!1 & sel) cyan
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select #2/E:124@CG1
1 atom, 1 residue, 1 model selected
> select #2/B:115@CA
1 atom, 1 residue, 1 model selected
> select #2/E:124@CG1
1 atom, 1 residue, 1 model selected
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1/D:275@CD1
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select #1/A:287
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> select #1/A:288
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> show sel atoms
> select #1/A:283
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:286
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> select #1/D:310@CG2
1 atom, 1 residue, 1 model selected
> select #1/A:286@CD
1 atom, 1 residue, 1 model selected
> select #1/A:287
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/A:288@N
1 atom, 1 residue, 1 model selected
> select #1/B:286
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> show #!2 models
> hide #!1 models
> hide #3 models
> show #3 models
> show #!1 models
> hide #!2 models
> select #1/B:65
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B:66
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:67
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:66
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/C:286
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:68
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:66
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:67
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:65
14 atoms, 13 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select clear
> select #1/B:286@CD
1 atom, 1 residue, 1 model selected
> select #1/B:286
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:286,C:286,A
24 atoms, 23 bonds, 1 residue, 1 model selected
> 286
Unknown command: 286
> select #1/B:286 #1/C:286 #1/A:286
72 atoms, 69 bonds, 3 residues, 1 model selected
> select #1/C:137 1/A:137 1/B:137
Expected a keyword
> select #1/C:137 #1/A:137 #11/B:137
38 atoms, 36 bonds, 2 residues, 1 model selected
> select #1/C:137 #1/A:137 #1/B:137
57 atoms, 54 bonds, 3 residues, 1 model selected
> select #1/C:136,137 #1/A:136,137 #1/B:136,137
114 atoms, 111 bonds, 6 residues, 1 model selected
> select clear
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> show sel surfaces
> select #1/E:208@CD1
1 atom, 1 residue, 1 model selected
> select #1/E:197@HE2
1 atom, 1 residue, 1 model selected
> select subtract #3
1 atom, 1 residue, 2 models selected
> hide sel surfaces
> hide #3 models
> select clear
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> hide sel surfaces
> select #1/E:201@HD13
1 atom, 1 residue, 1 model selected
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 4 models selected
> select subtract #1
6 models selected
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select #1/A:48@NE2
1 atom, 1 residue, 1 model selected
> select #1/F:123@CE2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 4 models selected
> hide sel surfaces
> select #1/D:94,102 #1/E:94,102 #1/F:94,102
114 atoms, 108 bonds, 6 residues, 1 model selected
> select #1/D:275 #1/E:275 #1/F:275
57 atoms, 54 bonds, 3 residues, 1 model selected
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 6 models selected
> show sel surfaces
> select #1/D:123 #1/E:123 #1/F:123
60 atoms, 60 bonds, 3 residues, 1 model selected
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 6 models selected
> select subtract #1
6 models selected
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> hide sel surfaces
> hide #!1 models
> show #!2 models
> select subtract #1
6 models selected
> select #2/B:140@CG1
1 atom, 1 residue, 1 model selected
> select #2/C:136,137 #2/A:136,137 #2/B:136,137
58 atoms, 55 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 58 atom styles
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 4 models selected
> select subtract #2
6 models selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> show sel surfaces
> select subtract #2
6 models selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel surfaces
> select #2/C:136,137 #2/A:130,131 #2/B:136,137
56 atoms, 53 bonds, 6 residues, 1 model selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 4 models selected
> show sel surfaces
> select #1/D:123 #1/E:123 #1/F:123
60 atoms, 60 bonds, 3 residues, 1 model selected
> hide #!2 models
> show #!1 models
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 6 models selected
> hide sel atoms
> show #!2 models
> select add #2
71818 atoms, 72446 bonds, 32 pseudobonds, 5846 residues, 10 models selected
> hide sel surfaces
> hide sel atoms
> select ::name="PHE"
2781 atoms, 2781 bonds, 171 residues, 2 models selected
> show sel atoms
> select clear
> select #2/A:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:116
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/F:123@HE2
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select #1/F:123@CE2
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select #1/C:116
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/C:214
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/C:211
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/C:212
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/C:213
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/C:210
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1/C:211
35 atoms, 33 bonds, 2 residues, 2 models selected
> select add #1/C:212
49 atoms, 46 bonds, 3 residues, 2 models selected
> select add #1/C:213
65 atoms, 61 bonds, 4 residues, 2 models selected
> select add #1/C:214
75 atoms, 70 bonds, 5 residues, 2 models selected
> select add #1/C:215
92 atoms, 86 bonds, 6 residues, 2 models selected
> select add #1/C:209
114 atoms, 107 bonds, 7 residues, 2 models selected
> select add #1/C:208
131 atoms, 123 bonds, 8 residues, 2 models selected
> select add #1/C:114
141 atoms, 132 bonds, 9 residues, 2 models selected
> select add #1/C:115
160 atoms, 150 bonds, 10 residues, 2 models selected
> select add #1/C:116
172 atoms, 161 bonds, 11 residues, 2 models selected
> select add #1/C:117
179 atoms, 167 bonds, 12 residues, 2 models selected
> select add #1/C:118
201 atoms, 188 bonds, 13 residues, 2 models selected
> select add #1/C:107
217 atoms, 203 bonds, 14 residues, 2 models selected
> select add #1/C:108
233 atoms, 218 bonds, 15 residues, 2 models selected
> select add #1/C:109
245 atoms, 229 bonds, 16 residues, 2 models selected
> select add #1/C:76@CE1
246 atoms, 229 bonds, 17 residues, 2 models selected
> select subtract #1/C:76@CE1
245 atoms, 229 bonds, 16 residues, 2 models selected
> select add #1/C:110
255 atoms, 238 bonds, 17 residues, 2 models selected
> hide sel atoms
> show sel atoms
> select #1/C:272
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/D:123 #1/E:123 #1/F:123
60 atoms, 60 bonds, 3 residues, 1 model selected
> select #1/A:213,214,107,115 #1/B:213,214,107,115 #1/C:213,214,107,115
183 atoms, 174 bonds, 12 residues, 1 model selected
> show sel atoms
> show #!2 models
> hide #!1 models
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 6 models selected
> select add #2
71818 atoms, 72446 bonds, 32 pseudobonds, 5846 residues, 10 models selected
> select subtract #1
27196 atoms, 27514 bonds, 2932 residues, 13 models selected
> select clear
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> show #!1 models
> select subtract #2
6 models selected
> hide #!1 models
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #2/A:213,214,107,115 #2/B:213,214,107,115 #2/C:213,214,107,115
105 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> select #2/D:123 #2/E:123 #2/F:123
39 atoms, 39 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #2/A:207,208,101,109 #2/B:213,214,107,115 #2/C:213,214,107,115
97 atoms, 88 bonds, 12 residues, 1 model selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 4 models selected
> select subtract #2
6 models selected
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel atoms
> select #2/A:207,208,101,109 #2/B:213,214,107,115 #2/C:213,214,107,115
97 atoms, 88 bonds, 12 residues, 1 model selected
> show sel atoms
> select #2/D:123 #2/E:123 #2/F:123
39 atoms, 39 bonds, 3 residues, 1 model selected
> show sel atoms
> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb"
Chain information for mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb #4
---
Chain | Description | UniProt
A | No description available | ATPA_MOUSE 1-553
B C | No description available |
D E F | No description available |
> select add #2
27196 atoms, 27514 bonds, 2932 residues, 4 models selected
> select subtract #2
6 models selected
> select subtract #3
Nothing selected
> select add #4
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> show #!1 models
> hide #!1 models
> hide #4 models
> show #!1 models
> hide #!2 models
> show #4 models
> matchmaker #4/F to #1/E pairing bs
Parameters
---
Chain pairing | bs
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 state_1_bovine_head_central_c-ring-coot-ABCDEF.pdb, chain E (#1)
with mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb, chain F (#4),
sequence alignment score = 2019.7
RMSD between 215 pruned atom pairs is 0.959 angstroms; (across all 467 pairs:
3.827)
> select subtract #3
Nothing selected
> select #4/F
4539 atoms, 4595 bonds, 475 residues, 1 model selected
> select subtract #3
4539 atoms, 4595 bonds, 475 residues, 1 model selected
> hide #4 models
> show #4 models
> select #4/F:123
13 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/C:213,214,107,115
35 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> hide #4 models
> select add #4
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> show #!2 models
> hide #!2 models
> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/state_1_bovine_head_central_c-ring-coot-head_central.pdb"
Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/state_1_bovine_head_central_c-ring-coot-head_central.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 MET 8 1
LEU 8 4 1 4
Start residue of secondary structure not found: HELIX 2 2 ASP 8 5 PHE 8 21 1
17
Start residue of secondary structure not found: HELIX 3 3 ILE 8 22 LYS 8 30 1
9
Start residue of secondary structure not found: HELIX 141 141 ILE K 2 ALA K 13
1 12
Start residue of secondary structure not found: HELIX 142 142 VAL K 16 ASN K
39 1 24
69 messages similar to the above omitted
Cannot find LINK/SSBOND residue LEU (69 )
Chain information for state_1_bovine_head_central_c-ring-coot-head_central.pdb
#5
---
Chain | Description
A B C | No description available
D E F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
S | No description available
h | No description available
> select add #5
83583 atoms, 84287 bonds, 32 pseudobonds, 6594 residues, 4 models selected
> hide sel & #!5 atoms
> show sel & #!5 cartoons
> hide #5
> select subtract #5
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> select add #5
83583 atoms, 84287 bonds, 32 pseudobonds, 6594 residues, 4 models selected
> select subtract #5
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> select add #5
83583 atoms, 84287 bonds, 32 pseudobonds, 6594 residues, 4 models selected
> hide sel & #!5 cartoons
> matchmaker #5 to #1/F pairing bs
Parameters
---
Chain pairing | bs
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 state_1_bovine_head_central_c-ring-coot-ABCDEF.pdb, chain F (#1)
with state_1_bovine_head_central_c-ring-coot-head_central.pdb, chain F (#5),
sequence alignment score = 2398.9
RMSD between 467 pruned atom pairs is 0.000 angstroms; (across all 467 pairs:
0.000)
> select subtract #5
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> select subtract #3
27196 atoms, 27514 bonds, 2932 residues, 1 model selected
> select subtract #4
Nothing selected
> select subtract #3
Nothing selected
> select add #5
56387 atoms, 56773 bonds, 32 pseudobonds, 3662 residues, 3 models selected
> show sel cartoons
> hide sel cartoons
> select #5/G
4300 atoms, 4326 bonds, 272 residues, 1 model selected
> show sel cartoons
> select clear
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/mus_compare_to_bovine_state_1_bovine-coot-926_head_central.pdb"
Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/mus_compare_to_bovine_state_1_bovine-coot-926_head_central.pdb
---
warning | PDB SEQRES record for chain S is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for mus_compare_to_bovine_state_1_bovine-
coot-926_head_central.pdb #6
---
Chain | Description | UniProt
A | No description available | ATPA_MOUSE 1-553
B C | No description available |
D E F | No description available |
G | No description available |
H | No description available |
I | No description available |
S | No description available |
h | No description available |
> select add #6
34004 atoms, 34394 bonds, 3633 residues, 1 model selected
> hide sel atoms
> matchmaker #6 to #2/F pairing bs
Parameters
---
Chain pairing | bs
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 mus_compare_to_bovine_state_1_bovine-coot_ABCDEF.pdb, chain F (#2)
with mus_compare_to_bovine_state_1_bovine-coot-926_head_central.pdb, chain F
(#6), sequence alignment score = 2347.9
RMSD between 469 pruned atom pairs is 0.000 angstroms; (across all 469 pairs:
0.000)
> select #6/G
2660 atoms, 2685 bonds, 273 residues, 1 model selected
> show sel cartoons
> select clear
> show #!5 models
> hide #6 models
> show #!1 models
> hide #!2 models
> select #1/F:390
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/F:391
38 atoms, 36 bonds, 2 residues, 2 models selected
> show sel atoms
> select #1/D:387
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/D:388
38 atoms, 36 bonds, 2 residues, 2 models selected
> select #1/D:390
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/D:391
38 atoms, 36 bonds, 2 residues, 2 models selected
> show sel atoms
> select add #1/E:390
57 atoms, 54 bonds, 3 residues, 2 models selected
> select add #1/E:391
76 atoms, 72 bonds, 4 residues, 3 models selected
> show sel atoms
> hide #!1 models
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 5 models selected
> select subtract #1
6 models selected
> show #!2 models
> hide #!5 models
> show #6 models
> select #2/D:390
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #2/D:391
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> select #2/E:390
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #2/E:391
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> select #2/B:406
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/C:492
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> color sel byhetero
> select #2/C:492@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select add #1
44622 atoms, 44932 bonds, 32 pseudobonds, 2914 residues, 3 models selected
> color #6#!2 bychain
> color #1 #8c8c8cff
> color #1 #848484ff
> show #!1 models
> select subtract #1
6 models selected
> color #1 #8c8c8cff
> color #1 #b1b1b1ff
> select clear
> hide #!1 models
> lighting shadows false
> graphics silhouettes true
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> view
> ui tool show "Side View"
> select #2/D:112
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D:112
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/D:113
24 atoms, 23 bonds, 2 residues, 2 models selected
> select ::name="ADP"
549 atoms, 579 bonds, 15 residues, 5 models selected
> show sel & #6#!2 atoms
> style sel & #6#!2 sphere
Changed 210 atom styles
> ui tool show "Color Actions"
> color sel black
> select clear
> hide #!2 models
> hide #6 models
> open
> C:/Users/2023.12/Desktop/mb/mb/ATPase/cryosparc_P13_J215_003_volume_map.mrc
Opened cryosparc_P13_J215_003_volume_map.mrc as #7, grid size 128,128,128,
pixel 3.28, shown at level 0.287, step 1, values float32
> volume #7 level 0.1904
> open "D:/liver_jxgsg/ATPase/ATP synthase model/bovine ATP synthase monomer
> state 1 (combined)_6ZPO.cif"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open "D:/liver_jxgsg/ATPase/ATP synthase model/bovine ATP synthase monomer
> state 1 (combined)_6ZPO.cif"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 教育版 (Build 19045)
Memory: 34,088,153,088
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Core(TM) i7-14700K
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
Send2Trash: 1.8.3
SEQCROW: 1.8.18
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError opening mmCIF files |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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