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Opened 4 years ago
Closed 4 years ago
#5378 closed defect (can't reproduce)
Unable to open file for writing PDB
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/CD1650CBDonly.cxs"
Log from Mon Sep 20 09:53:20 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\SC\Downloads\Superimpose CBD from different model tools
> (1).cxs" format session
Log from Sun Sep 5 23:26:28 2021UCSF 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 "/Users/wichuda/Downloads/CD16:50L CBD Hhpred.pdb"
Chain information for CD16:50L CBD Hhpred.pdb #1
---
Chain | Description
X | No description available
> open "/Users/wichuda/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/DB935D33-5A41-462C-80F2-730C24C78284/model_1_unrelaxed.pdb"
Chain information for model_1_unrelaxed.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 to #1
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 CD16:50L CBD Hhpred.pdb, chain X (#1) with model_1_unrelaxed.pdb,
chain A (#2), sequence alignment score = 445.2
RMSD between 76 pruned atom pairs is 0.732 angstroms; (across all 88 pairs:
2.502)
> open "/Volumes/GoogleDrive/My Drive/phage/Endolysin/Chrimera/CD16:50L CBD
> head on.pdb"
CD16:50L CBD head on.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for CD16:50L CBD head on.pdb #3
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #2-3 to #1
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 CD16:50L CBD Hhpred.pdb, chain X (#1) with model_1_unrelaxed.pdb,
chain A (#2), sequence alignment score = 445.2
RMSD between 76 pruned atom pairs is 0.732 angstroms; (across all 88 pairs:
2.502)
Matchmaker CD16:50L CBD Hhpred.pdb, chain X (#1) with CD16:50L CBD head
on.pdb, chain A (#3), sequence alignment score = 436.8
RMSD between 78 pruned atom pairs is 0.474 angstroms; (across all 88 pairs:
1.576)
> save "/Volumes/GoogleDrive/My Drive/phage/Endolysin/Chrimera/Superimpose CBD
> from different model tools.cxs"
——— End of log from Sun Sep 5 23:26:28 2021 ———
opened ChimeraX session
> hide #3 models
> hide #2 models
> select /X:257
Nothing selected
> select #1/X:257
Nothing selected
> select #1/X:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X
Alignment identifier is 1/X
> select #1/X:78
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/X:78
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:48
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:48
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #2 models
> hide #2 models
> show #3 models
> select #1/X:257
Nothing selected
> select #1/X:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X
Alignment identifier is 1/X
> select #1/X:78
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/X:78
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/X:74
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/X:73-74
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/X:47-48
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/X:47-48
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/X:38-39
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/X:38-39
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/X:24
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:24
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:23
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:23
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/X:24
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:24
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/X:9
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:9
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:3-4
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1/X:3
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:9
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:9
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:23-24
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #1/X:23-24
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/X:39-48
93 atoms, 96 bonds, 10 residues, 1 model selected
> select #1/X:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/X:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/X:54
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/X:54-59
47 atoms, 46 bonds, 6 residues, 1 model selected
> select #1/X:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/X:65-69
40 atoms, 40 bonds, 5 residues, 1 model selected
> select #1/X:70-71
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/X:70-74
40 atoms, 40 bonds, 5 residues, 1 model selected
> select #1/X:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/X:78-85
65 atoms, 66 bonds, 8 residues, 1 model selected
> select #1/X:90
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/X:86-90
46 atoms, 46 bonds, 5 residues, 1 model selected
> select #1/X:11
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/X:11-16
42 atoms, 41 bonds, 6 residues, 1 model selected
> select #1/X:19
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/X:19-21
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/X:18-19
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/X:18-19
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/X:20-21
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/X:20-22
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/X:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/X:15-16
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/X:14
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/X:14-18
35 atoms, 34 bonds, 5 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #3/A #3/B
Alignment identifier is 1
> select #2/A:72-89 #3/A-B:73-90
449 atoms, 458 bonds, 54 residues, 2 models selected
> select #2/A:72-89 #3/A-B:73-90
449 atoms, 458 bonds, 54 residues, 2 models selected
> select #2/A:77 #3/A-B:78
42 atoms, 45 bonds, 3 residues, 2 models selected
> select #2/A:77-89 #3/A-B:78-90
332 atoms, 338 bonds, 39 residues, 2 models selected
> select #2/A:77 #3/A-B:78
42 atoms, 45 bonds, 3 residues, 2 models selected
> select #2/A:77 #3/A-B:78
42 atoms, 45 bonds, 3 residues, 2 models selected
> show sel & #3 atoms
> select #2/A:38 #3/A-B:39
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:38 #3/A-B:39
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:30 #3/A-B:31
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:30 #3/A-B:31
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:22 #3/A-B:23
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:22-23 #3/A-B:23-24
72 atoms, 75 bonds, 6 residues, 2 models selected
> show sel & #3 atoms
> hide #1 models
> select #2/A:22 #3/A-B:23
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:22 #3/A-B:23
36 atoms, 36 bonds, 3 residues, 2 models selected
> hide sel & #3 atoms
> select #2/A:23 #3/A-B:24
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:23 #3/A-B:24
36 atoms, 36 bonds, 3 residues, 2 models selected
> hide sel & #3 atoms
> select #2/A:22 #3/A-B:23
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:22 #3/A-B:23
36 atoms, 36 bonds, 3 residues, 2 models selected
> show sel & #3 atoms
> select #1/X
721 atoms, 735 bonds, 88 residues, 1 model selected
> select #3/A
732 atoms, 746 bonds, 89 residues, 1 model selected
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
732 atoms, 89 residues, 1 surfaces, atom bfactor range 0.34 to 0.86
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for CD16:50L CBD head on.pdb_A SES surface #3.1: minimum,
-15.23, mean -0.05, maximum 15.90
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for CD16:50L CBD head on.pdb_A SES surface #3.1: minimum,
-15.23, mean -0.05, maximum 15.90
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> color sel byhetero
> rainbow sel
> color sel bychain
> mlp sel
Map values for surface "CD16:50L CBD head on.pdb_A SES surface": minimum
-24.05, mean -4.069, maximum 21.7
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X
Alignment identifier is 1/X
> select #1/X:11-23,36-38,52-59,61-63,77-88
300 atoms, 299 bonds, 39 residues, 1 model selected
> select #3/A
732 atoms, 746 bonds, 89 residues, 1 model selected
> hide sel surfaces
> select #1/X:5-9,33-35,46-50,70-72
133 atoms, 132 bonds, 16 residues, 1 model selected
> select #1/X:3-5
31 atoms, 32 bonds, 3 residues, 1 model selected
> select #1/X:3-9
65 atoms, 67 bonds, 7 residues, 1 model selected
> select #1/X:3-4
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1/X:3-7
46 atoms, 47 bonds, 5 residues, 1 model selected
> select #1/X:11-12
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/X:11-12
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/X:12-15
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/X:12-17
43 atoms, 42 bonds, 6 residues, 1 model selected
> select #1/X:21
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/X:21-44
212 atoms, 217 bonds, 24 residues, 1 model selected
> select #1/X:21-22
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/X:21-25
45 atoms, 46 bonds, 5 residues, 1 model selected
> select #1/X:71
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/X:18-71
445 atoms, 452 bonds, 54 residues, 1 model selected
> select #3/A
732 atoms, 746 bonds, 89 residues, 1 model selected
> select #3/A:39
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/X:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/X:18-19
16 atoms, 15 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #3/A #3/B
Alignment identifier is 1
> select #2/A:10-11 #3/A-B:11-12
36 atoms, 33 bonds, 6 residues, 2 models selected
> select #2/A:10-14 #3/A-B:11-15
108 atoms, 105 bonds, 15 residues, 2 models selected
> select #2/A:14 #3/A-B:15
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:14 #3/A-B:15
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:1 #3/A-B:2
33 atoms, 30 bonds, 3 residues, 2 models selected
> select #2/A:1-8 #3/A-B:2-9
228 atoms, 234 bonds, 24 residues, 2 models selected
> select #2/A:9-10 #3/A-B:10-11
30 atoms, 27 bonds, 6 residues, 2 models selected
> select #2/A:9-14 #3/A-B:10-15
126 atoms, 123 bonds, 18 residues, 2 models selected
> select #2/A:14 #3/A-B:15
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:14 #3/A-B:15
21 atoms, 18 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> select #2/A:16 #3/A-B:17
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #2/A:16 #3/A-B:17
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #2/A:18 #3/A-B:19
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:18 #3/A-B:19
24 atoms, 21 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> select #2/A:20 #3/A-B:21
12 atoms, 9 bonds, 3 residues, 2 models selected
> select #2/A:20 #3/A-B:21
12 atoms, 9 bonds, 3 residues, 2 models selected
> select #2/A:21 #3/A-B:22
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:21 #3/A-B:22
24 atoms, 21 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> select #2/A:22-23 #3/A-B:23-24
72 atoms, 75 bonds, 6 residues, 2 models selected
> select #2/A:22-23 #3/A-B:23-24
72 atoms, 75 bonds, 6 residues, 2 models selected
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:1-2 #3/A-B:2-3
69 atoms, 69 bonds, 6 residues, 2 models selected
> select #2/A:2-27 #3/A-B:3-28
648 atoms, 660 bonds, 78 residues, 2 models selected
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:4-8,30-34,45-49,69-71 #3/A-B:5-9,31-35,46-50,70-72
459 atoms, 459 bonds, 54 residues, 2 models selected
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:38 #3/A-B:39
36 atoms, 36 bonds, 3 residues, 2 models selected
> select #2/A:38-44 #3/A-B:39-45
195 atoms, 201 bonds, 21 residues, 2 models selected
> select #2/A:34 #3/A-B:35
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:34-38 #3/A-B:35-39
135 atoms, 135 bonds, 15 residues, 2 models selected
> select #2/A:44 #3/A-B:45
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:44-50 #3/A-B:45-51
168 atoms, 168 bonds, 21 residues, 2 models selected
> select #2/A:51 #3/A-B:52
12 atoms, 9 bonds, 3 residues, 2 models selected
> select #2/A:51-59 #3/A-B:52-60
201 atoms, 198 bonds, 27 residues, 2 models selected
> select #2/A:62 #3/A-B:63
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:62-68 #3/A-B:63-69
168 atoms, 168 bonds, 21 residues, 2 models selected
> select #2/A:67 #3/A-B:68
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:67-75 #3/A-B:68-76
228 atoms, 231 bonds, 27 residues, 2 models selected
> select #2/A:76 #3/A-B:77
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:76-77 #3/A-B:77-78
63 atoms, 66 bonds, 6 residues, 2 models selected
> select #2/A:76 #3/A-B:77
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:76 #3/A-B:77
21 atoms, 18 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> show sel & #!3 atoms
> show sel & #!3 atoms
> show sel & #!3 atoms
> select #2/A:79 #3/A-B:80
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:79-80 #3/A-B:80-81
45 atoms, 42 bonds, 6 residues, 2 models selected
> select #2/A:80 #3/A-B:81
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:80 #3/A-B:81
24 atoms, 21 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> select #2/A:81 #3/A-B:82
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:81 #3/A-B:82
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:82-83 #3/A-B:83-84
42 atoms, 39 bonds, 6 residues, 2 models selected
> select #2/A:82-83 #3/A-B:83-84
42 atoms, 39 bonds, 6 residues, 2 models selected
> select #2/A:83 #3/A-B:84
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #2/A:83 #3/A-B:84
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #2/A:84-85 #3/A-B:85-86
51 atoms, 48 bonds, 6 residues, 2 models selected
> select #2/A:84-85 #3/A-B:85-86
51 atoms, 48 bonds, 6 residues, 2 models selected
> select #2/A:85 #3/A-B:86
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:84-85 #3/A-B:85-86
51 atoms, 48 bonds, 6 residues, 2 models selected
> select #2/A:84 #3/A-B:85
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:84 #3/A-B:85
24 atoms, 21 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> select #2/A:88 #3/A-B:89
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:88 #3/A-B:89
27 atoms, 24 bonds, 3 residues, 2 models selected
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:87 #3/A-B:88
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #2/A:87 #3/A-B:88
21 atoms, 18 bonds, 3 residues, 2 models selected
> show sel & #!3 atoms
> hide sel & #!3 atoms
> select #2/A:74-89 #3/A-B:75-90
401 atoms, 407 bonds, 48 residues, 2 models selected
> select #2/A:1-89 #3/A-B:2-90
2195 atoms, 2237 bonds, 267 residues, 2 models selected
> select #2/A:89 #3/A-B:90
29 atoms, 26 bonds, 3 residues, 2 models selected
> select #2/A:1-89 #3/A-B:2-90
2195 atoms, 2237 bonds, 267 residues, 2 models selected
> select clear
> select #2/A:68-89 #3/A-B:69-90
554 atoms, 566 bonds, 66 residues, 2 models selected
> select #2/A:1-89 #3/A-B:2-90
2195 atoms, 2237 bonds, 267 residues, 2 models selected
Alignment identifier is 2
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:89 #3/A-B:90
29 atoms, 26 bonds, 3 residues, 2 models selected
> select #2/A:1-89 #3/A-B:2-90
2195 atoms, 2237 bonds, 267 residues, 2 models selected
> select #2/A:42-43 #3/A-B:43-44
54 atoms, 51 bonds, 6 residues, 2 models selected
> select #2/A:42-43 #3/A-B:43-44
54 atoms, 51 bonds, 6 residues, 2 models selected
> select #2/A:10-25,27-29,35-37,51-64,76-88
> #3/A-B:11-26,28-30,36-38,52-65,77-89
1164 atoms, 1164 bonds, 147 residues, 2 models selected
> select #2/A:22-23 #3/A-B:23-24
72 atoms, 75 bonds, 6 residues, 2 models selected
> select #2/A:22-23 #3/A-B:23-24
72 atoms, 75 bonds, 6 residues, 2 models selected
> select #2/A:12 #3/A-B:13
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #2/A:12-21 #3/A-B:13-22
213 atoms, 210 bonds, 30 residues, 2 models selected
> select clear
> select #3/B:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:23
12 atoms, 12 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:19
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:78
14 atoms, 15 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #3/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> save "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/CD1650CBDonly.cxs"
——— End of log from Mon Sep 20 09:53:20 2021 ———
opened ChimeraX session
> show #2 models
> show #1 models
> open "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/Superimpose of CBD from C. difficile
> endolysin CBD 210915.cxs"
> To Restore session:
>
> * update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
>
Unable to restore session: need to update bundle
> hide #2 models
> hide #1 models
No model chosen to save relative to
No model chosen to save relative to
> select clear
> save "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/CD16:50L CDB.pdb" displayedOnly true
> relModel #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CDB.pdb' for writing
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CDB.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb" relModel #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb' for writing
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save "G:/My Drive/# DrivWork@Mahidol_2020/My SC lab students/Bee
> Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb" displayedOnly true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb' for writing
OSError: Unable to open file 'G:/My Drive/# DrivWork@Mahidol_2020/My SC lab
students/Bee Wichuda/Endolysin manuscript/Others/CD16:50L CBD.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> save /CBD.pdb displayedOnly true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file '/CBD.pdb' for writing
OSError: Unable to open file '/CBD.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
> show #2 models
> show #1 models
> save /CBD.pdb displayedOnly true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save
pdb.save_pdb(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
OSError: Unable to open file '/CBD.pdb' for writing
OSError: Unable to open file '/CBD.pdb' for writing
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20HQS3U800
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 17,006,473,216
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300U CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unable to open file for writing PDB |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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