![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10245 closed defect (limitation)
Restore new session in old ChimeraX
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC folder/TBC-
> ChimeraX/Pie354-TBC-RAB8A complex.cxs"
Log from Tue Nov 28 18:05:43 2023UCSF ChimeraX version: 1.7.dev202305130100
(2023-05-13)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/obozkurt/Library/CloudStorage/Box-Box/TBC folder/TBC-
> ChimeraX/tbc-complex model.cxs"
Log from Tue Nov 28 01:05:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC folder/TBC-
> ChimeraX/Pie_TBC_R8a-2.cxs"
Log from Sat Jul 8 11:29:02 2023UCSF 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 "/Users/tolgabozkurt/Desktop/TBC-ChimeraX/Raw
> Models/PieTBCRab8a_f300c/PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
Chain information for
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> set bgColor white
> select /A:1-81
644 atoms, 654 bonds, 81 residues, 1 model selected
> color sel #fefa54ff
> color sel #fcea4fff
> select /B:1-607
4990 atoms, 5115 bonds, 607 residues, 1 model selected
> color sel black
Alignment identifier is 1/B
> select /B:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:1-140
1136 atoms, 1165 bonds, 140 residues, 1 model selected
> color sel #dc9de6ff
> color sel #d9a9e7ff
> select /D
Nothing selected
> select /C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
Alignment identifier is 1/C
> show sel surfaces
> color (#!1 & sel) cornflower blue
> transparency (#!1 & sel) 80
> select clear
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> select /B:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:1-140
1136 atoms, 1165 bonds, 140 residues, 1 model selected
> surface sel
> transparency (#!1 & sel) 90
> select clear
> select /B:305
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:305-427
1039 atoms, 1059 bonds, 123 residues, 1 model selected
> select /B:328
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:328-469
1194 atoms, 1223 bonds, 142 residues, 1 model selected
> select /B:328
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:328-565
2029 atoms, 2084 bonds, 238 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 80
> select clear
> select /B:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:1-140
1136 atoms, 1165 bonds, 140 residues, 1 model selected
> show sel surfaces
> select clear
> select /A
644 atoms, 654 bonds, 81 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 40
> select clear
> select /B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:141-380
1956 atoms, 2004 bonds, 240 residues, 1 model selected
> select /B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:141-427
2349 atoms, 2402 bonds, 287 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select /B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:141-415
2255 atoms, 2308 bonds, 275 residues, 1 model selected
> select /B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:141-318
1428 atoms, 1463 bonds, 178 residues, 1 model selected
> hide sel cartoons
> undo
> select /B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:141-293
1224 atoms, 1251 bonds, 153 residues, 1 model selected
> hide sel cartoons
> save /Users/tolgabozkurt/Desktop/TBC-ChimeraX/Pie_TBC_R8a-2.cxs
——— End of log from Sat Jul 8 11:29:02 2023 ———
opened ChimeraX session
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
> select /C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 resSeparation 4 interModel false intraMol
> false ignoreHiddenModels true select true color #010102 dashes 7 radius
> 0.165 reveal true
351 distances
> color #1.4 #6e71d5ff models
> color #1.4 #d5277aff models
> color #1.4 #d5042bff models
> color #1.4 #d54e50ff models
> color #1.4 #f0585aff models
> select clear
> select (/C & ::polymer_type>0 ) & ((/B & ::polymer_type>0 ) :<4)
241 atoms, 235 bonds, 28 residues, 1 model selected
> select (/B & ::polymer_type>0 ) & ((/C & ::polymer_type>0 ) :<4)
259 atoms, 248 bonds, 29 residues, 1 model selected
> select /B:510
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:510-607
831 atoms, 852 bonds, 98 residues, 1 model selected
> select /B:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:569-607
297 atoms, 300 bonds, 39 residues, 1 model selected
> select
> /B:51-57,64-66,102-112,133-140,193-214,216-218,275-292,304-310,320-330,334-336,338-344,354-376,380-385,387-402,408-410,416-431,441-452,455-473,478-494,496-504,511-519,527-539,546-557,559-564,569-579,585-606
2484 atoms, 2518 bonds, 294 residues, 1 model selected
> select /B:506
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:506-607
861 atoms, 882 bonds, 102 residues, 1 model selected
> color (#!1 & sel) #ffd271ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffc12fff
[Repeated 1 time(s)]
> hide sel surfaces
> select clear
[Repeated 2 time(s)]
> lighting soft
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 174311 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 298359 of 680238 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 314 atoms, 707 residues, 351 pseudobonds, 281 bonds
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> select clear
> alphafold contacts /A toResidues /B distance 4
Structure
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1 does not have PAE data opened
> select /A
644 atoms, 654 bonds, 81 residues, 1 model selected
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 10
> transparency (#!1 & sel) 0
> select clear
> select /C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:167-179
106 atoms, 106 bonds, 13 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select clear
> select /A
644 atoms, 654 bonds, 81 residues, 1 model selected
Alignment identifier is 1/A
> select clear
> select add #1.3
644 atoms, 81 residues, 1 model selected
> select subtract #1.3
1 model selected
> select add #1.1
1419 atoms, 179 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1.1
1419 atoms, 179 residues, 1 model selected
> transparency (#!1 & sel) 10
> select clear
> select /B:172
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:172-232
504 atoms, 513 bonds, 61 residues, 1 model selected
> hide sel atoms
> select clear
> hide #1.2 models
> select add #1.2
4990 atoms, 607 residues, 1 model selected
> select subtract #1.2
1 model selected
> show #1.2 models
> select add #1.2
4990 atoms, 607 residues, 1 model selected
> select subtract #1.2
1 model selected
> hide #1.2 models
> select clear
> select /B:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) magenta
> select clear
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> color #1.4 #76e559ff models
> color #1.4 #98e546ff models
> color #1.4 #64e568ff models
> color #1.4 #6be591ff models
> color #1.4 #40e57eff models
> color #1.4 #3ce515ff models
> color #1.4 #2de501ff models
> color #1.4 #08e511ff models
> color #1.4 #b3e51dff models
> color #1.4 #7ee531ff models
> color #1.4 #65e54dff models
> color #1.4 #56e569ff models
> color #1.4 #54e595ff models
> color #1.4 #33e585ff models
> color #1.4 #23e55cff models
> color #1.4 #1fe526ff models
> color #1.4 #5de53aff models
> color #1.4 #a1e58cff models
> color #1.4 #68e556ff models
> color #1.4 #2ae52fff models
> color #1.4 #10e513ff models
> select clear
> select /B:439
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) magenta
> select clear
> select /B:558-607
389 atoms, 393 bonds, 50 residues, 1 model selected
> select /B:459-607
1255 atoms, 1288 bonds, 149 residues, 1 model selected
> color (#!1 & sel) black
> select clear
> select /B:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:510-607
831 atoms, 852 bonds, 98 residues, 1 model selected
> color (#!1 & sel) dark gray
> select clear
> select /C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> transparency (#!1 & sel) 0
> select clear
> open "/Users/tolgabozkurt/Library/CloudStorage/Box-Box/Rab3GAP MS/Figure
> 5/Figure PDBs/6whe.pdb"
6whe.pdb title:
Structure of phosphomimetic RAB8A gtpase (T72E) In the GTP-bound state [more
info...]
Chain information for 6whe.pdb #2
---
Chain | Description | UniProt
A B | oncogene C-MEL | RAB8A_HUMAN 1-181
Non-standard residues in 6whe.pdb #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> 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
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain C (#1) with 6whe.pdb, chain B (#2), sequence alignment score = 662.2
RMSD between 154 pruned atom pairs is 0.546 angstroms; (across all 164 pairs:
1.155)
> select :GTP
64 atoms, 68 bonds, 2 residues, 1 model selected
> color sel orange
> select clear
Drag select of 123 atoms, 168 residues, 6 pseudobonds, 100 bonds
Drag select of 20 residues
Drag select of 123 atoms, 168 residues, 6 pseudobonds, 100 bonds
> select clear
> select #2/B:4-178
1418 atoms, 1439 bonds, 175 residues, 1 model selected
> select #2/A:4-175
1392 atoms, 1413 bonds, 172 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
Drag select of 41 atoms, 4 pseudobonds, 34 bonds
> hide sel cartoons
> hide sel atoms
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 165682 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 385 atoms, 876 residues, 176 pseudobonds, 325 bonds
> select ::name="HOH"
316 atoms, 316 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select all
10251 atoms, 10133 bonds, 363 pseudobonds, 1535 residues, 4 models selected
> select ::name="HOH"
316 atoms, 316 residues, 1 model selected
> hide #1.1 models
Drag select of 6 atoms, 5 bonds
> hide sel atoms
> close #1.4
> select #2/B:4-178
1418 atoms, 1439 bonds, 175 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 resSeparation 4 interModel false intraMol
> false ignoreHiddenModels true select true color #83e76e dashes 7 radius
> 0.165 reveal true
351 distances
> undo
> select add #1.4
121 atoms, 8 bonds, 351 pseudobonds, 30 residues, 4 models selected
> close #1.4
> select #1/C:174-179
48 atoms, 47 bonds, 6 residues, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel resSeparation 4 intraMol false ignoreHiddenModels true select
> true color #83e76e dashes 1 radius 0.165 reveal true
14410 contacts
> select #2/A:4-175
1392 atoms, 1413 bonds, 172 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> close #3
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select #2/A:4-175
1392 atoms, 1413 bonds, 172 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select ::name="HOH"
316 atoms, 316 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> close #2.1
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide sel cartoons
> select #2/B:4-178
1418 atoms, 1439 bonds, 175 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 6 atoms, 5 bonds
> hide sel cartoons
> hide sel atoms
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel resSeparation 4 intraMol false select true color #83e76e dashes
> 1 radius 0.165 reveal true
14410 contacts
> select #2/B:4-178
1418 atoms, 1439 bonds, 175 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> close #3
> select ::name="HOH"
316 atoms, 316 residues, 1 model selected
> hide sel atoms
> select #2/A:4-175
1392 atoms, 1413 bonds, 172 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel atoms
Drag select of 3 atoms, 5 bonds
> hide sel atoms
Drag select of 14 atoms, 7 residues, 12 bonds
> select clear
Drag select of 1 atoms
[Repeated 1 time(s)]
> hide sel atoms
> select add #2/B:203@O2
3 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:169-230
507 atoms, 516 bonds, 62 residues, 1 model selected
> hide sel atoms
> select #1/C:178-179
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> hide sel atoms
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> select clear
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 resSeparation 2 intraMol false select true
> color #83e76e dashes 8 radius 0.165 reveal true
613 distances
> select clear
Drag select of 182 atoms, 165 bonds, 219 pseudobonds
> hide sel atoms
> close #3
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 4160 of 97050 triangles, 380 atoms, 296 residues, 332 bonds, 1
pseudobonds
> select ::name="HOH"
316 atoms, 316 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select add #2.1
316 atoms, 1 pseudobond, 316 residues, 2 models selected
> close #2.1
> select #2/B:4-178
1418 atoms, 1439 bonds, 175 residues, 1 model selected
> hide sel atoms
> select add #1/B:401
1425 atoms, 1445 bonds, 176 residues, 2 models selected
> select clear
> select add #1/B:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> select #1/B:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:275-519
2060 atoms, 2113 bonds, 245 residues, 1 model selected
> select #1/B:275
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:275-607
2792 atoms, 2861 bonds, 333 residues, 1 model selected
> select add #2/B:201@C1'
2793 atoms, 2861 bonds, 334 residues, 3 models selected
> select subtract #2/B:201@C1'
2792 atoms, 2861 bonds, 333 residues, 2 models selected
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> select #1/B:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:455-607
1286 atoms, 1320 bonds, 153 residues, 1 model selected
> select #1/B:304
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:304-607
2550 atoms, 2612 bonds, 304 residues, 1 model selected
Drag select of 91 atoms, 36 residues, 87 bonds
Drag select of 144 atoms, 100 residues, 128 bonds
> ui tool show Contacts
> contacts sel restrict both distanceOnly 4.0 resSeparation 2 intraMol false
> select true color #83e76e dashes 8 radius 0.165 reveal true
78 distances
> select clear
> select add #1/B:402
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
Drag select of 94 atoms, 60 residues, 88 bonds, 4 pseudobonds
> select clear
Drag select of 263 atoms, 345 residues, 228 bonds, 78 pseudobonds
> ui tool show Contacts
> contacts sel restrict both distanceOnly 4.0 resSeparation 2 intraMol false
> select true color #83e76e dashes 8 radius 0.165 reveal true
92 distances
> select clear
> show #1.1 models
> select add #1.1
1419 atoms, 179 residues, 1 model selected
> show sel surfaces
> select clear
> hide #3 models
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> color sel #e6d28eff
[Repeated 1 time(s)]
> color sel #e6da62ff
[Repeated 1 time(s)]
> color sel #e6d25fff
> color sel #e6d061ff
> color sel #e6ac59ff
> color sel #e66d3cff
> color sel #e66739ff
> color sel #e66539ff
> color sel #e65837ff
> color sel #e6452eff
> color sel #e63125ff
> color sel #e62921ff
> color sel #e62820ff
> color sel #e62720ff
> color sel #e62620ff
> color sel #e61829ff
> color sel #e60632ff
> color sel #e60532ff
> color sel #e60a31ff
[Repeated 1 time(s)]
> color sel #e60b32ff
> color sel #e61837ff
> color sel #e63249ff
> color sel #e6384eff
> color sel #e63a4eff
> color sel #e63b4fff
> color sel #e64457ff
> color sel #e65e64ff
> color sel #e66267ff
> color sel #e66368ff
> color sel #e66564ff
> color sel #e66464ff
> color sel #e66364ff
> color sel #e66263ff
> color sel #e65a5bff
> color sel #e6595aff
> color sel #e65859ff
> color sel #e6544fff
> color sel #e64c3fff
> color sel #e6483aff
> color sel #e64638ff
[Repeated 1 time(s)]
> color sel #e64435ff
> color sel #e64234ff
> color sel #e63b2cff
> color sel #e63a2cff
> color sel #e6352cff
> color sel #e6332cff
> color sel #e62e27ff
> color sel #e62922ff
[Repeated 1 time(s)]
> color sel #e62923ff
> color sel #f12b24ff
> color sel #ff2e26ff
> color sel #ff3924ff
[Repeated 1 time(s)]
> select clear
> color #2#1.1,3#!1 #ff5d12ff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> color sel #ffc3daff
[Repeated 1 time(s)]
> color sel #fff1f1ff
[Repeated 1 time(s)]
> select clear
> color #2#1.1,3#!1 #f0e3e2ff
> select clear
[Repeated 1 time(s)]
> select #1/B:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:304-607
2550 atoms, 2612 bonds, 304 residues, 1 model selected
> color (#!1 & sel) black
> select clear
> undo
[Repeated 9 time(s)]
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:167-179
106 atoms, 106 bonds, 13 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select clear
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #e9f0cdff
[Repeated 1 time(s)]
> color sel #f0e1b8ff
[Repeated 1 time(s)]
> color sel #f0d899ff
[Repeated 1 time(s)]
> color sel #f0ee73ff
[Repeated 1 time(s)]
> color sel #f0ec62ff
> color sel #eef04cff
[Repeated 1 time(s)]
> color sel #d0f048ff
[Repeated 1 time(s)]
> color sel #e1f06fff
[Repeated 1 time(s)]
> color sel #eef06aff
[Repeated 1 time(s)]
> color sel #f0e35eff
[Repeated 1 time(s)]
> color sel #e5f061ff
[Repeated 1 time(s)]
> color sel #e9f048ff
[Repeated 1 time(s)]
> color sel #f0ec4dff
[Repeated 1 time(s)]
> select clear
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 165682 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 303 atoms, 701 residues, 265 bonds
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> select clear
> select #1/B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:141-303
1304 atoms, 1336 bonds, 163 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #1/B:304
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:304-607
2550 atoms, 2612 bonds, 304 residues, 1 model selected
> show sel surfaces
> select clear
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> transparency #1-2 100
> select clear
> undo
[Repeated 6 time(s)]
> redo
[Repeated 3 time(s)]
> undo
> hide #!1 models
> show #!1 models
> select #1/B:607
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:455-607
1286 atoms, 1320 bonds, 153 residues, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> show sel surfaces
> select add #1.2
6409 atoms, 1439 bonds, 786 residues, 2 models selected
> select subtract #1.2
1419 atoms, 1439 bonds, 179 residues, 3 models selected
> select add #1.3
2063 atoms, 1439 bonds, 260 residues, 2 models selected
> select subtract #1.3
1419 atoms, 1439 bonds, 179 residues, 3 models selected
> transparency (#!1 & sel) 0
> select clear
> select #1/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A
644 atoms, 654 bonds, 81 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 0
> select clear
[Repeated 1 time(s)]
> select add #1/B:422@CD
1 atom, 1 residue, 1 model selected
> select clear
> select add #1/B:397@OE1
1 atom, 1 residue, 1 model selected
> select add #1/B:393@CE
2 atoms, 2 residues, 2 models selected
> select add #1/B:375@CZ3
3 atoms, 3 residues, 2 models selected
> select add #1/B:426@CD1
4 atoms, 4 residues, 2 models selected
> select clear
> select add #1/B:401@CG2
1 atom, 1 residue, 1 model selected
> select subtract #1/B:401@CG2
1 model selected
> select add #1/B:401@CG2
1 atom, 1 residue, 1 model selected
> select subtract #1/B:401@CG2
1 model selected
> select add #1/B:414@OD1
1 atom, 1 residue, 1 model selected
> select add #1/B:401@CG2
2 atoms, 2 residues, 2 models selected
> select clear
> select #1/B:468
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:420-468
404 atoms, 415 bonds, 49 residues, 1 model selected
> select #1/B:476
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:476-483
61 atoms, 61 bonds, 8 residues, 1 model selected
> select clear
> select add #1/B:422@NH2
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select #1/B:422@NH2
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select add #1/B:422@CD
2 atoms, 1 residue, 2 models selected
> hide sel cartoons
> select add #1/B:375@CH2
3 atoms, 2 residues, 2 models selected
> hide sel cartoons
> select #1/B:318-374
484 atoms, 494 bonds, 57 residues, 1 model selected
> select #1/B:318-426
922 atoms, 939 bonds, 109 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> color sel #f00c9fff
[Repeated 1 time(s)]
> color sel #f01475ff
[Repeated 1 time(s)]
> color sel #f00d34ff
[Repeated 1 time(s)]
> color sel #f01006ff
[Repeated 1 time(s)]
> color sel #f05847ff
[Repeated 1 time(s)]
> color sel #f0908aff
[Repeated 1 time(s)]
> color sel #f0303cff
[Repeated 1 time(s)]
> color sel #f06970ff
[Repeated 1 time(s)]
> color sel #f05659ff
[Repeated 1 time(s)]
> color sel #f03157ff
[Repeated 1 time(s)]
> select clear
> select #1/C:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:1-148
1167 atoms, 1184 bonds, 148 residues, 1 model selected
> lighting shadows true intensity 0.5
> lighting shadows false
> select clear
> select add #1/B:422@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:422@NH2
2 atoms, 1 residue, 2 models selected
> select add #1/B:426@CD1
3 atoms, 2 residues, 2 models selected
> hide sel cartoons
> select clear
> select add #1/B:422@NH2
1 atom, 1 residue, 1 model selected
> select add #1/B:422@NH1
2 atoms, 1 residue, 2 models selected
> hide sel atoms
> select add #1/B:397@O
3 atoms, 2 residues, 2 models selected
> select add #1/B:397@C
4 atoms, 2 residues, 2 models selected
> hide sel cartoons
> select clear
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 870 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 383 of 680238 triangles, 6 residues, 1 bonds
> select clear
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 210 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 276 of 680238 triangles, 4 atoms, 4 residues, 3 bonds
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 586 of 189136 triangles,
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 376 of 680238 triangles, 1 atoms, 3 residues, 1 bonds
Drag select of
PieTBCRab8a_f300c_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C
SES surface, 256 of 189136 triangles, 2 residues
> select clear
> select #1/B:516
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:516-607
769 atoms, 786 bonds, 92 residues, 1 model selected
> hide sel cartoons
> select clear
> save "/Users/tolgabozkurt/Desktop/tbc-complex model.cxs"
——— End of log from Tue Nov 28 01:05:27 2023 ———
opened ChimeraX session
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.000000000000001 interModel false intraMol false
> ignoreHiddenModels true color #070309 dashes 8 reveal true
351 distances
> select #1/B:177-178
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/B:177-319
1179 atoms, 1207 bonds, 143 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> select clear
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select #1/B:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:565-607
331 atoms, 334 bonds, 1 pseudobond, 43 residues, 2 models selected
> hide sel atoms
> select #1/B:545
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:545-597
436 atoms, 443 bonds, 53 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/B:511
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:511-607
819 atoms, 839 bonds, 1 pseudobond, 97 residues, 2 models selected
> hide sel atoms
> select add #1.1
2238 atoms, 839 bonds, 276 residues, 2 models selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> transparency (#!1 & sel) 70
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 20
> transparency (#!1 & sel) 10
> transparency (#!1 & sel) 0
> select clear
> color #1.5 #9d55e5ff models
> color #1.5 #ae5efeff models
> color #1.5 #8dfea6ff models
> color #1.5 #8effa7ff models
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> color sel yellow
> select #1/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A
644 atoms, 654 bonds, 81 residues, 1 model selected
> color (#!1 & sel) #ffe174ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffbe61ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb15eff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffbd5bff
[Repeated 1 time(s)]
> color (#!1 & sel) #ff883dff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffa55bff
> color (#!1 & sel) #ffa65bff
> color (#!1 & sel) #ffb759ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb959ff
> color (#!1 & sel) #ffe18fff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffe08fff
> color (#!1 & sel) #ffdf8fff
> color (#!1 & sel) #ffb14cff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb132ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffa750ff
> color (#!1 & sel) #ffa54fff
> color (#!1 & sel) #ff803fff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb344ff
> select clear
> select #1/C:178-179
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> select #1/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A
644 atoms, 654 bonds, 81 residues, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 interModel false intraMol false
> ignoreHiddenModels true color #070309 dashes 7 radius 0.125 reveal true
351 distances
> undo
[Repeated 3 time(s)]
> close #1.5
> undo
[Repeated 4 time(s)]
> redo
> color #1.2 #d8b4ea00
> color #1.2 #54ea3900
> color #1.2 #5afb3d00
> select add #1.2
5634 atoms, 654 bonds, 688 residues, 2 models selected
> select subtract #1.2
644 atoms, 654 bonds, 81 residues, 3 models selected
> select add #1.2
5634 atoms, 654 bonds, 688 residues, 2 models selected
> hide #1.2 models
> select subtract #1.2
644 atoms, 654 bonds, 81 residues, 3 models selected
> hide #1.3 models
> show #1.3 models
> show #1.2 models
> select add #1.2
5634 atoms, 654 bonds, 688 residues, 2 models selected
> close #1.2
> select add #3
5634 atoms, 654 bonds, 92 pseudobonds, 688 residues, 3 models selected
> show #3 models
> hide #3 models
> select subtract #3
5634 atoms, 654 bonds, 688 residues, 2 models selected
> select clear
> select #1/B:142
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:142-346
1655 atoms, 1695 bonds, 205 residues, 1 model selected
> hide sel atoms
> select #1/B:505-506
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/B:505-607
870 atoms, 891 bonds, 2 pseudobonds, 103 residues, 2 models selected
> hide sel atoms
> ui tool show Contacts
> select #1/C:178-179
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/C
1419 atoms, 1439 bonds, 179 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 interModel false intraMol false color #070309
> dashes 7 radius 0.125 reveal true
351 distances
> color #1.2 #8548c2ff models
> color #1.2 #c2aca3ff models
> color #1.2 #ffe3d6ff models
> color #1.2 #ffdd98ff models
> color #1.2 #a2ff66ff models
> color #1.2 #6eff5dff models
> color #1.2 #40ff6fff models
> select #1/B:557-607
400 atoms, 404 bonds, 1 pseudobond, 51 residues, 2 models selected
> select #1/B:505-607
870 atoms, 891 bonds, 2 pseudobonds, 103 residues, 2 models selected
> hide sel atoms
> select #1/B:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:141-345
1659 atoms, 1699 bonds, 205 residues, 1 model selected
> hide sel atoms
> color #1.2 #e0f7d2ff models
> color #1.2 #e9f7ecff models
> select #1/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:1-140
1136 atoms, 1165 bonds, 140 residues, 1 model selected
> color #1.2 #f7c0eaff models
> color #1.2 #f757e3ff models
> color #1.2 #f742c4ff models
> hide sel cartoons
> show sel cartoons
> color sel hot pink
> color sel light gray
> undo
> select add #1.2
1136 atoms, 1165 bonds, 351 pseudobonds, 140 residues, 2 models selected
> hide #1.2 models
> show #1.2 models
> color #1.2 #e9a6ceff models
> color #1.2 #e9c297ff models
> color #1.2 #e9da7dff models
> color #1.2 #b7e95eff models
> color #1.2 #6be951ff models
> color #1.2 #43e96eff models
> color #1.2 #4ce9abff models
> color #1.2 #53e9deff models
> color #1.2 #40cfe9ff models
> color #1.2 #4ce9ceff models
> color #1.2 #1be969ff models
> color #1.2 #ade978ff models
> save /Users/obozkurt/Desktop/Pie354-TBC-Rab8acomplex.dcd
Models have different number of atoms
> save "/Users/obozkurt/Desktop/Pie354-TBC-RAB8A complex.cxs"
——— End of log from Tue Nov 28 18:05:43 2023 ———
opened ChimeraX session
> open "/Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC folder/TBC-
> ChimeraX/Pie354-TBC-RAB8A complex.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Failed opening file /Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC
folder/TBC-ChimeraX/Pie354-TBC-RAB8A complex.cxs:
'list' object has no attribute 'values'
> open "/Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC folder/TBC-
> ChimeraX/Pie354-TBC-RAB8A complex.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Failed opening file /Users/tolgabozkurt/Library/CloudStorage/Box-Box/TBC
folder/TBC-ChimeraX/Pie354-TBC-RAB8A complex.cxs:
'list' object has no attribute 'values'
OpenGL version: 4.1 ATI-4.6.21
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.7.10 (20G1427)
Kernel Version: Darwin 20.6.0
Time since boot: 10 days 15:45
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
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: 2021.10.8
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
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: 2022.2.22
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: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
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
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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