Opened 4 years ago
Closed 4 years ago
#6587 closed defect (not a bug)
PDB format
| 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: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Hello, When I save my model as a PDB file, colouring of the model is not preserved. If I reopen the newly created PDB in ChimeraX all the colour changes are lost. Am I saving incorrectly?
Many thanks for any advice, Cristina
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs
> format session
Log from Mon Apr 11 22:00:23 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
> format session
Log from Mon Feb 7 14:45:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
Log from Mon Feb 7 14:28:24 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/IRaligned_fn1.cxs
> To Restore session:
>
> * update Atomic bundle to version 1.31 or newer (have 1.13.2)
>
Unable to restore session: need to update bundle
> open
> /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_6SOFcolor.pdb.pdb
> /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_7pg0.pdb.pdb
> /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_dIR_01_real_space_refined_008.pdb.pdb
2_6SOFcolor.pdb.pdb title:
Human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for 2_6SOFcolor.pdb.pdb #1
---
Chain | Description
A C | IR
B D | IR
E G I K | insulin
F H J L | insulin
2_7pg0.pdb.pdb title:
Low resolution cryo-em structure of full-length insulin receptor bound to 3
insulin with visible DDM micelle, conf 1 [more info...]
Chain information for 2_7pg0.pdb.pdb #2
---
Chain | Description
A B | IR
C E I | insulin
D F J | insulin
Chain information for 2_dIR_01_real_space_refined_008.pdb.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
——— End of log from Mon Feb 7 14:28:24 2022 ———
opened ChimeraX session
> show atoms
> hide atoms
> show cartoons
> ui tool show Matchmaker
> ui tool show "Model Panel"
> select #3/A800-920
Nothing selected
> select #3/A:800-920
928 atoms, 946 bonds, 121 residues, 1 model selected
> matchmaker #!2 to #1 & sel
No 'to' model specified
> matchmaker #!2 to #3/A & sel 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 2_dIR_01_real_space_refined_008.pdb.pdb, chain A (#3) with
2_7pg0.pdb.pdb, chain A (#2), sequence alignment score = 157.6
RMSD between 63 pruned atom pairs is 0.946 angstroms; (across all 107 pairs:
7.304)
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> show #3 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
> matchmaker #1 to #3/A & sel 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 2_dIR_01_real_space_refined_008.pdb.pdb, chain A (#3) with
2_6SOFcolor.pdb.pdb, chain C (#1), sequence alignment score = 136
RMSD between 64 pruned atom pairs is 0.899 angstroms; (across all 106 pairs:
6.486)
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!2 models
> hide #3 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
——— End of log from Mon Feb 7 14:45:13 2022 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #3 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> show #1 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #3 models
> show #!2 models
> hide #!2 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs
> includeMaps true
> select up
1098 atoms, 1120 bonds, 143 residues, 1 model selected
> select down
928 atoms, 946 bonds, 121 residues, 1 model selected
> select up
1098 atoms, 1120 bonds, 143 residues, 1 model selected
> select up
6841 atoms, 6994 bonds, 863 residues, 1 model selected
> select #1/C:429-600
2713 atoms, 2754 bonds, 172 residues, 1 model selected
> select down
3811 atoms, 3874 bonds, 315 residues, 2 models selected
> select up
3845 atoms, 3910 bonds, 317 residues, 2 models selected
> select down
3811 atoms, 3874 bonds, 315 residues, 2 models selected
> select #1/C:429-600
2713 atoms, 2754 bonds, 172 residues, 1 model selected
> select #3/A:920-1200
1338 atoms, 1367 bonds, 161 residues, 1 model selected
> select #1/C:429-600
2713 atoms, 2754 bonds, 172 residues, 1 model selected
> select up
2747 atoms, 2790 bonds, 174 residues, 1 model selected
> select up
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select up
59218 atoms, 60367 bonds, 5607 residues, 3 models selected
> select up
59218 atoms, 60367 bonds, 5607 residues, 3 models selected
> select down
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select down
2747 atoms, 2790 bonds, 174 residues, 1 model selected
> select down
2713 atoms, 2754 bonds, 172 residues, 1 model selected
> select #1/D:600-810
859 atoms, 868 bonds, 55 residues, 1 model selected
> select #1/D:600-810
859 atoms, 868 bonds, 55 residues, 1 model selected
> select #2/A:700-900
1137 atoms, 1163 bonds, 1 pseudobond, 142 residues, 2 models selected
> show #!2 models
> select #2/A:700-900
1137 atoms, 1163 bonds, 1 pseudobond, 142 residues, 2 models selected
> ui tool show Matchmaker
> select #3/A800-920
Nothing selected
> select #3/A:800-920
928 atoms, 946 bonds, 121 residues, 1 model selected
> select up
1098 atoms, 1120 bonds, 143 residues, 1 model selected
> select up
6841 atoms, 6994 bonds, 863 residues, 1 model selected
> hide #3 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> show #1 models
> hide #3 models
> select #2/A:800-920
872 atoms, 895 bonds, 108 residues, 1 model selected
> select #1/A:800-920
Nothing selected
> select #1/D:600-810
859 atoms, 868 bonds, 55 residues, 1 model selected
> select up
893 atoms, 902 bonds, 58 residues, 1 model selected
> select up
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> select #1/A
11127 atoms, 11290 bonds, 719 residues, 1 model selected
> select #1/B
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> select #1/C
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select #1/D
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> show #3 models
> hide #3 models
> ui tool show "Color Actions"
> color sel slate blue
> select #1/C
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> color sel slate blue
> select #1/A
11127 atoms, 11290 bonds, 719 residues, 1 model selected
> color sel light salmon
> color sel salmon
> color sel dark salmon
> color sel salmon
> select #1/B
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> color sel salmon
> show #!2 models
> show #3 models
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #!2 models
> show #1 models
> hide #!2 models
> show #!2 models
> show #3 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs
> includeMaps true
> hide #!2 models
> hide #1 models
No model chosen to save relative to
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb
> relModel #3
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb
Summary of feedback from opening
/Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 ASP A 689
PHE A 714 1 26
Start residue of secondary structure not found: HELIX 11 11 ASN C 16 GLU C 24
1 9
Start residue of secondary structure not found: HELIX 12 12 ARG C 42 LEU C 49
1 8
Start residue of secondary structure not found: HELIX 13 13 ASN C 148 GLU C
153 1 6
Start residue of secondary structure not found: HELIX 14 14 PRO C 193 LYS C
197 1 5
157 messages similar to the above omitted
NAME_.pdb title:
Human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for NAME_.pdb
---
Chain | Description
4.1/A 4.1/C | IR
4.2/A | IR
4.3/A | IR
4.1/B 4.1/D | IR
4.2/B | IR
4.3/B | IR
4.2/C | IR
4.3/C | IR
4.2/D | IR
4.3/D | IR
4.1/E 4.2/E 4.1/G 4.1/I 4.2/I 4.1/K | insulin
4.3/E | insulin
4.1/F 4.1/H 4.1/J 4.1/L | insulin
4.2/F 4.2/J | insulin
4.3/F | insulin
4.3/G | insulin
4.3/H | insulin
4.3/I | insulin
4.3/J | insulin
> hide #4.1 models
> show #4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #4.3 models
> show #4.3 models
> close #4
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/[NAME]_.pdb
> relModel #3
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_6SOFcolor.pdb.pdb_.pdb
2_6SOFcolor.pdb.pdb_.pdb title:
Human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for 2_6SOFcolor.pdb.pdb_.pdb #4
---
Chain | Description
A C | IR
B D | IR
E G I K | insulin
F H J L | insulin
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_7pg0.pdb.pdb_.pdb
2_7pg0.pdb.pdb_.pdb title:
Low resolution cryo-em structure of full-length insulin receptor bound to 3
insulin with visible DDM micelle, conf 1 [more info...]
Chain information for 2_7pg0.pdb.pdb_.pdb #5
---
Chain | Description
A B | IR
C E I | insulin
D F J | insulin
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_dIR_01_real_space_refined_008.pdb.pdb_.pdb
Chain information for 2_dIR_01_real_space_refined_008.pdb.pdb_.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> hide #4 models
> show #4 models
> hide #3 models
> hide #4 models
> hide #!5 models
> hide #6 models
> show #3 models
> hide #3 models
> show #4 models
> show #!5 models
> show #6 models
> hide #6 models
> hide #!5 models
> hide #4 models
> show #1 models
> show #4 models
> show #!5 models
> show #6 models
> hide #1 models
> close #4,6#5
> show #3 models
> show #1 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs
> includeMaps true
——— End of log from Mon Apr 11 22:00:23 2022 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 15 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
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
matplotlib-inline: 0.1.2
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
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 → PDB format |
comment:2 by , 4 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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Hi Cristina,
--Eric