PDB format

[cristina.viola@…]

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

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> show #3 models

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> 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

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> 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

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> 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

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> 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

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> hide #6 models

> show #3 models

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> show #6 models

> hide #6 models

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> 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

[Eric Pettersen]

Hi Cristina,

The PDB format only contains information about the structure that was obtained by experiment, e.g. coordinates, secondary structure elements, crystallographic symmetry, etc. It does not contain depiction information like color, ball/stick vs. cartoon, etc. To preserve that information you would need to save a ChimeraX session file (.cxs extension) rather than a PDB file.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab