swapna

[hl.torresvera@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
The swapna command (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/swapna.html) does not seem to be implemented. 

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6TH6 format mmcif fromDatabase pdb

6th6 title:  
Cryo-EM Structure of T. kodakarensis 70S ribosome [more info...]  
  
Chain information for 6th6 #1  
---  
Chain | Description | UniProt  
Aa | 16S ribosomal RNA |  
Ab | 30S ribosomal protein S2 | RS2_THEKO  
Ac | 30S ribosomal protein S3 | RS3_THEKO  
Ad | 30S ribosomal protein S3Ae | RS3A_THEKO  
Ae | 30S ribosomal protein S4 | RS4_THEKO  
Af | 30S ribosomal protein S4e | RS4E_THEKO  
Ag | 30S ribosomal protein S5 | RS5_THEKO  
Ah | 30S ribosomal protein S6e | RS6E_THEKO  
Ai | 30S ribosomal protein S7 | RS7_THEKO  
Aj | 30S ribosomal protein S8 | RS8_THEKO  
Ak | 30S ribosomal protein S8e | RS8E_THEKO  
Al | 30S ribosomal protein S9 | RS9_THEKO  
Am | 30S ribosomal protein S10 | RS10_THEKO  
An | 30S ribosomal protein S11 | RS11_THEKO  
Ao | 30S ribosomal protein S12 | RS12_THEKO  
Ap | 30S ribosomal protein S13 | RS13_THEKO  
Aq | 30S ribosomal protein S15 | RS15_THEKO  
Ar | 30S ribosomal protein S14 type Z | RS14Z_THEKO  
As | 30S ribosomal protein S17 | RS17_THEKO  
At | 30S ribosomal protein S17e | RS17E_THEKO  
Au | 30S ribosomal protein S19 | RS19_THEKO  
Av | 30S ribosomal protein S19e | Q5JGN5_THEKO  
Aw | 30S ribosomal protein S24e | RS24_THEKO  
Ax | 30S ribosomal protein S27e | RS27_THEKO  
Ay | 30S ribosomal protein S28e | RS28_THEKO  
Az | Predicted zinc-ribbon RNA-binding protein involved in translation |
Q5JFE2_THEKO  
BA | 23S ribosomal RNA |  
BB | 5S ribosomal RNA |  
BC | 50S ribosomal protein L2 | RL2_THEKO  
BD | 50S ribosomal protein L3 | RL3_THEKO  
BE | 50S ribosomal protein L4 | RL4_THEKO  
BF | 50S ribosomal protein L5 | RL5_THEKO  
BG | 50S ribosomal protein L6 | RL6_THEKO  
BH BI | 50S ribosomal protein L7Ae | RL7A_THEKO  
BJ | 50S ribosomal protein L10e | RL10E_THEKO  
BK | 50S ribosomal protein L13 | RL13_THEKO  
BL | 50S ribosomal protein L14 | RL14_THEKO  
BM BN | 50S ribosomal protein L14e | RL14E_THEKO  
BO | 50S ribosomal protein L15 | RL15_THEKO  
BP | 50S ribosomal protein L15e | RL15E_THEKO  
BQ | 50S ribosomal protein L18 | RL18_THEKO  
BR | 50S ribosomal protein L18e | RL18E_THEKO  
BS | 50S ribosomal protein L19e | Q5JJG6_THEKO  
BT | 50S ribosomal protein L18Ae | RL18A_THEKO  
BU | 50S ribosomal protein L21e | RL21_THEKO  
BV | 50S ribosomal protein L22 | RL22_THEKO  
BW | 50S ribosomal protein L23 | RL23_THEKO  
BX | 50S ribosomal protein L24 | RL24_THEKO  
BY | 50S ribosomal protein L24e | RL24E_THEKO  
BZ | 50S ribosomal protein L29 | RL29_THEKO  
Ba | 50S ribosomal protein L30 | RL30_THEKO  
Bb | 50S ribosomal protein L30e | RL30E_THEKO  
Bc | 50S ribosomal protein L31e | RL31_THEKO  
Bd | 50S ribosomal protein L32e | RL32_THEKO  
Be | 50S ribosomal protein L34e | RL34_THEKO  
Bg | 50S ribosomal protein L37Ae | RL37A_THEKO  
Bh | 50S ribosomal protein L37e | RL37_THEKO  
Bi | 50S ribosomal protein L39e | RL39_THEKO  
Bj | 50S ribosomal protein L40e | RL40_THEKO  
Bk | LSU ribosomal protein L41E | Q5JEV0_THEKO  
Bl | 50S ribosomal protein L44e | Q5JE51_THEKO  
  
Non-standard residues in 6th6 #1  
---  
ZN — zinc ion  
  

> hide protein

> open 7k00

7k00 title:  
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]  
  
Chain information for 7k00 #2  
---  
Chain | Description | UniProt  
0 | 50S ribosomal protein L33 | D7Z9P0_ECOLX  
1 | 50S ribosomal protein L34 | RL34_ECO45  
2 | 50S ribosomal protein L35 | D7Z814_ECOLX  
3 | 50S ribosomal protein L36 | A0A0E2L017_ECOU3  
4 | 50S ribosomal protein L31 | D7ZFP6_ECOLX  
5 | E-site tRNA |  
A | 16S rRNA |  
B | 30S ribosomal protein S2 | D7ZK99_ECOLX  
C | 30S ribosomal protein S3 | RS3_ECO45  
D | 30S ribosomal protein S4 | D7Z9H7_ECOLX  
E | 30S ribosomal protein S5 | D7Z9H2_ECOLX  
F | 30S ribosomal protein S6 | RS6_ECOLI  
G | 30S ribosomal protein S7 | A0A5Q2GFB5_ECOLX  
H | 30S ribosomal protein S8 | D7Z9G9_ECOLX  
I | 30S ribosomal protein S9 | D7ZES9_ECOLX  
J | 30S ribosomal protein S10 | D7Z9F4_ECOLX  
K | 30S ribosomal protein S11 | S1ELC2_ECOLX  
L | 30S ribosomal protein S12 | I2UHF1_ECOLX  
M | 30S ribosomal protein S13 | H4UQ02_ECOLX  
N | 30S ribosomal protein S14 | D7Z9G8_ECOLX  
O | 30S ribosomal protein S15 | D7ZEL4_ECOLX  
P | 30S ribosomal protein S16 | RS16_ECO45  
Q | 30S ribosomal protein S17 | D7Z9G4_ECOLX  
R | 30S ribosomal protein S18 | A0A0E2KXL3_ECOU3  
S | 30S ribosomal protein S19 | D7Z9F9_ECOLX  
T | 30S ribosomal protein S20 | D7ZAS2_ECOLX  
U | 30S ribosomal protein S21 | A0A0E2L2J1_ECOU3  
X | mRNA |  
Y | A-site tRNA-val |  
Z | P-site tRNA-fMet |  
a | 23S rRNA |  
b | 5S rRNA |  
c | 50S ribosomal protein L2 | RL2_ECOLI  
d | 50S ribosomal protein L3 | I2X6U5_ECOLX  
e | 50S ribosomal protein L4 | D7Z9F6_ECOLX  
f | 50S ribosomal protein L5 | D7Z9G7_ECOLX  
g | 50S ribosomal protein L6 | D7Z9H0_ECOLX  
h | 50S ribosomal protein L9 | D7ZI15_ECOLX  
i | 50S ribosomal protein L13 | D7ZET0_ECOLX  
j | 50S ribosomal protein L14 | D7Z9G5_ECOLX  
k | 50S ribosomal protein L15 | A0A037Y8L6_ECOLX  
l | 50S ribosomal protein L16 | L4V2J8_ECOLX  
m | 50S ribosomal protein L17 | D6I1Y5_ECOLX  
n | 50S ribosomal protein L18 | D7Z9H1_ECOLX  
o | 50S ribosomal protein L19 | D7ZKU3_ECOLX  
p | 50S ribosomal protein L20 | RL20_ECO45  
q | 50S ribosomal protein L21 | D7ZEN7_ECOLX  
r | 50S ribosomal protein L22 | D7Z9G0_ECOLX  
s | 50S ribosomal protein L23 | D7X2Z9_ECOLX  
t | 50S ribosomal protein L24 | D7Z9G6_ECOLX  
u | 50S ribosomal protein L25 | D7XH79_ECOLX  
v | 50S ribosomal protein L27 | RL27_ECOLI  
w | 50S ribosomal protein L28 | S0YB49_ECOLX  
x | 50S ribosomal protein L29 | D7Z9G3_ECOLX  
y | 50S ribosomal protein L30 | D7Z9H3_ECOLX  
z | 50S ribosomal protein L32 | D7ZGG2_ECOLX  
  
Non-standard residues in 7k00 #2  
---  
MG — magnesium ion  
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol  
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
ZN — zinc ion  
  

> hide protein

> mmaker #1 to #2 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 7k00, chain a (#2) with 6th6, chain BA (#1), sequence alignment
score = 5512.8  
RMSD between 914 pruned atom pairs is 1.404 angstroms; (across all 2610 pairs:
11.535)  
  

> zone #1/Aa:648

> show #1/Aa & sidechain

> view #1/Aa:648

> zone #1/Aa:648

> style stick

Changed 310846 atom styles  

> style stick

Changed 310846 atom styles  

> hide #!1 models

> hide #!2 atoms

[Repeated 1 time(s)]

> zone #1/Aa:648

> show #1/Aa & sidechain

> show #!2 cartoons

> style #!2 stick

Changed 149338 atom styles  

> show #1/Aa & sidechain

> hide #!2 models

> show #!1 models

> select #1/Aa:648

20 atoms, 21 bonds, 1 residue, 1 model selected  

> swapaa #1/Aa:648 G

No amino acid residues specified for swapping  

> swapna #1/Aa:648 G

Unknown command: swapna #1/Aa:648 G  

> swapna

Unknown command: swapna  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,2
      Model Number: Z15Z000RELL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 7 days, 3 hours, 2 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
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    ChimeraX-ModelPanel: 1.3.6
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    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
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    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
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    Jinja2: 3.1.2
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    msgpack: 1.0.4
    nest-asyncio: 1.5.6
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    networkx: 2.8.5
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    sphinxcontrib-devhelp: 1.0.2
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    tifffile: 2022.7.31
    tinyarray: 1.2.4
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    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[pett]

Hi Hector,

The swapna command was only implemented fairly recently, so you need to get the ChimeraX daily build to use it -- it's not in the 1.5 release.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab