The following bug report has been submitted:
Platform: macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I am trying to mutate a residue to ALANINE. But using this version of ChimeraX does not allow me to do so and come back with error "No rotamers for ALA in Richardson.common rotamer library".
Is it possible to fix this?
Thanks
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/sudattlam/Downloads/fold_2025_01_13_10_55/fold_2025_01_13_10_55_model_0.cif
> format mmcif
Chain information for fold_2025_01_13_10_55_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> hbonds reveal true
598 hydrogen bonds found
> ~hbonds
> ui tool show Contacts
> contacts ignoreHiddenModels true
3366 contacts
Drag select of 6 atoms, 9 residues, 6 bonds, 8 pseudobonds
Alignment identifier is 1/A
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 64 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
/A ASP 361: phi -83.0, psi -33.9 trans
Changed 90 bond radii
> swapaa #!1/A:361 ASP criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Applying ASP rotamer (chi angles: -67.9 -19.5) to
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361
> swapaa interactive sel ASP rotLib Dunbrack
/A ASP 361: phi -83.0, psi -33.9 trans
Changed 90 bond radii
> swapaa #!1/A:361 ASP criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Applying ASP rotamer (chi angles: -67.9 -19.5) to
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
/A ASP 361: phi -83.0, psi -33.9 trans
Changed 600 bond radii
> swapaa interactive sel ARG rotLib Dunbrack
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Changed 600 bond radii
> swapaa #!1/A:361 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Applying ARG rotamer (chi angles: -69.1 178.4 -179.9 174.7) to
fold_2025_01_13_10_55_model_0.cif #!1/A ARG 361
> swapaa interactive sel ARG rotLib Dunbrack
fold_2025_01_13_10_55_model_0.cif #!1/A ARG 361: phi -83.0, psi -33.9 trans
Changed 600 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!1/A:361 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
fold_2025_01_13_10_55_model_0.cif #!1/A ARG 361: phi -83.0, psi -33.9 trans
Applying ARG rotamer (chi angles: -69.1 178.4 -179.9 174.7) to
fold_2025_01_13_10_55_model_0.cif #!1/A ARG 361
> ~hbonds
> hbonds sel reveal true
5 hydrogen bonds found
> close session
> open
> /Users/sudattlam/Downloads/fold_2025_01_13_10_55/fold_2025_01_13_10_55_model_0.cif
> format mmcif
Chain information for fold_2025_01_13_10_55_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
Alignment identifier is 1/A
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
/A ASP 361: phi -83.0, psi -33.9 trans
Changed 600 bond radii
> swapaa #!1/A:361 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Applying ARG rotamer (chi angles: -69.1 178.4 -179.9 174.7) to
fold_2025_01_13_10_55_model_0.cif #!1/A ARG 361
> swapaa interactive sel ARG rotLib Dunbrack
/A ARG 361: phi -83.0, psi -33.9 trans
Changed 600 bond radii
> hbonds #!1 & ~#!1/A:361 & ~solvent reveal true restrict #1.1 & ~@c,ca,n
40 hydrogen bonds found
No rotamers selected
> ~hbonds
[Repeated 1 time(s)]
> hbonds sel reveal true
5 hydrogen bonds found
> select #!1/A
4932 atoms, 5050 bonds, 1 pseudobond, 606 residues, 2 models selected
> ~hbonds
> hbonds sel reveal true
717 hydrogen bonds found
> select #!1/A:361
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #!1/A:361
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel GLY rotLib Dunbrack
No rotamers for GLY in Dunbrack rotamer library
> hide sel target a
> ui tool show Rotamers
> swapaa interactive sel GLY rotLib Dunbrack
No rotamers for GLY in Dunbrack rotamer library
> ui tool show Rotamers
> swapaa interactive sel GLY rotLib Richardson.common
No rotamers for GLY in Richardson.common rotamer library
> close session
> open
> /Users/sudattlam/Downloads/fold_2025_01_13_10_55/fold_2025_01_13_10_55_model_0.cif
> format mmcif
Chain information for fold_2025_01_13_10_55_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
Alignment identifier is 1/A
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ILE rotLib Richardson.common
/A ASP 361: phi -83.0, psi -33.9 trans
Changed 35 bond radii
> swapaa #!1/A:361 ILE criteria 1 rotLib Richardson.common
Using Richardson.common library
fold_2025_01_13_10_55_model_0.cif #!1/A ASP 361: phi -83.0, psi -33.9 trans
Applying ILE rotamer (chi angles: -65.0 170.0) to
fold_2025_01_13_10_55_model_0.cif #!1/A ILE 361
> swapaa interactive sel ILE rotLib Richardson.common
/A ILE 361: phi -83.0, psi -33.9 trans
Changed 35 bond radii
> swapaa #!1/A:361 ILE criteria 1 rotLib Richardson.common retain false
Using Richardson.common library
fold_2025_01_13_10_55_model_0.cif #!1/A ILE 361: phi -83.0, psi -33.9 trans
Applying ILE rotamer (chi angles: -65.0 170.0) to
fold_2025_01_13_10_55_model_0.cif #!1/A ILE 361
> hbonds sel reveal true
1 hydrogen bonds found
> select /A
4929 atoms, 5047 bonds, 1 pseudobond, 606 residues, 2 models selected
> ~hbonds
> hbonds sel reveal true
598 hydrogen bonds found
> ~hbonds
> ui tool show Contacts
> contacts ignoreHiddenModels true
3372 contacts
> select /A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:361
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Richardson.common
No rotamers for ALA in Richardson.common rotamer library
> ui tool show Rotamers
> swapaa interactive sel VAL rotLib Richardson.common
/A ILE 361: phi -83.0, psi -33.9 trans
Changed 12 bond radii
> swapaa #!1/A:361 VAL criteria 1 rotLib Richardson.common
Using Richardson.common library
fold_2025_01_13_10_55_model_0.cif #!1/A ILE 361: phi -83.0, psi -33.9 trans
Applying VAL rotamer (chi angles: 175.0) to fold_2025_01_13_10_55_model_0.cif
#!1/A VAL 361
> swapaa interactive sel VAL rotLib Richardson.common
/A VAL 361: phi -83.0, psi -33.9 trans
Changed 12 bond radii
> swapaa #!1/A:361 VAL criteria 1 rotLib Richardson.common retain false
Using Richardson.common library
fold_2025_01_13_10_55_model_0.cif #!1/A VAL 361: phi -83.0, psi -33.9 trans
Applying VAL rotamer (chi angles: 175.0) to fold_2025_01_13_10_55_model_0.cif
#!1/A VAL 361
> ui tool show Contacts
> contacts ignoreHiddenModels true
3367 contacts
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Richardson.common
No rotamers for ALA in Richardson.common rotamer library
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3ZP/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 1 day, 18 hours, 33 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Su Datt,
--Eric