Opened 4 years ago

Last modified 4 years ago

#5464 accepted defect

better template residue support

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
Description
Residue.is_missing_heavy_template_atoms() throws a RuntimeError if ChimeraX doesn't already have its template loaded. Would probably be better if it tries to fetch the template from the components dictionary first, and raise a more friendly UserError if it still fails.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3rvg structureFactors true

Summary of feedback from opening 3rvg fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
phase_calc, fom  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 3rvg from
http://files.rcsb.org/download/3rvg.cif  
Fetching CCD 17P from http://ligand-expo.rcsb.org/reports/1/17P/17P.cif  
Fetching CCD PTR from http://ligand-expo.rcsb.org/reports/P/PTR/PTR.cif  
Fetching compressed 3rvg structure factors from
http://files.rcsb.org/download/3rvg-sf.cif  
Resolution: 2.498  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 48,36,32, pixel 0.83,0.83,0.765,
shown at level 0.389, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 48,36,32, pixel 0.83,0.83,0.765,
shown at level -0.138,0.138, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_1 as #1.1.1.4, grid size 48,36,32, pixel
0.83,0.83,0.765, shown at level 0.538, step 1, values float32  
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 48,36,32, pixel
0.83,0.83,0.765, shown at level -0.798,0.798, step 1, values float32  
3rvg title:  
Crystals structure of Jak2 with a 1-amino-5H-pyrido[4,3-b]indol-4-carboxamide
inhibitor [more info...]  
  
Chain information for 3rvg  
---  
Chain | Description | UniProt  
1.2/A | Tyrosine-protein kinase JAK2 | JAK2_HUMAN  
  
Non-standard residues in 3rvg #1.2  
---  
17P —
1-(cyclohexylamino)-7-(1-methyl-1H-pyrazol-4-yl)-5H-pyrido[4,3-b]indole-4-carboxamide  
  

> addh

Summary of feedback from adding hydrogens to 3rvg #1.2  
---  
warnings | Not adding hydrogens to /A ASN 859 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 1069 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLN 1070 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLN 1072 CB because it is missing heavy-atom bond
partners  
notes | Termini for 3rvg (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 841, /A SER 1016  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 1010, /A GLY 1132  
283 hydrogen bonds  
Adding 'H' to /A SER 1016  
/A GLY 1132 is not terminus, removing H atom from 'C'  
2379 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\cmd\cmd.py", line 29, in isolde_start  
get_singleton(session)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\cmd\cmd.py", line 20, in get_singleton  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=create)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 317, in __init__  
self._start_gui(gui)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 482, in _start_gui  
self._update_model_list(None, None, force=True)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1042, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2517, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\atomic\util.py", line 17, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CA','CB','CG','CD1')):  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\atomic\util.py", line 57, in flip_if_necessary  
if residue.is_missing_heavy_template_atoms():  
File "atomic_cpp\cymol.pyx", line 1631, in
chimerax.atomic.cymol.CyResidue.is_missing_heavy_template_atoms  
RuntimeError: No residue template found for PTR  
  
RuntimeError: No residue template found for PTR  
  
File "atomic_cpp\cymol.pyx", line 1631, in
chimerax.atomic.cymol.CyResidue.is_missing_heavy_template_atoms  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110222254
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.2
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.4
    ChimeraX-ModelPanel: 1.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.0
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Hmm... still throws the error even if I preload the template for PTR using `mmcif.find_template_residue()`.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 25 October 2021 15:27
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #5464: ChimeraX bug report submission

#5464: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19041
 ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
 Description
 Residue.is_missing_heavy_template_atoms() throws a RuntimeError if
 ChimeraX doesn't already have its template loaded. Would probably be
 better if it tries to fetch the template from the components dictionary
 first, and raise a more friendly UserError if it still fails.

 Log:
 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color {arguments} bychain; color {arguments} byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open 3rvg structureFactors true

 Summary of feedback from opening 3rvg fetched from pdb
 ---
 warning | WARNING: multiple experimental reflection datasets found:
 F_meas_au, F_meas_sigma_au,
 phase_calc, fom
 Automatically choosing "F_meas_au, F_meas_sigma_au".
 notes | Fetching compressed mmCIF 3rvg from
 http://files.rcsb.org/download/3rvg.cif
 Fetching CCD 17P from http://ligand-expo.rcsb.org/reports/1/17P/17P.cif
 Fetching CCD PTR from http://ligand-expo.rcsb.org/reports/P/PTR/PTR.cif
 Fetching compressed 3rvg structure factors from
 http://files.rcsb.org/download/3rvg-sf.cif
 Resolution: 2.498

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 48,36,32, pixel
 0.83,0.83,0.765,
 shown at level 0.389, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 48,36,32, pixel
 0.83,0.83,0.765,
 shown at level -0.138,0.138, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_1 as #1.1.1.4, grid size 48,36,32, pixel
 0.83,0.83,0.765, shown at level 0.538, step 1, values float32
 Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 48,36,32, pixel
 0.83,0.83,0.765, shown at level -0.798,0.798, step 1, values float32
 3rvg title:
 Crystals structure of Jak2 with a 1-amino-5H-
 pyrido[4,3-b]indol-4-carboxamide
 inhibitor [more info...]

 Chain information for 3rvg
 ---
 Chain | Description | UniProt
 1.2/A | Tyrosine-protein kinase JAK2 | JAK2_HUMAN

 Non-standard residues in 3rvg #1.2
 ---
 17P —
 1-(cyclohexylamino)-7-(1-methyl-1H-pyrazol-4-yl)-5H-
 pyrido[4,3-b]indole-4-carboxamide


 > addh

 Summary of feedback from adding hydrogens to 3rvg #1.2
 ---
 warnings | Not adding hydrogens to /A ASN 859 CB because it is missing
 heavy-
 atom bond partners
 Not adding hydrogens to /A LYS 1069 CB because it is missing heavy-atom
 bond
 partners
 Not adding hydrogens to /A GLN 1070 CA because it is missing heavy-atom
 bond
 partners
 Not adding hydrogens to /A GLN 1072 CB because it is missing heavy-atom
 bond
 partners
 notes | Termini for 3rvg (#1.2) chain A determined from SEQRES records
 Chain-initial residues that are actual N termini:
 Chain-initial residues that are not actual N termini: /A PRO 841, /A SER
 1016
 Chain-final residues that are actual C termini:
 Chain-final residues that are not actual C termini: /A VAL 1010, /A GLY
 1132
 283 hydrogen bonds
 Adding 'H' to /A SER 1016
 /A GLY 1132 is not terminus, removing H atom from 'C'
 2379 hydrogens added


 > isolde start

 > set selectionWidth 4

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 Traceback (most recent call last):
 File "C:\Program Files\ChimeraX\bin\lib\site-
 packages\chimerax\cmd_line\tool.py", line 297, in execute
 cmd.run(cmd_text)
 File "C:\Program Files\ChimeraX\bin\lib\site-
 packages\chimerax\core\commands\cli.py", line 2856, in run
 result = ci.function(session, **kw_args)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\cmd\cmd.py", line 29, in isolde_start
 get_singleton(session)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\cmd\cmd.py", line 20, in get_singleton
 return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE',
 create=create)
 File "C:\Program Files\ChimeraX\bin\lib\site-
 packages\chimerax\core\tools.py",
 line 193, in get_singleton
 tinst = tool_class(session, tool_name, **kw)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\tool.py", line 186, in __init__
 self.isolde = isolde.Isolde(self)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\isolde.py", line 317, in __init__
 self._start_gui(gui)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\isolde.py", line 482, in _start_gui
 self._update_model_list(None, None, force=True)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\isolde.py", line 1042, in _update_model_list
 self._change_selected_model(model=current_model)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\isolde.py", line 2517, in _change_selected_model
 correct_pseudosymmetric_sidechain_atoms(session, m.residues)
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\atomic\util.py", line 17, in
 correct_pseudosymmetric_sidechain_atoms
 if flip_if_necessary(r, ('CA','CB','CG','CD1')):
 File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
 packages\chimerax\isolde\atomic\util.py", line 57, in flip_if_necessary
 if residue.is_missing_heavy_template_atoms():
 File "atomic_cpp\cymol.pyx", line 1631, in
 chimerax.atomic.cymol.CyResidue.is_missing_heavy_template_atoms
 RuntimeError: No residue template found for PTR

 RuntimeError: No residue template found for PTR

 File "atomic_cpp\cymol.pyx", line 1631, in
 chimerax.atomic.cymol.CyResidue.is_missing_heavy_template_atoms

 See log for complete Python traceback.





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 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
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 Manufacturer: Notebook
 Model: P7xxTM1
 OS: Microsoft Windows 10 Education (Build 19041)
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 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5464>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

Cc: Greg Couch added
Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → better template residue support

Asking about a residue with a missing template throws the Cython standard RuntimeError and perhaps it should throw UserError instead. I could change that. Using mmcif.find_residue_template() doesn't seem to make the template known to atomic's builtin template library. Should it?

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