Opened 3 years ago

Closed 3 years ago

#8464 closed defect (duplicate)

ISOLDE: Unparameterised residue detected

Reported by: emcrae@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-58-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF 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 "/home/ewan/ELK_data/QT for modelling/model.pdb"

Summary of feedback from opening /home/ewan/ELK_data/QT for
modelling/model.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK - File Generated by RNA_build.pl - written by Cody Geary  
  
Ignored bad PDB record found on line 2  
REMARK - Building a total of 360 nts.  
  
Ignored bad PDB record found on line 3  
REMARK Add GNRA 31-37  
  
Ignored bad PDB record found on line 4  
REMARK Add Crossover 45,22,46,158  
  
Ignored bad PDB record found on line 5  
REMARK Add Kturn-A 62-68  
  
18 messages similar to the above omitted  
  
Chain information for model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for model.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Done loading forcefield  

> open "/home/ewan/ELK_data/QT for
> modelling/cryosparc_P799_J638_map_sharp.mrc"

Opened cryosparc_P799_J638_map_sharp.mrc as #2, grid size 256,256,256, pixel
1.29, shown at level 0.000115, step 1, values float32  

> volume #2 level 0.1096

> close #1

> close #2

> open "/home/ewan/ELK_data/QT for modelling/model.pdb" format pdb

Summary of feedback from opening /home/ewan/ELK_data/QT for
modelling/model.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK - File Generated by RNA_build.pl - written by Cody Geary  
  
Ignored bad PDB record found on line 2  
REMARK - Building a total of 360 nts.  
  
Ignored bad PDB record found on line 3  
REMARK Add GNRA 31-37  
  
Ignored bad PDB record found on line 4  
REMARK Add Crossover 45,22,46,158  
  
Ignored bad PDB record found on line 5  
REMARK Add Kturn-A 62-68  
  
17 messages similar to the above omitted  
  
Chain information for model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for model.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> open "/home/ewan/ELK_data/QT for
> modelling/cryosparc_P799_J635_003_volume_map_sharp.mrc"

Opened cryosparc_P799_J635_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.29, shown at level 0.0157, step 1, values float32  

> volume #2 level 0.1528

> close #2

> open "/home/ewan/ELK_data/QT for
> modelling/cryosparc_P799_J638_map_sharp.mrc"

Opened cryosparc_P799_J638_map_sharp.mrc as #2, grid size 256,256,256, pixel
1.29, shown at level 0.000115, step 1, values float32  

> volume #2 level 0.01038

> surface dust #2 size 12.9

> volume #2 level 0.02748

> volume #2 level 0.02064

> hide #!2 models

Opened cryosparc_P799_J638_map_sharp.mrc as #1.1.1.1, grid size 256,256,256,
pixel 1.29, shown at step 1, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> nucleotides sel fill

> style nucleic & sel stick

Changed 7671 atom styles  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to model.pdb #1.2  
---  
warning | Not adding hydrogens to /A G 1 P because it is missing heavy-atom
bond partners  
notes | Termini for model.pdb (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A G 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A A 360  
Chain-final residues that are not actual C termini:  
564 hydrogen bonds  
3875 hydrogens added  
  
Traceback (most recent call last):  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2760, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 594, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1347, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2760, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 594, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1347, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/ewan/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 510.47.03
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       4.4Gi       109Gi       115Mi        11Gi       120Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:87af]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
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: 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
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    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
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    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
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    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
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    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
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    ChimeraX-CoreFormats: 1.0
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    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-ISOLDE: 1.2.2
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    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
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    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
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    ChimeraX-RNALayout: 1.0
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
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    ChimeraX-Segger: 1.0
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    ChimeraX-SpaceNavigator: 1.0
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    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
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    ChimeraX-uniprot: 2.1
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    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
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    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
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    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
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    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
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    tifffile: 2020.9.3
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    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: Unparameterised residue detected

Reported by Ewan McRae

comment:2 by Tristan Croll, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Updating to ISOLDE 1.5 (by first updating to ChimeraX 1.5) should take care of this.

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