Opened 3 years ago
Closed 3 years ago
#7730 closed defect (fixed)
Buried Volume: KeyError: 'Ni'
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| 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: Windows-10-10.0.19041
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
Successfully installed 'SEQCROW==1.5.4'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Collecting SEQCROW==1.5.4
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/seqcrow/releases/1.5.4/SEQCROW-1.5.4-py3-none-
any.whl (3.1 MB)
Requirement already satisfied: scipy in c:\program files\chimerax
1.2.5\bin\lib\site-packages (from SEQCROW==1.5.4) (1.5.2)
Requirement already satisfied: Send2Trash in
c:\users\chand\appdata\local\ucsf\chimerax\1.2\site-packages (from
SEQCROW==1.5.4) (1.8.0)
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.2.5\bin\lib\site-packages (from SEQCROW==1.5.4) (2.11.2)
Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program
files\chimerax 1.2.5\bin\lib\site-packages (from SEQCROW==1.5.4) (1.2.5)
Requirement already satisfied: psutil in c:\program files\chimerax
1.2.5\bin\lib\site-packages (from SEQCROW==1.5.4) (5.7.2)
Requirement already satisfied: MarkupSafe>=0.23 in c:\program files\chimerax
1.2.5\bin\lib\site-packages (from jinja2->SEQCROW==1.5.4) (2.0.1)
Requirement already satisfied: numpy>=1.14.5 in c:\program files\chimerax
1.2.5\bin\lib\site-packages (from scipy->SEQCROW==1.5.4) (1.19.2)
Installing collected packages: SEQCROW
Attempting uninstall: SEQCROW
Found existing installation: SEQCROW 1.5.3
Uninstalling SEQCROW-1.5.3:
Successfully uninstalled SEQCROW-1.5.3
Successfully installed SEQCROW-1.5.4
WARNING: You are using pip version 21.0.1; however, version 22.2.2 is
available.
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.2.5\bin\ChimeraX.exe -m pip install --upgrade pip' command.
> open Files\\\ChimeraX
'Files\\\ChimeraX' has no suffix
> open 1.2.5\\\bin\\\ChimeraX.exe
Unrecognized file suffix '.exe'
> open F:/Post_Doc_Vetticatt/Jarvo_BSSE_Analysis/Figures_XYZ/TS_OA_F17.xyz
Opened TS_OA_F17.xyz as an XYZ file
> select ::name="UNK"
74 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select up
74 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select down
4 pseudobonds, 1 model selected
> select down
4 pseudobonds, 1 model selected
> select up
74 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select down
4 pseudobonds, 1 model selected
> select clear
> select /a:1@Ni1
1 atom, 1 residue, 1 model selected
> select /a:1@C14
1 atom, 1 residue, 1 model selected
> select /a:1@P2
1 atom, 1 residue, 1 model selected
> select /a:1@P2
1 atom, 1 residue, 1 model selected
> select /a:1@C12
1 atom, 1 residue, 1 model selected
> select /a:1@C12
1 atom, 1 residue, 1 model selected
> select /a:1@P2
1 atom, 1 residue, 1 model selected
> select up
74 atoms, 70 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
74 atoms, 70 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select @C20, C19, H23, H24, H25, H22, H21
7 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select /a:1@Ni1
1 atom, 1 residue, 1 model selected
> select sel @< 1
1 atom, 1 residue, 1 model selected
> select sel @< 2
2 atoms, 1 pseudobond, 1 residue, 2 models selected
> select sel @< 2
5 atoms, 3 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select clear
Drag select of 15 atoms, 14 bonds
Drag select of 3 atoms, 4 bonds
Drag select of 15 atoms, 1 pseudobonds, 16 bonds
Drag select of 22 atoms, 2 pseudobonds, 20 bonds
Drag select of 29 atoms, 2 pseudobonds, 24 bonds
> select /a:1@H23
1 atom, 1 residue, 1 model selected
Drag select of 23 atoms, 2 pseudobonds, 21 bonds
> ui tool show "Buried Volume"
Traceback (most recent call last):
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\tools\percent_Vbur.py", line 582, in calc_vbur
info = percent_vbur_cmd(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\commands\percent_Vbur.py", line 307, in percent_vbur
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
KeyError: 'Ni'
KeyError: 'Ni'
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
See log for complete Python traceback.
> select /a:1@Ni1
1 atom, 1 residue, 1 model selected
> select /a:1@Ni1
1 atom, 1 residue, 1 model selected
Drag select of 23 atoms, 2 pseudobonds, 22 bonds
Traceback (most recent call last):
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\tools\percent_Vbur.py", line 582, in calc_vbur
info = percent_vbur_cmd(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\commands\percent_Vbur.py", line 307, in percent_vbur
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
KeyError: 'Ni'
KeyError: 'Ni'
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
See log for complete Python traceback.
> select clear
Drag select of 43 atoms, 43 bonds
Drag select of 47 atoms, 2 pseudobonds, 46 bonds
> select ~sel
27 atoms, 24 bonds, 2 pseudobonds, 1 residue, 2 models selected
Traceback (most recent call last):
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\tools\percent_Vbur.py", line 582, in calc_vbur
info = percent_vbur_cmd(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\commands\percent_Vbur.py", line 307, in percent_vbur
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
KeyError: 'Ni'
KeyError: 'Ni'
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\tools\percent_Vbur.py", line 582, in calc_vbur
info = percent_vbur_cmd(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\SEQCROW\commands\percent_Vbur.py", line 307, in percent_vbur
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
KeyError: 'Ni'
KeyError: 'Ni'
File "C:\Users\chand\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\AaronTools\geometry.py", line 2848, in steric_map
and dist_ip[i] - radii_dict[atom.element] < radius
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 388.16
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Predator G3-571
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 17,057,812,480
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: en-US
Locale: ('en_US', '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: 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
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
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
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
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.8.0
SEQCROW: 1.5.4
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
WMI: 1.5.1
Change History (4)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Buried Volume: KeyError: 'Ni' |
follow-up: 2 comment:2 by , 3 years ago
follow-up: 3 comment:3 by , 3 years ago
steric maps should be working in 1.5.5
________________________________
From: Anthony James Schaefer <tony.schaefer@uga.edu>
Sent: Wednesday, October 5, 2022 1:37 PM
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7730: Buried Volume: KeyError: 'Ni' (was: ChimeraX bug report submission)
This person reached out to me as well (he graduated from the Wheeler group a couple years ago). We figured out that he was using the Bondi radii, which aren't defined for Ni. I can probably add a clear error message for that. Switching to the UMN radii worked. He may have also accidentally selected the Ni when defining the ligand. We did find another potential bug with steric maps in SEQCROW that I'll try to fix this week.
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, October 5, 2022 1:17 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7730: Buried Volume: KeyError: 'Ni' (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7730: Buried Volume: KeyError: 'Ni'
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------------+---------------------------
Changes (by pett):
* status: new => assigned
* component: Unassigned => Third Party
* project: => ChimeraX
* platform: => all
* owner: (none) => Tony Schaefer
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7730#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
This person reached out to me as well (he graduated from the Wheeler group a couple years ago). We figured out that he was using the Bondi radii, which aren't defined for Ni. I can probably add a clear error message for that. Switching to the UMN radii worked. He may have also accidentally selected the Ni when defining the ligand. We did find another potential bug with steric maps in SEQCROW that I'll try to fix this week. Tony ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Wednesday, October 5, 2022 1:17 PM Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu> Subject: Re: [ChimeraX] #7730: Buried Volume: KeyError: 'Ni' (was: ChimeraX bug report submission) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] #7730: Buried Volume: KeyError: 'Ni' --------------------------------------------+--------------------------- Reporter: chimerax-bug-report@… | Owner: Tony Schaefer Type: defect | Status: assigned Priority: normal | Milestone: Component: Third Party | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------------+--------------------------- Changes (by pett): * status: new => assigned * component: Unassigned => Third Party * project: => ChimeraX * platform: => all * owner: (none) => Tony Schaefer -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7730#comment:1> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker