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Opened 4 years ago
Last modified 4 years ago
#4753 assigned defect
Tolman cone angle not implemented for tridentate or more ligands
| 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: Linux-5.11.0-20-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)set lgand to current selectio
calculate cone angle for sellected center
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 https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open 2bbv
Summary of feedback from opening 2bbv fetched from pdb
---
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description
A B C | protein (black beetle virus capsid protein)
D E F | protein (black beetle virus capsid protein)
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> lighting full
> style /b stick
Changed 2382 atom styles
> ribbon /c
> surface #1
> style solvent sphere
Changed 208 atom styles
> style ~solvent stick
Changed 7609 atom styles
> sym #1 assembly 3 newModel false
> view
> set bgColor white
> set silhouettes true
> save /home/pi/Desktop/2bbv.png
Directory "/home/pi/Desktop" does not exist
> measure buriedarea /a withAtoms2 /b
Buried area between /a and /b = 14796
area /a = 65737, area /b = 74944, area both = 1.1109e+05
> measure sasa #1 & ~solvent
Solvent accessible area for #1 & ~solvent = 34093
> interfaces #1 & protein
6 buried areas: C A 1675, C B 1671, A B 1663, C F 739, A D 714, B E 699
> close
> set bgColor black
> set silhouettes false
> open 1080 fromDatabase emdb
Summary of feedback from opening 1080 fetched from emdb
---
note | Fetching compressed map 1080 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> lighting full
> volume #1 level 0.9
> set bgColor gray
> set silhouettes true
> open 1grl
Summary of feedback from opening 1grl fetched from pdb
---
note | Fetching compressed mmCIF 1grl from
http://files.rcsb.org/download/1grl.cif
1grl title:
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]
Chain information for 1grl #2
---
Chain | Description
A B C D E F G | groel (HSP60 class)
1grl mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> lighting default
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> volume subtract #1 #3 minRms true
Opened volume difference as #4, grid size 100,100,100, pixel 2.7, shown at
step 1, values float32
Minimum RMS scale factor for "1grl map 10 #3" above level 0.061077 is 1.4121
> volume #4 color pink transparency 0
> hide atoms
> show ribbons
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> close
> set bgColor black
> set silhouettes false
> open 1a0m fromDatabase eds
Summary of feedback from opening 1a0m fetched from eds
---
note | Fetching map 1a0m from
http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4
Opened eds 1a0m as #1, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at
level 2.28, step 1, values float32
> open 1a0m
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description
A B | α-conotoxin [TYR15]-epi
Non-standard residues in 1a0m #2
---
NH2 — amino group
> hide ribbons
> show
> volume #1 level 1.0 style mesh
> volume zone #1 nearAtoms #2 range 2
> volume #1 level 0.5 transparency 0.6
> close
> open 1273 fromDatabase emdb
Summary of feedback from opening 1273 fetched from emdb
---
note | Fetching compressed map 1273 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8
> volume #1 region all showOutlineBox true
> close session
> help help:seqcrow/tutorials.html
> ui tool show "Managed Models"
> ui tool show "Job Queue"
paused SEQCROW queue
> show"Structure Modification
Unknown command: ui tool show"Structure Modification
> ui tool show "Structure Modification"
> lighting soft
> close session
> open
> https://raw.githubusercontent.com/QChASM/AaronTools.py/master/test/test_files/catalysts/tm_multi-
> lig.xyz
Summary of feedback from opening
//raw.githubusercontent.com/QChASM/AaronTools.py/master/test/test_files/catalysts/tm_multi-
lig.xyz fetched from https
---
notes | Fetching compressed tm_multi-lig.xyz from
https://raw.githubusercontent.com/QChASM/AaronTools.py/master/test/test_files/catalysts/tm_multi-
lig.xyz
Downloaded tm_multi-lig.xyz to /home/pi/Downloads/tm_multi-lig.xyz
Opened tm_multi-lig.xyz as an XYZ file
> ui tool show "Cone Angle"
> ui mousemode right "select fragment"
> select P
2 atoms, 1 residue, 1 model selected
> select connected"
Expected an objects specifier or a keyword
> select P
2 atoms, 1 residue, 1 model selected
> select connected
78 atoms, 85 bonds, 1 residue, 1 model selected
Traceback (most recent call last):
File "/home/pi/.local/share/ChimeraX/1.2/site-
packages/SEQCROW/tools/cone_angle.py", line 290, in calc_cone
cone_angle = comp.cone_angle(
File "/home/pi/.local/share/ChimeraX/1.2/site-
packages/AaronTools/component.py", line 439, in cone_angle
raise NotImplementedError(
NotImplementedError: Tolman cone angle not implemented for tridentate or more
ligands
NotImplementedError: Tolman cone angle not implemented for tridentate or more
ligands
File "/home/pi/.local/share/ChimeraX/1.2/site-
packages/AaronTools/component.py", line 439, in cone_angle
raise NotImplementedError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 460.80
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450M S2H
OS: Ubuntu 21.04 hirsute
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 2.3Gi 2.6Gi 101Mi 10Gi 12Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 710] [10de:128b] (rev a1)
Subsystem: Micro-Star International Co., Ltd. [MSI] GK208B [GeForce GT 710] [1462:8c93]
Kernel driver in use: nvidia
Locale: ('fr_FR', '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
biopython: 1.78
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-Clipper: 0.16.0
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-Cytoscape: 0.1
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
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 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-StrudelScore: 0.1.4
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
distro: 1.5.0
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
MolecularDynamicsViewer: 1.1
mrcfile: 1.3.0
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
pandas: 1.2.4
ParmEd: 3.2.0
parso: 0.7.1
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
recordtype: 1.3
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.5.0
SEQCROW: 1.0.2
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
threed-strudel: 0.9.3
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: 1.2.0
Change History (3)
comment:1 by , 4 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Tolman cone angle not implemented for tridentate or more ligands |
follow-up: 2 comment:2 by , 4 years ago
It looks like you're working through the SEQCROW tutorial for cone angles, so this case has been tested and should work. The process should be:
1. select the diphosphine ligand and nothing else - the suggested command is `select P; select connected` (you can click this command in the tutorial to run it)
2. press the "set ligand to current selection" button on the tool interface
3. select the Ru atom and nothing else - I would CTRL+click on it, but you could also use the `select Ru` command
4. press the "calculate cone angle for ligand on selected center" button
Hope this helps
I'll look at catching NotImplementedErrors and turning them into chimerax.core.errors.LimitationErrors.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, June 9, 2021 12:02 PM
Cc: aishen@free.fr <aishen@free.fr>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #4753: Tolman cone angle not implemented for tridentate or more ligands (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#4753: Tolman cone angle not implemented for tridentate or more ligands
----------------------------------+---------------------------
Reporter: aishen@… | 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 Eric Pettersen):
* status: new => assigned
* component: Unassigned => Third Party
* project: => ChimeraX
* platform: => all
* owner: (none) => Tony Schaefer
Comment:
Might want to raise chimerax.core.errors.LimitationError if you don't want
bug reports in these situations.
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4753#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:3 by , 4 years ago
Conversely, of course, if you do want bug reports in these situations, leave them be! :-)
Note:
See TracTickets
for help on using tickets.
Might want to raise chimerax.core.errors.LimitationError if you don't want bug reports in these situations.