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Opened 3 years ago
Last modified 3 years ago
#6776 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-5.4.0-107-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo
Current working directory is:
/mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo
> open *coot*.pdb
No such file/path: *coot*.pdb
> select #1:550-584, 630-665, 817-839
Nothing selected
> select ~sel
Nothing selected
> delete sel
> save
> /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo/TMD-
> pore/apo-TMD-porealt.pdb
No structures to save
> close
> cd /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo
Current working directory is:
/mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo
> open *coot*.pdb
Chain information for FINAL_apo-
fromcls5-input_real_space_refined_022-coot-0.pdb #1
---
Chain | Description
A B C D | No description available
> select #1:550-584, 630-665, 817-839
2776 atoms, 2840 bonds, 4 pseudobonds, 360 residues, 2 models selected
> select ~sel
21352 atoms, 21838 bonds, 4 pseudobonds, 2655 residues, 2 models selected
> delete sel
> save
> /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo/TMD-
> pore/apo-TMD-porealt.pdb
> close
[Repeated 2 time(s)]
> tool show "Side View"
> open 3w7f
Summary of feedback from opening 3w7f fetched from pdb
---
notes | Fetching compressed mmCIF 3w7f from
http://files.rcsb.org/download/3w7f.cif
Fetching CCD FPS from http://ligand-expo.rcsb.org/reports/F/FPS/FPS.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
3w7f title:
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]
Chain information for 3w7f #1
---
Chain | Description | UniProt
A B | Dehydrosqualene synthase | CRTM_STAAU
Non-standard residues in 3w7f #1
---
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)
MG — magnesium ion
3w7f mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete /b
> view ligand
> label ligand
> label height 1.0
> lighting soft
> delete solvent
> label @@display
> view #1:21
> select /A:21@OG
1 atom, 1 residue, 1 model selected
> select add /A:302@O1B
2 atoms, 2 residues, 1 model selected
> distance /A:21@OG /A:302@O1B
Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å
> distance :21@OG :302@O1B
Distance already exists; modify distance properties with 'distance style'
> distance :248@OH :302@O1B
Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å
> hbonds
312 hydrogen bonds found
> hbonds hide
Expected a keyword
> hide hbonds
> select :FPS
48 atoms, 46 bonds, 2 residues, 1 model selected
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3w7f
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A
/A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A
/A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A
/A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A
/A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A
/A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A
/A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A
/A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A
/A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A
/A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A
/A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A
/A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A
/A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A
13 hydrogen bonds found
> ~hbonds
> ~distance
> contacts sel restrict cross reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
86 contacts
atom1 atom2 overlap distance
/A FPS 301 C10 /A CYS 44 CB 0.472 3.288
/A FPS 302 O2A /A SER 19 CB 0.387 2.913
/A FPS 301 PB /A ARG 45 NH1 0.248 3.492
/A FPS 302 O2A /A SER 19 CA 0.242 3.058
/A FPS 302 O1B /A SER 21 CB 0.215 3.085
/A FPS 302 C14 /A ALA 157 CB 0.208 3.552
/A FPS 301 C7 /A CYS 44 CB 0.207 3.433
/A FPS 302 C14 /A ALA 157 CA 0.191 3.569
/A FPS 301 C6 /A ASP 48 CB 0.166 3.474
/A FPS 301 C15 /A TYR 41 CD2 0.158 3.482
/A FPS 301 O2A /A MG 303 MG 0.156 1.834
/A FPS 302 PB /A ARG 171 NH1 0.139 3.601
/A FPS 301 PA /A ASN 168 ND2 0.116 3.624
/A FPS 301 C14 /A LEU 141 CD1 0.106 3.654
/A FPS 302 O1A /A MG 304 MG 0.098 1.892
/A FPS 301 C8 /A CYS 44 CB 0.097 3.393
/A FPS 301 O2A /A ASN 168 OD1 0.097 2.743
/A FPS 301 O2A /A ASP 172 OD2 0.088 2.752
/A FPS 302 O1B /A SER 21 OG 0.075 2.405
/A FPS 301 O3B /A ARG 45 NH1 0.075 2.585
/A FPS 302 PB /A SER 21 OG 0.073 3.487
/A FPS 302 O3B /A MG 304 MG 0.039 1.951
/A FPS 301 C15 /A TYR 41 CE2 0.036 3.604
/A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307
/A FPS 302 PA /A ARG 45 NH2 -0.011 3.751
/A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535
/A FPS 302 PB /A SER 21 CB -0.023 4.003
/A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685
/A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558
/A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688
/A FPS 301 O2B /A MG 304 MG -0.054 2.044
/A FPS 301 C2 /A ASP 48 CG -0.073 3.713
/A FPS 302 C10 /A GLY 161 CA -0.084 3.844
/A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611
/A FPS 302 C5 /A ALA 134 CB -0.095 3.855
/A FPS 301 O1A /A MG 304 MG -0.097 2.087
/A FPS 301 O3B /A MG 305 MG -0.103 2.093
/A FPS 302 C5 /A LEU 164 CB -0.104 3.864
/A FPS 302 O2A /A TYR 41 OH -0.105 2.585
/A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945
/A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476
/A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866
/A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627
/A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750
/A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669
/A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794
/A FPS 301 C5 /A ASP 48 CG -0.159 3.919
/A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681
/A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802
/A FPS 302 C1 /A TYR 248 OH -0.174 3.394
/A FPS 301 C9 /A ARG 45 CA -0.175 3.935
/A FPS 302 C4 /A ASN 168 CB -0.185 3.945
/A FPS 302 PB /A ARG 265 NH2 -0.191 3.931
/A FPS 302 C14 /A PHE 233 CZ -0.192 3.832
/A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713
/A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965
/A FPS 302 C4 /A GLN 165 CA -0.212 3.972
/A FPS 301 C15 /A MET 15 CE -0.215 3.975
/A FPS 302 PA /A SER 19 CB -0.217 4.197
/A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407
/A FPS 302 C11 /A GLY 161 CA -0.230 3.870
/A FPS 302 C10 /A GLY 138 CA -0.231 3.991
/A FPS 302 PA /A SER 19 CA -0.232 4.212
/A FPS 302 C12 /A GLY 138 CA -0.237 3.877
/A FPS 302 PA /A SER 19 OG -0.239 3.799
/A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889
/A FPS 301 C5 /A ASP 48 CB -0.250 4.010
/A FPS 301 PA /A ASN 168 OD1 -0.251 3.771
/A FPS 302 PA /A TYR 41 OH -0.259 3.819
/A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754
/A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039
/A FPS 301 C6 /A ASP 48 CG -0.284 3.924
/A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936
/A FPS 301 C9 /A ARG 45 CZ -0.312 3.802
/A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077
/A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507
/A FPS 302 C7 /A ALA 134 CB -0.333 3.973
/A FPS 302 PB /A TYR 248 OH -0.356 3.916
/A FPS 302 C10 /A GLY 138 N -0.356 3.876
/A FPS 301 O2A /A ASN 168 CG -0.361 3.391
/A FPS 302 C7 /A GLY 161 CA -0.379 4.019
/A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022
/A FPS 302 O2A /A HIS 18 O -0.390 3.230
/A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150
/A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052
/A FPS 302 C6 /A ALA 134 CB -0.396 4.036
86 contacts
> ui tool show "Cone Angle"
> select clear
> select FPS
Expected an objects specifier or a keyword
> select FPS
Expected an objects specifier or a keyword
> select :FPS
48 atoms, 46 bonds, 2 residues, 1 model selected
WARNING AaronTools.atoms.Atom._set_saturation
Saturation not found for element: Mg
Traceback (most recent call last):
File "/home/user/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/tools/cone_angle.py", line 307, in calc_cone
cone_angle = comp.cone_angle(
File "/home/user/.local/share/ChimeraX/1.3/site-
packages/AaronTools/component.py", line 494, 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/user/.local/share/ChimeraX/1.3/site-
packages/AaronTools/component.py", line 494, in cone_angle
raise NotImplementedError(
See log for complete Python traceback.
> select clear
> select /A:FPS
48 atoms, 46 bonds, 2 residues, 1 model selected
> select /A:301
24 atoms, 23 bonds, 1 residue, 1 model selected
WARNING AaronTools.atoms.Atom._set_saturation
Saturation not found for element: Mg
Traceback (most recent call last):
File "/home/user/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/tools/cone_angle.py", line 307, in calc_cone
cone_angle = comp.cone_angle(
File "/home/user/.local/share/ChimeraX/1.3/site-
packages/AaronTools/component.py", line 494, 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/user/.local/share/ChimeraX/1.3/site-
packages/AaronTools/component.py", line 494, in cone_angle
raise NotImplementedError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA T600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Linux Mint 20.3 una
Architecture: 64bit ELF
Virutal Machine: none
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 24Gi 5.2Gi 449Mi 1.3Gi 5.6Gi
Swap: 8.0Gi 8.0Gi 47Mi
Graphics:
65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GL [T600] [10de:1fb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:1488]
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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
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: 1.31
ChimeraX-AtomicLibrary: 4.2
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: 2.6.1
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: 2.2.2
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: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
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
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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: 2.0.4
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: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
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: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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: 2.4.6
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: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
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: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
Send2Trash: 1.8.0
SEQCROW: 1.3.2
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
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: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (3)
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 → Tolman cone angle not implemented for tridentate or more ligands |
follow-up: 2 comment:2 by , 3 years ago
It looks like you're trying to calculate the cone angle of the FPS ligands that are coordinating the Mg ions. You would have to do this one ligand at a time by:
1. selecting one of the FPS ligands
2. clicking the 'set ligand to current selection' button on the tool
3. selecting an Mg atom
4. clicking 'calculate cone angle for ligand on selected center'.
I've tried this out for the /A:301 FPS ligand, and I got a strangely small result of 150 degrees. It seems to either ignore the bridge or the aliphatic chain. I'll take a closer look at that; it might be a bug. I'd suggest trying the 'exact' cone angle if you want to stick with cone angles. That gave me a larger 180 degrees for the same Mg, and it also works for ligands of any denticity.
For a ligand this long, I think buried volume might be a better metric at gauging how accessible those Mg atoms are. The long aliphatic tail, which is far from the coordination site, might be inflating the size of the ligand. Buried volume only looks within a few angstroms of the center. The procedure for calculating %Vbur is roughly the same, but it doesn't matter of something is coordinating or not. With the "Buried Volume" tool open, you could
1. select everything except solvent and Mg (sel ~:HOH & ~Mg), or just the FPS ligands if you prefer
2. click 'set ligand to current selection'
3. make sure 'use centroid of centers' is unchecked
4. select Mg atoms (sel Mg)
5. click 'calculate % buried volume for selected centers'
I get around 50-70% buried volume around each of the Mg atoms when I do this. You could play around with the settings, but the defaults should be pretty much standard. You can also create a visualization of either the buried or free volume around an Mg by going over to the "volume cutout" tab of the tool and choosing one of those to display.
Best,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, May 5, 2022 5:50 PM
Cc: nxb318@case.edu <nxb318@case.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #6776: Tolman cone angle not implemented for tridentate or more ligands (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#6776: Tolman cone angle not implemented for tridentate or more ligands
----------------------------------+---------------------------
Reporter: nxb318@… | 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
Comment:
Reported by Nebojsa Bogdanovic
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6776#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 3 comment:3 by , 3 years ago
I've looked into it, and the 150 degree cone angle is consistent with the Tolman method. Or maybe it's more accurate to say that diphosphate ligands are not handled sensibly, as Tolman was only considering mono- and diphosphine ligands. In the Tolman algorithm, you look at the angle of each substituent/fragment coming off of the chelating atom. For this diphosphate ligand, oxygen atoms are coordinating the metal. The only other thing bonded to these O atoms are the phosphorus atoms. Because the phosphorus atoms are part of the path connecting the coordinating oxygens, Tolman's method says to use the L-M-L angle. Thus, the Tolman cone angle is 150 degrees - double the L-M-L angle.
Basically, I don't see any bugs in the calculation of Tolman cone angles or the tool. Please try using the method outlined in my last comment, with only one Mg atom selected when clicking the "calculate cone angle for ligand on selected center" button. There is also a tutorial for this tool. On the ChimeraX menu, go to Help -> SEQCROW Tutorials -> Calculating Ligand Cone Angles.
Best,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, May 5, 2022 7:12 PM
To: nxb318@case.edu <nxb318@case.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #6776: Tolman cone angle not implemented for tridentate or more ligands
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#6776: Tolman cone angle not implemented for tridentate or more ligands
----------------------------------+---------------------------
Reporter: nxb318@… | 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 |
----------------------------------+---------------------------
Comment (by Tony Schaefer):
{{{
It looks like you're trying to calculate the cone angle of the FPS ligands
that are coordinating the Mg ions. You would have to do this one ligand at
a time by:
1. selecting one of the FPS ligands
2. clicking the 'set ligand to current selection' button on the tool
3. selecting an Mg atom
4. clicking 'calculate cone angle for ligand on selected center'.
I've tried this out for the /A:301 FPS ligand, and I got a strangely small
result of 150 degrees. It seems to either ignore the bridge or the
aliphatic chain. I'll take a closer look at that; it might be a bug. I'd
suggest trying the 'exact' cone angle if you want to stick with cone
angles. That gave me a larger 180 degrees for the same Mg, and it also
works for ligands of any denticity.
For a ligand this long, I think buried volume might be a better metric at
gauging how accessible those Mg atoms are. The long aliphatic tail, which
is far from the coordination site, might be inflating the size of the
ligand. Buried volume only looks within a few angstroms of the center. The
procedure for calculating %Vbur is roughly the same, but it doesn't matter
of something is coordinating or not. With the "Buried Volume" tool open,
you could
1. select everything except solvent and Mg (sel ~:HOH & ~Mg), or just
the FPS ligands if you prefer
2. click 'set ligand to current selection'
3. make sure 'use centroid of centers' is unchecked
4. select Mg atoms (sel Mg)
5. click 'calculate % buried volume for selected centers'
I get around 50-70% buried volume around each of the Mg atoms when I do
this. You could play around with the settings, but the defaults should be
pretty much standard. You can also create a visualization of either the
buried or free volume around an Mg by going over to the "volume cutout"
tab of the tool and choosing one of those to display.
Best,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, May 5, 2022 5:50 PM
Cc: nxb318@case.edu <nxb318@case.edu>; Anthony James Schaefer
<tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #6776: Tolman cone angle not implemented for
tridentate or more ligands (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#6776: Tolman cone angle not implemented for tridentate or more ligands
----------------------------------+---------------------------
Reporter: nxb318@… | 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
Comment:
Reported by Nebojsa Bogdanovic
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6776#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6776#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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Reported by Nebojsa Bogdanovic