id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4753 Tolman cone angle not implemented for tridentate or more ligands aishen@… Tony Schaefer "{{{ 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: 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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 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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 }}} " defect assigned normal Third Party all ChimeraX