id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7481 QMainWindowLayout::tabPosition called with out-of-bounds value '0' disha-gajanan.hiregange@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.14 ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2 (2021-04-27) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7ls2 Summary of feedback from opening 7ls2 fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""GDP"" near line 263968 notes | Fetching compressed mmCIF 7ls2 from http://files.rcsb.org/download/7ls2.cif Fetching CCD B8Q from http://ligand-expo.rcsb.org/reports/B/B8Q/B8Q.cif Fetching CCD I4U from http://ligand-expo.rcsb.org/reports/I/I4U/I4U.cif Fetching CCD E7G from http://ligand-expo.rcsb.org/reports/E/E7G/E7G.cif Fetching CCD B9H from http://ligand-expo.rcsb.org/reports/B/B9H/B9H.cif Fetching CCD B8W from http://ligand-expo.rcsb.org/reports/B/B8W/B8W.cif Fetching CCD E6G from http://ligand-expo.rcsb.org/reports/E/E6G/E6G.cif Fetching CCD MHG from http://ligand-expo.rcsb.org/reports/M/MHG/MHG.cif Fetching CCD B8T from http://ligand-expo.rcsb.org/reports/B/B8T/B8T.cif Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif Fetching CCD DDE from http://ligand-expo.rcsb.org/reports/D/DDE/DDE.cif 7ls2 title: 80S ribosome from mouse bound to eEF2 (Class I) [more info...] Chain information for 7ls2 #1 --- Chain | Description A | Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein A1 | 60S ribosomal protein L7 A2 | 28S rRNA A3 | 40S ribosomal protein S18 B1 | 60S ribosomal protein L7a B2 | 5S rRNA B3 | 40S ribosomal protein S19 C1 | 60S ribosomal protein L9 C2 | 5.8S rRNA C3 | 40S ribosomal protein S20 D1 | 60S ribosomal protein L10-like D2 | 60S ribosomal protein L8 D3 | 40S ribosomal protein S21 E1 | 60S ribosomal protein L11 E2 | 60S ribosomal protein L3 E3 | 40S ribosomal protein S23 F1 | 60S ribosomal protein L13 F2 | 60S ribosomal protein L4 F3 | 40S ribosomal protein S26 G1 | 60S ribosomal protein L14 G2 | 60S ribosomal protein L5 G3 | 40S ribosomal protein S28 H1 | 60S ribosomal protein L15 H2 | 60S ribosomal protein L6 H3 | 40S ribosomal protein S29 I2 | 60S ribosomal protein L13a I3 | Receptor of activated protein C kinase 1 J2 | 60S ribosomal protein L17 J3 | 40S ribosomal protein S2 K2 | 60S ribosomal protein L18 K3 | 40S ribosomal protein S6 L1 | 60S ribosomal protein L10a L2 | 60S ribosomal protein L19 L3 | 40S ribosomal protein S9 M2 | 60S ribosomal protein L18a M3 | 40S ribosomal protein S12 N2 | 60S ribosomal protein L21 N3 | 40S ribosomal protein S13 O2 | 60S ribosomal protein L22 O3 | 40S ribosomal protein S14 P2 | 60S ribosomal protein L23 P3 | 40S ribosomal protein S15a Q2 | 60S ribosomal protein L24 Q3 | 40S ribosomal protein S24 R2 | 60S ribosomal protein L23a R3 | 40S ribosomal protein S25 S2 | 60S ribosomal protein L26 S3 | 40S ribosomal protein S27-like T2 | 60S ribosomal protein L27 T3 | 40S ribosomal protein S30 U2 | 60S ribosomal protein L27a U3 | Ubiquitin-40S ribosomal protein S27a V2 | 60S ribosomal protein L29 W2 | 60S ribosomal protein L30 X2 | 60S ribosomal protein L31 Y2 | 60S ribosomal protein L32 Z2 | 60S ribosomal protein L35a a2 | 60S ribosomal protein L34 b2 | 60S ribosomal protein L35 c2 | 60S ribosomal protein L36 d2 | 60S ribosomal protein L37 e2 | 60S ribosomal protein L38 f2 | 60S ribosomal protein L39 g2 | Ubiquitin-60S ribosomal protein L40 h2 | 60S ribosomal protein L41 i2 | 60S ribosomal protein L36a j | 60S acidic ribosomal protein P0 j2 | 60S ribosomal protein L37a k | 60S ribosomal protein L12 k2 | 60S ribosomal protein L28 m | Elongation factor 2 m2 | 18S rRNA n2 | tRNA o2 | 40S ribosomal protein SA p2 | 40S ribosomal protein S3a q2 | 40S ribosomal protein S3 r2 | 40S ribosomal protein S4, X isoform s2 | 40S ribosomal protein S5 t | 40S ribosomal protein S7 u | 40S ribosomal protein S8 v2 | 40S ribosomal protein S10 w2 | 40S ribosomal protein S11 x2 | 40S ribosomal protein S15 y2 | 40S ribosomal protein S16 z2 | 40S ribosomal protein S17 Non-standard residues in 7ls2 #1 --- B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid MG — magnesium ion ZN — zinc ion > set bgColor white > open 7cpu Summary of feedback from opening 7cpu fetched from pdb --- note | Fetching compressed mmCIF 7cpu from http://files.rcsb.org/download/7cpu.cif 7cpu title: Cryo-EM structure of 80S ribosome from mouse kidney [more info...] Chain information for 7cpu #2 --- Chain | Description L5 | Mus musculus 28S ribosomal RNA L7 | Mus musculus 5S ribosomal RNA L8 | Mus musculus 5.8S ribosomal RNA LA | 60S ribosomal protein L8 LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4 LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6 LF | 60S ribosomal protein L7 LG | 60S ribosomal protein L7a LH | 60S ribosomal protein L9 LI | 60S ribosomal protein L10 LJ | 60S ribosomal protein L11 LL | 60S ribosomal protein L13 LM | 60S ribosomal protein L14 LN | 60S ribosomal protein L15 LO | 60S ribosomal protein L13a LP | 60S ribosomal protein L17 LQ | 60S ribosomal protein L18 LR | 60S ribosomal protein L19 LS | 60S ribosomal protein L18a LT | 60S ribosomal protein L21 LU | 60S ribosomal protein L22 LV | 60S ribosomal protein L23 LW | 60S ribosomal protein L24 LX | 60S ribosomal protein L23a LY | 60S ribosomal protein L26 LZ | 60S ribosomal protein L27 La | 60S ribosomal protein L27a Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31 Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L35a Lg | 60S ribosomal protein L34 Lh | 60S ribosomal protein L35 Li | 60S ribosomal protein L36 Lj | 60S ribosomal protein L37 Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41 Lo | 60S ribosomal protein L36a Lp | 60S ribosomal protein L37a Lr | 60S ribosomal protein L28 S2 | Mus musculus 18S ribosomal RNA S6 | Met-tRNA SA | 40S ribosomal protein SA SB | 40S ribosomal protein S3a SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4, X isoform SF | 40S ribosomal protein S5 SG | 40S ribosomal protein S6 SH | 40S ribosomal protein S7 SI | 40S ribosomal protein S8 SJ | 40S ribosomal protein S9 SK | 40S ribosomal protein S10 SL | 40S ribosomal protein S11 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14 SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16 SR | 40S ribosomal protein S17 SS | 40S ribosomal protein S18 ST | 40S ribosomal protein S19 SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21 SW | 40S ribosomal protein S15a SX | 40S ribosomal protein S23 SY | 40S ribosomal protein S24 SZ | 40S ribosomal protein S25 Sa | 40S ribosomal protein S26 Sb | 40S ribosomal protein S27 Sc | 40S ribosomal protein S28 Sd | 40S ribosomal protein S29 Se | 40S ribosomal protein S30 Sg | Receptor of activated protein C kinase 1 Non-standard residues in 7cpu #2 --- MG — magnesium ion ZN — zinc ion > open 7cpv Summary of feedback from opening 7cpv fetched from pdb --- note | Fetching compressed mmCIF 7cpv from http://files.rcsb.org/download/7cpv.cif 7cpv title: Cryo-EM structure of 80S ribosome from mouse testis [more info...] Chain information for 7cpv #3 --- Chain | Description L5 | Mus musculus 28S ribosomal RNA L7 | Mus musculus 5S ribosomal RNA L8 | Mus musculus 5.8S ribosomal RNA LA | 60S ribosomal protein L8 LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4 LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6 LF | 60S ribosomal protein L7 LG | 60S ribosomal protein L7a LH | 60S ribosomal protein L9 LI | 60S ribosomal protein L10-like LJ | 60S ribosomal protein L11 LL | 60S ribosomal protein L13 LM | 60S ribosomal protein L14 LN | 60S ribosomal protein L15 LO | 60S ribosomal protein L13a LP | 60S ribosomal protein L17 LQ | 60S ribosomal protein L18 LR | 60S ribosomal protein L19 LS | 60S ribosomal protein L18a LT | 60S ribosomal protein L21 LU | 60S ribosomal protein L22 LV | 60S ribosomal protein L23 LW | 60S ribosomal protein L24 LX | 60S ribosomal protein L23a LY | 60S ribosomal protein L26 LZ | 60S ribosomal protein L27 La | 60S ribosomal protein L27a Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31 Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L35a Lg | 60S ribosomal protein L34 Lh | 60S ribosomal protein L35 Li | 60S ribosomal protein L36 Lj | 60S ribosomal protein L37 Lk | 60S ribosomal protein L38 Ll | Ribosomal protein L39-like Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41 Lo | 60S ribosomal protein L36a Lp | 60S ribosomal protein L37a Lr | 60S ribosomal protein L28 S2 | Mus musculus 18S ribosomal RNA S6 | Met-tRNA SA | 40S ribosomal protein SA SB | 40S ribosomal protein S3a SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4, X isoform SF | 40S ribosomal protein S5 SG | 40S ribosomal protein S6 SH | 40S ribosomal protein S7 SI | 40S ribosomal protein S8 SJ | 40S ribosomal protein S9 SK | 40S ribosomal protein S10 SL | 40S ribosomal protein S11 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14 SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16 SR | 40S ribosomal protein S17 SS | 40S ribosomal protein S18 ST | 40S ribosomal protein S19 SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21 SW | 40S ribosomal protein S15a SX | 40S ribosomal protein S23 SY | 40S ribosomal protein S24 SZ | 40S ribosomal protein S25 Sa | 40S ribosomal protein S26 Sb | 40S ribosomal protein S27 Sc | 40S ribosomal protein S28 Sd | 40S ribosomal protein S29 Se | 40S ribosomal protein S30 Sg | Receptor of activated protein C kinase 1 Non-standard residues in 7cpv #3 --- MG — magnesium ion ZN — zinc ion > select all 639400 atoms, 686465 bonds, 16371 pseudobonds, 51984 residues, 12 models selected > show sel cartoons > hide sel atoms > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > ui tool show Matchmaker > matchmaker #!2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7ls2, chain E2 (#1) with 7cpu, chain LB (#2), sequence alignment score = 1938.9 RMSD between 391 pruned atom pairs is 0.597 angstroms; (across all 397 pairs: 0.731) Matchmaker 7ls2, chain E2 (#1) with 7cpv, chain LB (#3), sequence alignment score = 1971.9 RMSD between 391 pruned atom pairs is 0.586 angstroms; (across all 397 pairs: 0.717) > matchmaker #!2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7ls2, chain E2 (#1) with 7cpu, chain LB (#2), sequence alignment score = 1938.9 RMSD between 391 pruned atom pairs is 0.597 angstroms; (across all 397 pairs: 0.731) Matchmaker 7ls2, chain E2 (#1) with 7cpv, chain LB (#3), sequence alignment score = 1971.9 RMSD between 391 pruned atom pairs is 0.586 angstroms; (across all 397 pairs: 0.717) QMainWindowLayout::tabPosition called with out-of-bounds value '0' QMainWindowLayout::tabPosition called with out-of-bounds value '0' Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 2149, in dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File ""/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 620, in close_request all_windows = self.tool_instance_to_windows[tool_instance] KeyError: KeyError: File ""/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 620, in close_request all_windows = self.tool_instance_to_windows[tool_instance] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.113 OpenGL renderer: Quadro RTX 4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUS Model: System Product Name OS: CentOS Stream 8 Architecture: 64bit ELF Virutal Machine: none CPU: 24 AMD Ryzen 9 5900X 12-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 62Gi 23Gi 29Gi 518Mi 9.6Gi 37Gi Swap: 31Gi 13Gi 17Gi Graphics: 05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1) Subsystem: NVIDIA Corporation Device [10de:12a0] 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: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 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: 1.13.3 ChimeraX-AtomicLibrary: 3.1.2 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: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2 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: 1.1.1 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-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 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 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: 1.7.3 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: 5.0.7 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: 1.1.1 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 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 scipy: 1.5.2 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: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 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: 1.2.0 }}} " defect accepted normal Window Toolkit Tom Goddard all ChimeraX