id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7044 kerning jack.stevenson@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description In all text boxes, kerning is weird after some letters. In particular, I notice problems after capital C and D: Cw, Cy, Cz, Cx, and Cv are kerned noticeably too wide. I see this at least in the command line, in this feedback text box and in the model panel. Haven't checked every letter. Thanks! Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 30xz Fetching url http://files.rcsb.org/download/30xz.cif failed: HTTP Error 404: Not Found > open 3oxz Summary of feedback from opening 3oxz fetched from pdb --- notes | Fetching compressed mmCIF 3oxz from http://files.rcsb.org/download/3oxz.cif Fetching CCD 0LI from http://ligand-expo.rcsb.org/reports/0/0LI/0LI.cif 3oxz title: Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 [more info...] Chain information for 3oxz #1 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE Non-standard residues in 3oxz #1 --- 0LI — 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (Ponatinib) > open 3cs9 Summary of feedback from opening 3cs9 fetched from pdb --- notes | Fetching compressed mmCIF 3cs9 from http://files.rcsb.org/download/3cs9.cif Fetching CCD NIL from http://ligand-expo.rcsb.org/reports/N/NIL/NIL.cif 3cs9 title: Human ABL kinase in complex with nilotinib [more info...] Chain information for 3cs9 #2 --- Chain | Description | UniProt A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN Non-standard residues in 3cs9 #2 --- NIL — Nilotinib (4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide) 3cs9 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > ui tool show Matchmaker > matchmaker #!2 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 3oxz, chain A (#1) with 3cs9, chain B (#2), sequence alignment score = 1373.8 RMSD between 242 pruned atom pairs is 0.591 angstroms; (across all 244 pairs: 0.623) > select #1 2280 atoms, 2249 bonds, 3 pseudobonds, 358 residues, 2 models selected > ~select #1 Nothing selected > log metadata #1 Metadata for 3oxz #1 --- Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats, J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C., Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x Non-standard residue | 0LI — 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (Ponatinib) Gene source | Mus musculus (mouse) Experimental method | X-ray diffraction Resolution | 2.2Å > log chains #1 Chain information for 3oxz #1 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE > show #!1 target m > view #1 clip false > help help:user/tools/modelpanel.html > hide #!1 target m > show #!1 target m > log metadata #1 Metadata for 3oxz #1 --- Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats, J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C., Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x Non-standard residue | 0LI — 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (Ponatinib) Gene source | Mus musculus (mouse) Experimental method | X-ray diffraction Resolution | 2.2Å > log chains #1 Chain information for 3oxz #1 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE > log metadata #1 Metadata for 3oxz #1 --- Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats, J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C., Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x Non-standard residue | 0LI — 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (Ponatinib) Gene source | Mus musculus (mouse) Experimental method | X-ray diffraction Resolution | 2.2Å > log chains #1 Chain information for 3oxz #1 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE > ui tool show ""Selection Inspector"" > log metadata #1 Metadata for 3oxz #1 --- Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 Citation | Zhou, T., Commodore, L., Huang, W.S., Wang, Y., Thomas, M., Keats, J., Xu, Q., Rivera, V.M., Shakespeare, W.C., Clackson, T., Dalgarno, D.C., Zhu, X. (2011). Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Chem.Biol.Drug Des., 77, 1-11. PMID: 21118377. DOI: 10.1111/j.1747-0285.2010.01054.x Non-standard residue | 0LI — 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide (Ponatinib) Gene source | Mus musculus (mouse) Experimental method | X-ray diffraction Resolution | 2.2Å > log chains #1 Chain information for 3oxz #1 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_MOUSE > help help:user > rename #1 Abl ponatinib Expected a keyword > rename #1 ""Abl ponatinib"" > rename #2 ""Abl nilotinib"" > sym #2 Abl nilotinib mmCIF Assemblies --- 1| author_and_software_defined_assembly| 1 copy of chain A 2| author_and_software_defined_assembly| 1 copy of chain B 3| author_and_software_defined_assembly| 1 copy of chain C 4| author_and_software_defined_assembly| 1 copy of chain D > log metadata #2 Metadata for Abl nilotinib #2 --- Title | Human ABL kinase in complex with nilotinib Citations | Weisberg, E., Manley, P.W., Breitenstein, W., Brueggen, J., Cowan- Jacob, S.W., Ray, A., Huntly, B., Fabbro, D., Fendrich, G., Hall-Meyers, E., Kung, A.L., Mestan, J., Daley, G.Q., Callahan, L., Catley, L., Cavazza, C., Azam, M., Neuberg, D., Wright, R.D., Gilliland, D.G., Griffin, J.D. (2005). Characterization of AMN107, a selective inhibitor of native and mutant Bcr- Abl. Cancer Cell, 7, 129-141. PMID: 15710326. DOI: 10.1016/j.ccr.2005.01.007 Vajpai, N., Strauss, A., Fendrich, G., Cowan-Jacob, S.W., Manley, P.W., Grzesiek, S., Jahnke, W. (?). Solution conformations and dynamics of ABL kinase inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. To be Published Non-standard residue | NIL — Nilotinib (4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide) Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.20Å > log chains #2 Chain information for Abl nilotinib #2 --- Chain | Description | UniProt A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN > rename #2 ""Abl nilotinib 3cs9"" > rename #1 ""Abl ponatinib 3oxz"" > open 2gqg Summary of feedback from opening 2gqg fetched from pdb --- warning | Atom P has no neighbors to form bonds with according to residue template for PTR /A:393 notes | Fetching compressed mmCIF 2gqg from http://files.rcsb.org/download/2gqg.cif Fetching CCD 1N1 from http://ligand-expo.rcsb.org/reports/1/1N1/1N1.cif Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif Fetching CCD PTR from http://ligand-expo.rcsb.org/reports/P/PTR/PTR.cif 2gqg title: X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain [more info...] Chain information for 2gqg #3 --- Chain | Description | UniProt A B | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN Non-standard residues in 2gqg #3 --- 1N1 — N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide (Dasatinib) GOL — glycerol (glycerin; propane-1,2,3-triol) 2gqg mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > rename #3 ""Abl dasatinib 2gqg"" > open 1iep Summary of feedback from opening 1iep fetched from pdb --- notes | Fetching compressed mmCIF 1iep from http://files.rcsb.org/download/1iep.cif Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif 1iep title: Crystal structure of the C-abl kinase domain In complex with sti-571. [more info...] Chain information for 1iep #4 --- Chain | Description | UniProt A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE Non-standard residues in 1iep #4 --- CL — chloride ion STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl- pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib) 1iep mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > rename #4 ""Abl imatinib 1iep"" > open 3ue4 Summary of feedback from opening 3ue4 fetched from pdb --- warning | Unable to fetch template for 'DB8': might have incorrect bonds note | Fetching compressed mmCIF 3ue4 from http://files.rcsb.org/download/3ue4.cif 3ue4 title: Structural and spectroscopic analysis of the kinase inhibitor bosutinib binding to the Abl tyrosine kinase domain [more info...] Chain information for 3ue4 #5 --- Chain | Description | UniProt A B | Tyrosine-protein kinase ABL1 | ABL1_HUMAN Non-standard residues in 3ue4 #5 --- DB8 — 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile (Bosutinib) 3ue4 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > rename #5 ""Abl bosutinib 3ue4"" > open 1opl Summary of feedback from opening 1opl fetched from pdb --- notes | Fetching compressed mmCIF 1opl from http://files.rcsb.org/download/1opl.cif Fetching CCD MYR from http://ligand-expo.rcsb.org/reports/M/MYR/MYR.cif Fetching CCD P16 from http://ligand-expo.rcsb.org/reports/P/P16/P16.cif 1opl title: Structural basis for the auto-inhibition of c-Abl tyrosine kinase [more info...] Chain information for 1opl #6 --- Chain | Description | UniProt A B | proto-oncogene tyrosine-protein kinase | ABL1_HUMAN Non-standard residues in 1opl #6 --- MYR — myristic acid P16 — 6-(2,6-dichlorophenyl)-2-{[3-(hydroxymethyl)phenyl]amino}-8-methylpyrido[2,3-D]pyrimidin-7(8H)-one (PD166326) 1opl mmCIF Assemblies --- 1| author_defined_assembly 2| author_and_software_defined_assembly 3| software_defined_assembly > rename #6 ""Abl myristic acid 1opl"" > open 5mo4 Summary of feedback from opening 5mo4 fetched from pdb --- notes | Fetching compressed mmCIF 5mo4 from http://files.rcsb.org/download/5mo4.cif Fetching CCD AY7 from http://ligand-expo.rcsb.org/reports/A/AY7/AY7.cif 5mo4 title: ABL1 kinase (T334I_D382N) in complex with asciminib and nilotinib [more info...] Chain information for 5mo4 #7 --- Chain | Description | UniProt A | Tyrosine-protein kinase ABL1 | ABL1_HUMAN Non-standard residues in 5mo4 #7 --- AY7 — asciminib NIL — Nilotinib (4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide) > rename #7 ""Abl asciminib nilotonib 5mo4"" > ui tool show Matchmaker > matchmaker #3-4#!2,5-7 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 Abl ponatinib 3oxz, chain A (#1) with Abl dasatinib 2gqg, chain B (#3), sequence alignment score = 1361.8 RMSD between 233 pruned atom pairs is 0.585 angstroms; (across all 256 pairs: 2.409) Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl imatinib 1iep, chain A (#4), sequence alignment score = 1423.3 RMSD between 248 pruned atom pairs is 0.529 angstroms; (across all 255 pairs: 0.929) Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl nilotinib 3cs9, chain B (#2), sequence alignment score = 1373.8 RMSD between 242 pruned atom pairs is 0.591 angstroms; (across all 244 pairs: 0.623) Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl bosutinib 3ue4, chain B (#5), sequence alignment score = 1388.5 RMSD between 238 pruned atom pairs is 0.619 angstroms; (across all 252 pairs: 2.418) Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl myristic acid 1opl, chain A (#6), sequence alignment score = 1404.8 RMSD between 230 pruned atom pairs is 0.619 angstroms; (across all 268 pairs: 4.522) Matchmaker Abl ponatinib 3oxz, chain A (#1) with Abl asciminib nilotonib 5mo4, chain A (#7), sequence alignment score = 1398.8 RMSD between 227 pruned atom pairs is 0.742 angstroms; (across all 260 pairs: 3.986) > open 5u8l Summary of feedback from opening 5u8l fetched from pdb --- notes | Fetching compressed mmCIF 5u8l from http://files.rcsb.org/download/5u8l.cif Fetching CCD O44 from http://ligand-expo.rcsb.org/reports/O/O44/O44.cif Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif 5u8l title: Crystal structure of EGFR kinase domain in complex with a sulfonyl fluoride probe XO44 [more info...] Chain information for 5u8l #8 --- Chain | Description | UniProt A | Epidermal growth factor receptor | EGFR_HUMAN Non-standard residues in 5u8l #8 --- GOL — glycerol (glycerin; propane-1,2,3-triol) O44 — 4-[(4-{4-[(3-cyclopropyl-1H-pyrazol-5-yl)amino]-6-[(prop-2-yn-1-yl)carbamoyl]pyrimidin-2-yl}piperazin-1-yl)methyl]benzene-1-sulfonyl fluoride SO4 — sulfate ion > rename #8 ""EGFR XO44 5u8l"" > open 1fin Summary of feedback from opening 1fin fetched from pdb --- notes | Fetching compressed mmCIF 1fin from http://files.rcsb.org/download/1fin.cif Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif 1fin title: Cyclin A-cyclin-dependent kinase 2 complex [more info...] Chain information for 1fin #9 --- Chain | Description | UniProt A C | cyclin-dependent kinase 2 | CDK2_HUMAN B D | cyclin A | CCNA2_HUMAN Non-standard residues in 1fin #9 --- ATP — adenosine-5'-triphosphate 1fin mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > rename #9 ""CDK2 CycA ATP active 1fin"" OpenGL version: 4.1 INTEL-18.5.8 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 429.140.8.0.0 OS Loader Version: 540.100.7~23 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 2:46 Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 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-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-ItemsInspection: 1.0 ChimeraX-Label: 1.1 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 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 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: 21.0 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 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 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 File attachment: Screen Shot 2022-06-07 at 13.27.04.png }}} [attachment:""Screen Shot 2022-06-07 at 13.27.04.png""] " defect closed normal Platform fixed Tom Goddard all ChimeraX