id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8607 SEQCROW sticks preset sets key_light_color to 4 values instead of 3 joegair@… tony.schaefer@… "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description presets... sticks command: lighting Log: > color name grey80 #333333 Color 'grey80' is opaque: gray(20%) hex: #333333 > color name grey65 #595959 Color 'grey65' is opaque: gray(34.9%) hex: #595959 > color name grey40 #999999 Color 'grey40' is opaque: gray(60%) hex: #999999 > color name grey20 #CCCCCC Color 'grey20' is opaque: gray(80%) hex: #cccccc > color name grey10 #E6E6E6 Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6 > color name grey3 #F7F7F7 Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7 > color name spartan #18453B Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b > color name msu_yellow #E6BF5C Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c > color name teal_light #49B0AB Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab > color name teal_dark #1C7B81 Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81 > color name msu_blue #004583 Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583 > color name excel #0B9A6D Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d > preset Ball-Stick-Endcap Using preset: SEQCROW / Ball-Stick-Endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out --- note | 2R_3_pyridyl_pyrrolidine_eq_02_opt.out has 0 imaginary harmonic vibrational modes Opened 2R_3_pyridyl_pyrrolidine_eq_02_opt.out as an ORCA output file > preset seqcrow ball-stick-endcap Using preset: SEQCROW / Ball-Stick-Endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > close session > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_piperidine_eq_01_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_piperidine_eq_01_opt.out --- note | 2R_3_pyridyl_piperidine_eq_01_opt.out has 0 imaginary harmonic vibrational modes Opened 2R_3_pyridyl_piperidine_eq_01_opt.out as an ORCA output file > close session > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_02_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_02_opt.out --- note | 3R_3_pyridyl_piperidine_eq_02_opt.out has 0 imaginary harmonic vibrational modes Opened 3R_3_pyridyl_piperidine_eq_02_opt.out as an ORCA output file > close session > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_01_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_01_opt.out --- note | 3R_3_pyridyl_piperidine_eq_01_opt.out has 0 imaginary harmonic vibrational modes Opened 3R_3_pyridyl_piperidine_eq_01_opt.out as an ORCA output file > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_01_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_01_opt.out --- note | 2R_3_pyridyl_pyrrolidine_eq_01_opt.out has 0 imaginary harmonic vibrational modes Opened 2R_3_pyridyl_pyrrolidine_eq_01_opt.out as an ORCA output file > open > /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out Summary of feedback from opening /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out --- note | 2R_3_pyridyl_pyrrolidine_eq_02_opt.out has 0 imaginary harmonic vibrational modes Opened 2R_3_pyridyl_pyrrolidine_eq_02_opt.out as an ORCA output file > close #3 > preset seqcrow ball-stick-endcap Using preset: SEQCROW / Ball-Stick-Endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide H > ui mousemode right translate > ui mousemode right ""translate selected models"" > select add #1 26 atoms, 27 bonds, 1 residue, 1 model selected > view matrix models #1,1,0,0,-0.25648,0,1,0,-2.4108,0,0,1,-0.043008 > ui mousemode right translate > select subtract #1 Nothing selected > color N msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #*/a N msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #*/a&N msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select all 49 atoms, 51 bonds, 2 residues, 2 models selected > color N red > color N msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-0.21399,0,1,0,-3.0451,0,0,1,1.309 > color N msu_blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color name msu_blue #004583 Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583 > select subtract #1 Nothing selected > ui mousemode right select > select #1/a:1@N1 1 atom, 1 residue, 1 model selected > color sel msu_blue > select #1/a:1@N1 1 atom, 1 residue, 1 model selected > select clear > color N msu_blue > color C grey40 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > color sel grey40 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color name grey40 #999999 Color 'grey40' is opaque: gray(60%) hex: #999999 > color C grey40 [Repeated 1 time(s)] > color C grey > color C grey40 > color name excel #0B9A6D Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d > color #1&C excel > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > select #2/a:1@N2 1 atom, 1 residue, 1 model selected > select add #2/a:1@C6 2 atoms, 1 residue, 1 model selected > select add #2/a:1@C7 3 atoms, 1 residue, 1 model selected > select add #2/a:1@C8 4 atoms, 1 residue, 1 model selected > select subtract #2/a:1@C6 3 atoms, 1 residue, 1 model selected > select subtract #2/a:1@C7 2 atoms, 1 residue, 1 model selected > select subtract #2/a:1@C8 1 atom, 1 residue, 1 model selected > select subtract #2/a:1@N2 Nothing selected > select add #2/a:1@N1 1 atom, 1 residue, 1 model selected > select add #2/a:1@C5 2 atoms, 1 residue, 1 model selected > select add #2/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #2/a:1@C3 4 atoms, 1 residue, 1 model selected > select add #2/a:1@C1 5 atoms, 1 residue, 1 model selected > select add #2/a:1@C2 6 atoms, 1 residue, 1 model selected > select #2/a:1@C6 1 atom, 1 residue, 1 model selected > select #2/a:1@C6 1 atom, 1 residue, 1 model selected > select #1/a:1@N1 1 atom, 1 residue, 1 model selected > select #1/a:1@C9 1 atom, 1 residue, 1 model selected > select #1/a:1@C8 1 atom, 1 residue, 1 model selected > select #1/a:1@N1 1 atom, 1 residue, 1 model selected > align #1/a:1@O4,C2,C3,C4,C5 toAtoms #2/a:1@N1,C5, Invalid ""toAtoms"" argument: only initial part ""#2/a:1@N1,C5"" of atom specifier valid > align #1/a:1@N1, C9,C8, toAtoms #2/a:1@N1,C5,C4,C3,C1, C2,C6 Missing required ""to_atoms"" argument > view > select #1/a:1@N1 1 atom, 1 residue, 1 model selected > select add #1 26 atoms, 27 bonds, 1 residue, 1 model selected > select subtract #1 Nothing selected > align #1/a:1@N1, C9,C8,C7,C5,C6,C2 toAtoms #2/a:1@N1,C5,C4,C3,C1, C2,C6 RMSD between 7 atom pairs is 0.014 angstroms > preset seqcrow sticks Using preset: SEQCROW / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow ""ball-stick-endcap 2"" Using preset: SEQCROW / Ball-Stick-Endcap 2 Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow ""sticks 2"" Using preset: SEQCROW / Sticks 2 Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #1/a:1@N1, C9,C8,C7,C5,C6,C2 > hide #1/a:1@N1, C9,C8,C7,C5,C6 > hide #1 models > show #1 models > hide #2 models > show #2 models > color #1 grey40 > color #2 grey40 > color #1 excel > color N msu_blue > set bgColor white > lighting soft > undo [Repeated 1 time(s)] > preset seqcrow sticks Using preset: SEQCROW / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > color #2 grey40 > color #1 excel > color N msu_blue > size #1&2 stickRadius 0.15 Expected a keyword > size #1 stickRadius 0.15 Changed 27 bond radii > size stickRadius 0.15 Changed 51 bond radii > size stickRadius 0.18 Changed 51 bond radii > preset seqcrow ""ball-stick-endcap 2"" Using preset: SEQCROW / Ball-Stick-Endcap 2 Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow sticks Using preset: SEQCROW / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow ""sticks 2"" Using preset: SEQCROW / Sticks 2 Preset implemented in Python; no expansion to individual ChimeraX commands available. > size stickRadius 0.18 Changed 51 bond radii > size stickRadius 0.2 Changed 51 bond radii > size stickRadius 0.18 Changed 51 bond radii > color #1 grey40 > color#2 excel Unknown command: color#2 excel > color #2 excel > color #1 excel > color #2 grey40 > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > select #2/a:1@C1 1 atom, 1 residue, 1 model selected > color #2 msu_yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2 spartan Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color name spartan #18453B Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b > color #2 spartan > select add #2/a:1@C3 2 atoms, 1 residue, 1 model selected > select add #2/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #2/a:1@C5 4 atoms, 1 residue, 1 model selected > select add #2/a:1@N1 5 atoms, 1 residue, 1 model selected > select add #2/a:1@C2 6 atoms, 1 residue, 1 model selected > color sel grey40 > color N msu_blue > view > select add #2 23 atoms, 24 bonds, 1 residue, 1 model selected > select subtract #2 Nothing selected > select clear > ui mousemode right clip [Repeated 1 time(s)] > lighting full > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting flat > lighting full > lighting soft > lighting simple > color name msu_yellow #E6BF5C Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c > view > size stickRadius 0.17 Changed 51 bond radii > color #1 msu_yellow > color #2 msu_yellow > color #1 excel > undo > color #1 excel > ui mousemode right select Drag select of 6 atoms, 6 bonds > color sel grey40 > select clear > color N msu_blue > color name teal_light #49B0AB Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab > color name teal_dark #1C7B81 Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81 > color #2 teal_light > color N msu_blue > color #2 teal_dark Drag select of 6 atoms, 6 bonds > color sel grey40 > color N msu_blue > select add #2 23 atoms, 24 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > lighting Intensity: 1 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0.5 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 0.4 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01) > fill intensity .2 Unknown command: fill intensity .2 > lighting fill intensity 0.2 Expected keyword ""fillColor"", ""fillDirection"", or ""fillIntensity"" > lighting fillIntensity 0.2 > lighting fillIntensity 0.3 > lighting intensity 0.3 > lighting intensity 0.5 > lighting intensity 0.8 > lighting fillIntensity 0.8 > lighting fillIntensity 0.5 > lighting ambientIntensity 0.5 > lighting ambientIntensity 0.1 > lighting ambientIntensity 0.2 > lighting ambientIntensity 0.3 > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > lighting gentle > lighting depthCue false > preset seqcrow sticks Using preset: SEQCROW / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/lighting.py"", line 100, in lighting 'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color), TypeError: not all arguments converted during string formatting TypeError: not all arguments converted during string formatting File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/lighting.py"", line 100, in lighting 'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color), See log for complete Python traceback. > lighting Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/lighting.py"", line 100, in lighting 'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color), TypeError: not all arguments converted during string formatting TypeError: not all arguments converted during string formatting File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/lighting.py"", line 100, in lighting 'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color), See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0) OS Loader Version: 540.120.3~19 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 24 days 13:08 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 Send2Trash: 1.8.0 SEQCROW: 1.5.14 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect assigned normal General Controls all ChimeraX