id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7256 Crash in swapaa afrance2@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000130d5000 (most recent call first): File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000001095c2600 (most recent call first): File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/clashes/clashes.py"", line 120 in find_clashes File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py"", line 739 in process_clashes File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py"", line 97 in swap_aa File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/cmd.py"", line 45 in swap_aa File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 332 in event_loop File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2022-07-11 16:23:05.00 -0400"",""app_version"":""1.5.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.5.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.0.1 (21A559)"",""incident_id"":""5082318E-B788-4D55-9C10-EF9BFCCF5CA3"",""name"":""ChimeraX""} { ""uptime"" : 1600000, ""procLaunch"" : ""2022-07-10 15:01:50.9925 -0400"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 504, ""deployVersion"" : 210, ""modelCode"" : ""iMac20,1"", ""procStartAbsTime"" : 1566490417338423, ""coalitionID"" : 78064, ""osVersion"" : { ""train"" : ""macOS 12.0.1"", ""build"" : ""21A559"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-07-11 16:22:54.8263 -0400"", ""incident"" : ""5082318E-B788-4D55-9C10-EF9BFCCF5CA3"", ""bug_type"" : ""309"", ""pid"" : 65355, ""procExitAbsTime"" : 1657755977135567, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.5.0"",""CFBundleVersion"":""1.5.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""31B0C3D6-302F-5CA1-AC22-678F30BF7167"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""B648F3E9-3C05-5922-1609-51E501149E1F"", ""bridgeVersion"" : {""build"":""19P549"",""train"":""6.0""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/amandaghilardi/Desktop/sdf/py145.sdf format sdf > close session > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt Summary of feedback from opening /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.445 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -11.764 Ignored bad PDB record found on line 4 REMARK INTER: -11.390 Ignored bad PDB record found on line 5 REMARK INTRA: -0.375 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.098 139 messages similar to the above omitted Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds) > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt Chain information for hAhR_49.pdb #2 --- Chain | Description ? | No description available Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds) > hide #1.9 models > hide #1.8 models > hide #1.7 models > hide #1.6 models > hide #1.5 models > hide #1.4 models > hide #1.3 models > hide #1.2 models > select ::name=""UNL"" 180 atoms, 198 bonds, 9 residues, 9 models selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > select clear Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > ui tool show ViewDockX > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > ZOOM Unknown command: ZOOM > zoom Pixel size at center of rotation is 0.0695 > zoom Pixel size at center of rotation is 0.0695 > zoom Pixel size at center of rotation is 0.0695 > color bfactor #2#1.1 1166 atoms, 114 residues, atom bfactor range 0 to 0 > color bfactor #2#1.1 1166 atoms, 114 residues, atom bfactor range 0 to 0 > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 1146 atoms, 1165 bonds, 113 residues, 1 model selected > color bfactor sel 1146 atoms, 113 residues, atom bfactor range 0 to 0 > color bfactor sel 1146 atoms, 113 residues, atom bfactor range 0 to 0 > mlp sel Map values for surface ""hAhR_49.pdb_ SES surface"": minimum -25.13, mean -2.884, maximum 26.25 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""hAhR_49.pdb_ SES surface"": minimum -25.13, mean -2.884, maximum 26.25 To also show corresponding color key, enter the above mlp command and add key true > select clear > mlp #1.1#!2 Map values for surface ""hAhR_49.pdb_ SES surface"": minimum -25.13, mean -2.884, maximum 26.25 To also show corresponding color key, enter the above mlp command and add key true > mlp #1.1#!2 Map values for surface ""hAhR_49.pdb_ SES surface"": minimum -25.13, mean -2.884, maximum 26.25 To also show corresponding color key, enter the above mlp command and add key true > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 1146 atoms, 1165 bonds, 113 residues, 1 model selected > mlp sel Map values for surface ""hAhR_49.pdb_ SES surface"": minimum -25.13, mean -2.884, maximum 26.25 To also show corresponding color key, enter the above mlp command and add key true > rainbow sel > color sel bypolymer > color sel byhetero > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 1146 atom styles > style sel sphere Changed 1146 atom styles > hide sel surfaces > show sel cartoons > show sel atoms > hide sel atoms > close session > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/complex.pdb Chain information for complex.pdb #1 --- Chain | Description ? | No description available > color bfactor 1166 atoms, 114 residues, atom bfactor range 0 to 0 > close session > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdb Chain information for hAhR_49.pdb #1 --- Chain | Description ? | No description available > close session > open > /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb 1iep.pdb title: Crystal structure of the C-abl kinase domain In complex with sti-571. [more info...] Chain information for 1iep.pdb #1 --- Chain | Description | UniProt A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE Non-standard residues in 1iep.pdb #1 --- 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) > color bfactor 4710 atoms, 728 residues, atom bfactor range 23.6 to 114 > select ::name=""STI"" 74 atoms, 82 bonds, 2 residues, 1 model selected > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > style sel sphere Changed 74 atom styles > select /B:225-498 2229 atoms, 2288 bonds, 274 residues, 1 model selected > select /B:225-498 2229 atoms, 2288 bonds, 274 residues, 1 model selected > select clear > color bfactor 4710 atoms, 728 residues, atom bfactor range 23.6 to 114 > ui tool show ""Side View"" > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > undo > coulombic Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62, maximum 9.00 Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > close session > open > /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb 1iep.pdb title: Crystal structure of the C-abl kinase domain In complex with sti-571. [more info...] Chain information for 1iep.pdb #1 --- Chain | Description | UniProt A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE Non-standard residues in 1iep.pdb #1 --- 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) > select :CL 6 atoms, 6 residues, 1 model selected > delete Missing or invalid ""atoms"" argument: empty atom specifier > delete CL Missing or invalid ""atoms"" argument: invalid atoms specifier > delete 'CL' Missing or invalid ""atoms"" argument: invalid atoms specifier > delete ""CL"" Missing or invalid ""atoms"" argument: invalid atoms specifier > select :CL 6 atoms, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > color bfactor 4704 atoms, 722 residues, atom bfactor range 23.6 to 114 > open 1iep fromDatabase Database eds Invalid ""fromDatabase"" argument: Should be one of 'alphafold', 'ccd', 'cellpack', 'eds', 'edsdiff', 'emdb', 'emdb_china', 'emdb_europe', 'emdb_japan', 'emdb_us', 'ftp', 'help', 'http', 'https', 'pdb', 'pdbdev', 'pdbe', 'pdbe_bio', 'pdbj', 'pubchem', 'rcsb_bio', 'smiles', or 'uniprot' > ui tool show ""Side View"" > ui tool show ""Volume Viewer"" > modelcol white Unknown command: modelcol white > open 1iep fromDatabse eds 'fromDatabse' has no suffix > open 1iep fromDatabase eds Summary of feedback from opening 1iep fetched from eds --- note | Fetching map 1iep from http://www.ebi.ac.uk/pdbe/coordinates/files/1iep.ccp4 Opened eds 1iep as #2, grid size 93,142,147, pixel 0.706,0.709,0.697, shown at level 0.514, step 1, values float32 > volume #2 level 0.4502 > volume #2 level 0.3734 > volume #2 color #2700d7 > undo > volume #2 color #d77692 > color bfactor 4704 atoms, 722 residues, atom bfactor range 23.6 to 114 > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > volume #2 level 0.5849 > hide #!2 models > delete /A > combine #1 > rename #ligand Missing or invalid ""models"" argument: invalid models specifier > rename #1 ligand > hide #3 models > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 4458 atoms, 4576 bonds, 548 residues, 2 models selected > delete atoms (#1 & sel) > delete bonds (#1 & sel) > select ::name=""HOH"" 146 atoms, 146 residues, 2 models selected > delete atoms (#1 & sel) > delete bonds (#1 & sel) > show #3 models > hide #1 models > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 2229 atoms, 2288 bonds, 274 residues, 1 model selected > select ~sel 147 atoms, 82 bonds, 75 residues, 4 models selected > delete atoms (#3 & sel) > delete bonds (#3 & sel) > show #1 models > select ::name=""STI"" 37 atoms, 41 bonds, 1 residue, 1 model selected > color sel magenta > color sel byhetero > select clear > select ligand 37 atoms, 41 bonds, 1 residue, 1 model selected > select zone Missing or invalid ""near"" argument: empty atom specifier > select Zone... Expected an objects specifier or a keyword > select sel @ show sel atoms > hbonds sel reveal true 16 hydrogen bonds found > select clear > hbonds reveal true 251 hydrogen bonds found > hide #4 models > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > show #4 models > select clear > select ligand 37 atoms, 41 bonds, 1 residue, 1 model selected > select invert Expected an objects specifier or a keyword > invert Unknown command: invert > select ~sel 2229 atoms, 2288 bonds, 274 residues, 3 models selected > show sel surfaces > select clear > mlp Map values for surface ""copy of 1iep.pdb_B SES surface"": minimum -26.69, mean -3.94, maximum 23.19 To also show corresponding color key, enter the above mlp command and add key true > select ::name=""STI"" 37 atoms, 41 bonds, 1 residue, 1 model selected > mlp sel mlp: no amino acids specified > ui tool show ""Surface Color"" > transparency sel 50 > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 2229 atoms, 2288 bonds, 274 residues, 1 model selected > transparency (#!3 & sel) 60 > select clear Alignment identifier is 3/B > select > #3/B:238-240,249-252,263-265,279-291,322-330,336-357,365-367,373-375,383-387,402-414,417-434,444-454,465-476,479-483,485-496 1099 atoms, 1109 bonds, 136 residues, 1 model selected > select clear > select #3/B:302-303 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3/B:302-303 12 atoms, 11 bonds, 2 residues, 1 model selected > select clear > select ::name=""STI"" 37 atoms, 41 bonds, 1 residue, 1 model selected > style sel ball Changed 37 atom styles > style sel sphere Changed 37 atom styles > style sel ball Changed 37 atom styles > show sel surfaces > hide sel surfaces Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 0 maps. Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > volume show > volume hide > ui mousemode right ""mark surface"" > ui mousemode right ""mark point"" > ui mousemode right ""link markers"" > ui mousemode right distance > show sel surfaces > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > view sel > side view Unknown command: side view > sideview Unknown command: sideview > ui tool show ""Side View"" > distance #3/B:326@CA #3/B:260@CB Distance between copy of 1iep.pdb #3/B TYR 326 CA and VAL 260 CB: 23.969Å > distance #3/B:317@CE2 #3/B:258@OE1 Distance between copy of 1iep.pdb #3/B PHE 317 CE2 and GLU 258 OE1: 6.675Å > distance #3/B:258@CG #3/B:312@OH Distance between copy of 1iep.pdb #3/B GLU 258 CG and TYR 312 OH: 12.629Å > distance #3/B:250@CA #3/B:266@CD2 Distance between copy of 1iep.pdb #3/B GLY 250 CA and LEU 266 CD2: 19.784Å > distance #3/B:317@CZ #3/B:258@CD Distance between copy of 1iep.pdb #3/B PHE 317 CZ and GLU 258 CD: 4.712Å > slect ligand Unknown command: slect ligand > hide sel surfaces > hide #!5 models > hide #4 models > hide #!3 models > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-3.1412,0,1,0,0.85101,0,0,1,0.10614 > view matrix models #1,1,0,0,-5.6603,0,1,0,1.7873,0,0,1,-0.10158 > view matrix models #1,1,0,0,-8.7063,0,1,0,1.4387,0,0,1,-1.8774 > view matrix models #1,1,0,0,-6.0654,0,1,0,-0.87088,0,0,1,-3.027 > view matrix models #1,1,0,0,-6.1034,0,1,0,-1.4409,0,0,1,-3.9743 > show #!3 models > slect ligand Unknown command: slect ligand > slect clear Unknown command: slect clear > mlp sel mlp: no amino acids specified > hide sel surfaces > select ligand 37 atoms, 41 bonds, 1 residue, 1 model selected > select ~sel 2229 atoms, 2288 bonds, 5 pseudobonds, 274 residues, 7 models selected > mlp sel Map values for surface ""copy of 1iep.pdb_B SES surface"": minimum -26.69, mean -3.94, maximum 23.19 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > view matrix models > #2,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#3,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#1.1.1,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#5,1,0,0,0,0,1,0,0,0,0,1,0 > undo > select clear > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > close session > open > /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb > format pdb 1iep.pdb title: Crystal structure of the C-abl kinase domain In complex with sti-571. [more info...] Chain information for 1iep.pdb #1 --- Chain | Description | UniProt A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE Non-standard residues in 1iep.pdb #1 --- 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) > select ::name=""CL"" 6 atoms, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > select ::name=""HOH"" 172 atoms, 172 residues, 1 model selected > delete atoms sel > delete bonds sel > delecte /B Unknown command: delecte /B > delete /B > combina #1 Unknown command: combina #1 > combine #1 > rename #2 ligand > hide #2 models > select ::name=""STI"" 74 atoms, 82 bonds, 2 residues, 2 models selected > delete atoms (#1 & sel) > delete bonds (#1 & sel) > show #2 models > hide #1 models > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 4458 atoms, 4576 bonds, 548 residues, 2 models selected > delete atoms (#2 & sel) > delete bonds (#2 & sel) > show #1 models > select clear > select ligand Nothing selected > style ball Changed 2266 atom styles > color light sea green > undo > select ligand Nothing selected > color cyan > select clear > select ::name=""STI"" 37 atoms, 41 bonds, 1 residue, 1 model selected > color sel light sea green > color sel byhetero > select clear > select ::name=""STI"" 37 atoms, 41 bonds, 1 residue, 1 model selected > select sel @ show sel atoms > style sel stick Changed 149 atom styles > color sel byhetero > select clear > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > hbonds intraModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > view matrix models > #1,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471,#2,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471 > view matrix models > #1,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374,#2,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374 > close session > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt Summary of feedback from opening /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.445 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -11.764 Ignored bad PDB record found on line 4 REMARK INTER: -11.390 Ignored bad PDB record found on line 5 REMARK INTRA: -0.375 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.098 139 messages similar to the above omitted Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds) > open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt Chain information for hAhR_49.pdb #2 --- Chain | Description ? | No description available Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds) > hide #1.9 models > hide #1.8 models > hide #1.7 models > hide #1.6 models > hide #1.5 models > hide #1.4 models > hide #1.3 models > hide #1.2 models > hide #2 models > show #2 models > ui tool show ViewDockX > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.2 models > hide #1.2 models > show #1.1 models > hide #1.1 models > show #1.2 models > hide #1.2 models > show #1.3 models > hide #1.3 models > show #1.4 models > hide #1.4 models > show #1.5 models > hide #1.5 models > show #1.6 models > hide #1.6 models > show #1.7 models > hide #1.7 models > show #1.8 models > hide #1.8 models > show #1.9 models > hide #1.9 models > show #1.8 models > hide #1.8 models > show #1.7 models > hide #1.7 models > show #1.6 models > hide #1.6 models > show #1.5 models > hide #1.5 models > show #1.4 models > hide #1.4 models > show #1.3 models > hide #1.3 models > show #1.2 models > hide #1.2 models > show #1.1 models > Add H Unknown command: Add H > hide #2 models > select ::name=""UNL"" 180 atoms, 198 bonds, 9 residues, 9 models selected > addh Summary of feedback from adding hydrogens to multiple structures --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 0 hydrogen bonds No usable SEQRES records for hAhR_49.pdb (#2) chain (blank); guessing termini instead Chain-initial residues that are actual N termini: hAhR_49.pdb #2/? GLU 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: hAhR_49.pdb #2/? GLY 113 Chain-final residues that are not actual C termini: 80 hydrogen bonds 774 hydrogens added > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > close session > open help:user/tutorial/binding-sites.html Opened help:user/tutorial/binding-sites.html No help found for 'help:user/tutorial/binding-sites.html' > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > open 2hyy Summary of feedback from opening 2hyy fetched from pdb --- notes | Fetching compressed mmCIF 2hyy from http://files.rcsb.org/download/2hyy.cif Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif 2hyy title: Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more info...] Chain information for 2hyy #1 --- Chain | Description | UniProt A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN Non-standard residues in 2hyy #1 --- STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl- pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib) 2hyy mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > panel Unknown command: modeller panel > close session > log clear > open 1fpp Summary of feedback from opening 1fpp fetched from pdb --- notes | Fetching compressed mmCIF 1fpp from http://files.rcsb.org/download/1fpp.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif Fetching CCD PO4 from http://ligand-expo.rcsb.org/reports/P/PO4/PO4.cif Fetching CCD FPP from http://ligand-expo.rcsb.org/reports/F/FPP/FPP.cif 1fpp title: Protein farnesyltransferase complex with farnesyl diphosphate [more info...] Chain information for 1fpp #1 --- Chain | Description | UniProt A | protein farnesyltransferase | PFTA_RAT B | protein farnesyltransferase | PFTB_RAT Non-standard residues in 1fpp #1 --- FPP — farnesyl diphosphate PO4 — phosphate ion ZN — zinc ion > mlp Map values for surface ""1fpp_A SES surface"": minimum -28.46, mean -4.976, maximum 24.73 Map values for surface ""1fpp_B SES surface"": minimum -27.83, mean -4.111, maximum 22.2 > surface zone #1 nearAtoms :fpp distance 8 maxComponents 1 > hide ~:fpp target ar > close > open 4xt3 Summary of feedback from opening 4xt3 fetched from pdb --- notes | Fetching compressed mmCIF 4xt3 from http://files.rcsb.org/download/4xt3.cif Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif 4xt3 title: Structure of a viral GPCR bound to human chemokine CX3CL1 [more info...] Chain information for 4xt3 #1 --- Chain | Description | UniProt A | G-protein coupled receptor homolog US28 | US28_HCMVA B | Fractalkine | X3CL1_HUMAN Non-standard residues in 4xt3 #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PO4 — phosphate ion UNL — unknown ligand > mlp Map values for surface ""4xt3_A SES surface"": minimum -28.71, mean 1.122, maximum 23.28 Map values for surface ""4xt3_B SES surface"": minimum -25.15, mean -4.785, maximum 22.04 > close > open 1g74 Summary of feedback from opening 1g74 fetched from pdb --- notes | Fetching compressed mmCIF 1g74 from http://files.rcsb.org/download/1g74.cif Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif 1g74 title: Toward changing specificity: adipocyte lipid binding protein mutant, oleic acid bound form [more info...] Chain information for 1g74 #1 --- Chain | Description | UniProt A | adipocyte lipid-binding protein | FABPA_MOUSE Non-standard residues in 1g74 #1 --- OLA — oleic acid PO4 — phosphate ion > surface > cliup Unknown command: cliup > clip > volume planes z style image imageMode ""full region"" No volumes specified > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right translate > ui mousemode right rotate > ui mousemode right ""clip rotate"" > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right translate > clip model #!1 false > hide ~:ola target ar > color :ola & C green > mlp Map values for surface ""1g74_A SES surface"": minimum -27.91, mean -5.662, maximum 22.39 > mlp protein surfaces #1.1.1 Map values for surface ""cap front"": minimum -53.62, mean 0.8646, maximum 49.31 > transparency #1.1.1 30 > coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1g74_A SES surface #1.1: minimum, -11.34, mean -0.02, maximum 10.80 > coulombic protein surfaces #1.1.1 offset 0 Coulombic values for cap front #1.1.1: minimum, -2199.36, mean 4.92, maximum 1486.74 > close session > open 3d6y fromDatabase rcsb_bio maxAssemblies 1 Summary of feedback from opening 3d6y fetched from rcsb_bio --- notes | Fetching compressed 3d6y bioassembly 1 from https://files.rcsb.org/download/3d6y-assembly1.cif Fetching CCD BER from http://ligand-expo.rcsb.org/reports/B/BER/BER.cif Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif 3d6y bioassembly 1 title: Crystal structure of R275E mutant of BMRR bound to DNA and berberine [more info...] Chain information for 3d6y bioassembly 1 #1 --- Chain | Description A A-2 | Multidrug-efflux transporter 1 regulator B B-2 | BMR promoter DNA Non-standard residues in 3d6y bioassembly 1 #1 --- BER — berberine GOL — glycerol (glycerin; propane-1,2,3-triol) Opened 1 biological assemblies for 3d6y > select :BER 50 atoms, 58 bonds, 2 residues, 1 model selected > select :BER 50 atoms, 58 bonds, 2 residues, 1 model selected > select :BER 50 atoms, 58 bonds, 2 residues, 1 model selected > select :BER 50 atoms, 58 bonds, 2 residues, 1 model selected > select :GOL 24 atoms, 20 bonds, 4 residues, 1 model selected > hide :gol > hide solvent > hide protein > select clear > coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84, mean -2.11, maximum 14.59 Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17, mean -2.12, maximum 15.04 > color nucleic tan > cartoon style nucleic xsection round width 1.5 thickness 1.5 > nucleotides tubs Missing or invalid ""representation"" argument: Should be one of 'atoms', 'fill', 'ladder', 'slab', 'stubs', or 'tube/slab' > nucleotides stubs > nucleotides tube/slab shape muffler > nucleotides tube/slab shape ellipsoid > nucleotides tube/slab shape box > nucleotides slab > style nucleic stick Changed 976 atom styles > nucleotides fill > style nucleic stick Changed 976 atom styles > nucleotides atoms > style nucleic stick Changed 976 atom styles > nucleotides stubs > size :ber stickRadius .7 Changed 58 bond radii > color C & :ber limegreen > set bgColor white > set bgColor gray > set bgColor black > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting full > lighting soft > lighting simple > graphics silhouettes false > coulombic protein key true Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84, mean -2.11, maximum 14.59 Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17, mean -2.12, maximum 15.04 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > 2dlabels text ""electrostatic potential"" > hide #!3 models > hide #2 models > show #!3 models > show #2 models > set bgColor white > ui mousemode right label > label delete residues > select clear > label delete residues > select clear > label delete residues > ui mousemode right label > ui mousemode right select > select //chain_id='A-2':20@NZ 1 atom, 1 residue, 1 model selected > select //chain_id='B-2':-5 19 atoms, 20 bonds, 1 residue, 1 model selected > select /A:26@O 1 atom, 1 residue, 1 model selected > select /A:32@CB 1 atom, 1 residue, 1 model selected > slect clear Unknown command: slect clear > ui mousemode right label > ui mousemode right ""move label"" > 2dlabels #3.1 xpos 0.658 ypos 0.140 > ui mousemode right translate > close session > open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation- coloring/conservation-coloring.html > open 121p Summary of feedback from opening 121p fetched from pdb --- notes | Fetching compressed mmCIF 121p from http://files.rcsb.org/download/121p.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD GCP from http://ligand-expo.rcsb.org/reports/G/GCP/GCP.cif 121p title: Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal verkuerzten menschlichen krebsproteins P21-H-ras [more info...] Chain information for 121p #1 --- Chain | Description | UniProt A | H-ras P21 protein | RASH_HUMAN Non-standard residues in 121p #1 --- GCP — phosphomethylphosphonic acid guanylate ester MG — magnesium ion 121p mmCIF Assemblies --- 1| author_defined_assembly > hide solvent > style ligand ball Changed 32 atom styles > open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/121p-consurf.aln Summary of feedback from opening //www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln fetched from https --- notes | Fetching 121p-consurf.aln from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln Downloaded 121p-consurf.aln to /Users/amandaghilardi/Downloads/121p-consurf.aln Alignment identifier is 121p-consurf.aln Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 121p-consurf.aln Opened 150 sequences from 121p-consurf.aln > color byattr_conservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color byattribute seq_conservation 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > color byattribute seq_conservation palette cyanmaroon range -1.4,1.4 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > color byattribute seq_conservation palette blue:red:yellow 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > color byattribute seq_conservation palette cyanmaroon 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > color byattribute seq_conservation palette cyanmaroon range -1.4,1.4 1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83 > open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation- coloring/conservation-coloring.html > hide protein > show ::seq_conservation>1.8 > label ::seq_conservation>1.8 > label height 1.3 > preset pub Multiple preset names match 'pub': publication 1 (silhouettes); publication 2 (depth-cued) > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > label delete > surface > color fromatoms > preset inter Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > close session > open 3sn6 Summary of feedback from opening 3sn6 fetched from pdb --- notes | Fetching compressed mmCIF 3sn6 from http://files.rcsb.org/download/3sn6.cif Fetching CCD P0G from http://ligand-expo.rcsb.org/reports/P/P0G/P0G.cif 3sn6 title: Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more info...] Chain information for 3sn6 #1 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(s) subunit α isoforms short | GNAS2_BOVIN B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN N | Camelid antibody VHH fragment | R | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN Non-standard residues in 3sn6 #1 --- P0G — 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one > preset cylinders Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 10247 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cylinders Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > color /R yellow > hide /N cartoons > open /Users/amandaghilardi/Desktop/81321.ali.rtf Unrecognized file suffix '.rtf' > open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali Summary of feedback from opening //www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali fetched from https --- notes | Fetching 81321.ali from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali Downloaded 81321.ali to /Users/amandaghilardi/Downloads/81321.ali Alignment identifier is 81321.ali Showing conservation header (""seq_conservation"" residue attribute) for alignment 81321.ali Opened 10 sequences from 81321.ali > sequence associate /N 81321.ali Associated 3sn6 chain N to d1m0ka- with 128 mismatches and/or gaps > sequence associate /R 81321.ali Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps > sequence associate /R 81321.ali Disassociated 3sn6 chain R from d2rh1a1 Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps > color byattribute seq_conservation /R & protein range -1.5,3 noValueColor > gray 3433 atoms, 443 residues, atom seq_conservation range -1.76 to 4.75 > show :: seq_conversation>2 > size stickRadius .5 Changed 10478 bond radii > color ligand byhetero > lighting soft > color ligand byhetero > lighting soft > lighting simple > close session > open 1kmo Summary of feedback from opening 1kmo fetched from pdb --- notes | Fetching compressed mmCIF 1kmo from http://files.rcsb.org/download/1kmo.cif Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif Fetching CCD HTO from http://ligand-expo.rcsb.org/reports/H/HTO/HTO.cif 1kmo title: Crystal structure of the Outer Membrane Transporter FecA [more info...] Chain information for 1kmo #1 --- Chain | Description | UniProt A | Iron(III) dicitrate transport protein fecA | FECA_ECOLI Non-standard residues in 1kmo #1 --- HTO — heptane-1,2,3-triol LDA — lauryl dimethylamine-N-oxide > hide > open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali Summary of feedback from opening //www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali fetched from https --- notes | Fetching 56935.ali from https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali Downloaded 56935.ali to /Users/amandaghilardi/Downloads/56935.ali Alignment identifier is 56935.ali Associated 1kmo chain A to d1kmoa- with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 56935.ali Opened 13 sequences from 56935.ali > color byattribute attr seq_conservation Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword > color byattribute seq_conservation 5862 atoms, 1066 residues, atom seq_conservation range -2.29 to 4.37 > select ~::seq_conservation 2540 atoms, 2148 bonds, 653 residues, 1 model selected > sequence header conservation setting al2co_gap 0.51 > sequence header conservation setting al2co_gap 0.52 > sequence header conservation setting al2co_gap 0.6 > select ~::seq_conservation 1364 atoms, 946 bonds, 496 residues, 1 model selected > select clear > color byattrseq_convservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color byattribute seq_convservation No known/registered numeric attribute seq_convservation > color byattribute seq_conservation 5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18 > color byattribute seq_conservation palette cyanmaroon range -2,3 > noValueColor silver key true > key cyan-white-maroon :-2.0 :0.5 :3.0 showTool true > ui mousemode right ""color key"" 5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18 > ui mousemode right translate > windowsize 600 600 > preset pub Multiple preset names match 'pub': publication 1 (silhouettes); publication 2 (depth-cued) > ui windowfill toggle > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) > set bgColor #ffffff00 Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > set bgColor steelblue > set bgColor #4682b400 > lighting flat > graphics silhouettes depthJump 0.003 > graphics silhouettes depthJump 0.03 > 2dlabels text ""Conservation (AL2CO entropy measure)"" > ui mousemode right ""move label"" > 2dlabels #3.1 xpos 0.406 ypos 0.157 > 2dlabels #3.1 xpos 0.349 ypos 0.141 > 2dlabels #3.1 xpos 0.354 ypos 0.018 > key labelSide left/top > key pos 0.06,0.1 size 0.3,0.04 > 2dlabels xpos 0.021 ypos 0.021 > close session > open 6ddf Summary of feedback from opening 6ddf fetched from pdb --- notes | Fetching compressed mmCIF 6ddf from http://files.rcsb.org/download/6ddf.cif Fetching CCD DAL from http://ligand-expo.rcsb.org/reports/D/DAL/DAL.cif Fetching CCD MEA from http://ligand-expo.rcsb.org/reports/M/MEA/MEA.cif Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif 6ddf title: μ Opioid Receptor-Gi Protein Complex [more info...] Chain information for 6ddf #1 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN D | DAMGO | R | Mu-type opioid receptor | OPRM_MOUSE Non-standard residues in 6ddf #1 --- ETA — ethanolamine > set bgColor black > set bgColor transparent > close > open 4n6h Summary of feedback from opening 4n6h fetched from pdb --- notes | Fetching compressed mmCIF 4n6h from http://files.rcsb.org/download/4n6h.cif Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif Fetching CCD TLA from http://ligand-expo.rcsb.org/reports/T/TLA/TLA.cif Fetching CCD EJ4 from http://ligand-expo.rcsb.org/reports/E/EJ4/EJ4.cif Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif 4n6h title: 1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target) [more info...] Chain information for 4n6h #1 --- Chain | Description | UniProt A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein | OPRD_HUMAN Non-standard residues in 4n6h #1 --- EJ4 — (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol (Naltrindole) NA — sodium ion OLA — oleic acid OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol) PGE — triethylene glycol TLA — L(+)-tartaric acid > surface > mlp Map values for surface ""4n6h_A SES surface"": minimum -26.77, mean -0.8566, maximum 23.81 > hide solvent > hide > show > lighting soft > lighting simple > hide surfaces > delete :1002-1106 > hbonds 582 hydrogen bonds found > hide solvent > select protein 2314 atoms, 2370 bonds, 327 pseudobonds, 303 residues, 2 models selected > hide > hide sel atoms > select clear > hbonds :EH4 Atom specifier selects no atoms > hbonds :EJ4 10 hydrogen bonds found > select ::name=""EJ4"" 31 atoms, 38 bonds, 1 residue, 1 model selected > select sel @ show sel atoms > select clear > color :EJ orange > color :EJ4 orange > color byhetero > hide cartoons > clip off > hide atoms > show :EJ4 : addh Summary of feedback from adding hydrogens to 4n6h #1 --- warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy- atom bond partners Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond partners 10 messages similar to the above omitted notes | Termini for 4n6h (#1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A GLY 36 Chain-final residues that are actual C termini: /A GLY 338 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A GLY 338 581 hydrogen bonds Adding 'H' to /A GLY 36 3076 hydrogens added > open 4n6h fromDatabase eds Summary of feedback from opening 4n6h fetched from eds --- note | Fetching map 4n6h from http://www.ebi.ac.uk/pdbe/coordinates/files/4n6h.ccp4 Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown at level 0.799, step 1, values float32 > volume #2 level 1.201 > volume zone #2 nearAtoms :EJ4 range 6 newMap false > volume #2 level 0.7072 > delete H > volume level .5 > close #2 > style :EJ4 sphere Changed 31 atom styles > surface :EJ4 : ui mousemode right translate > transparency 50 > close session > open 6pt2 Summary of feedback from opening 6pt2 fetched from pdb --- notes | Fetching compressed mmCIF 6pt2 from http://files.rcsb.org/download/6pt2.cif Fetching CCD CLR from http://ligand-expo.rcsb.org/reports/C/CLR/CLR.cif Fetching CCD DI7 from http://ligand-expo.rcsb.org/reports/D/DI7/DI7.cif Fetching CCD DAR from http://ligand-expo.rcsb.org/reports/D/DAR/DAR.cif Fetching CCD SAR from http://ligand-expo.rcsb.org/reports/S/SAR/SAR.cif Fetching CCD OXJ from http://ligand-expo.rcsb.org/reports/O/OXJ/OXJ.cif 6pt2 title: Crystal structure of the active δ opioid receptor in complex with the peptide agonist KGCHM07 [more info...] Chain information for 6pt2 #1 --- Chain | Description A B | δ opioid receptor C D | Peptide agonist KGCHM07 Non-standard residues in 6pt2 #1 --- CLR — cholesterol OLA — oleic acid OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol) OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine > hide #1 models > view > open 4n6h 4n6h title: 1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target) [more info...] Chain information for 4n6h #2 --- Chain | Description | UniProt A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein | OPRD_HUMAN Non-standard residues in 4n6h #2 --- EJ4 — (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol (Naltrindole) NA — sodium ion OLA — oleic acid OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol) PGE — triethylene glycol TLA — L(+)-tartaric acid > open 4pt2 Summary of feedback from opening 4pt2 fetched from pdb --- note | Fetching compressed mmCIF 4pt2 from http://files.rcsb.org/download/4pt2.cif 4pt2 title: Myxococcus xanthus encapsulin protein (EncA) [more info...] Chain information for 4pt2 #3 --- Chain | Description | UniProt A B P | Encapsulin protein | Q1D6H4_MYXXD 4pt2 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > hide #1 models > hide #!2 models > view > delete /B,D > delete :999-1106 > color #2:73,90,95,108,131,143,268,309,323 red > show #1 models > matchmaker #1 to #2 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 4n6h, chain A (#2) with 6pt2, chain A (#1), sequence alignment score = 1850 RMSD between 198 pruned atom pairs is 1.026 angstroms; (across all 289 pairs: 3.234) > show #!2 models > hide #3 models > show #1 cartoons > style stick Changed 9427 atom styles > hide surfaces > morph #1,2 same true Computed 51 frame morph #4 > coordset #4 1,51 > morph #1,2 same true Computed 51 frame morph #5 > coordset #5 1,51 > morph #1,2 same true Computed 51 frame morph #6 > coordset #6 1,51 > hide #3 > hide #3 models > show #2 models > show :128 > color :128 & C yellow > color /C & C pink > hbonds /C distSlop 0.6 47 hydrogen bonds found > swapaa #2:128 ASN Using Dunbrack library 4n6h #2/A ASP 128: phi -58.3, psi -44.7 trans ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.7.29 OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,1 Processor Name: 8-Core Intel Core i7 Processor Speed: 3.8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0) OS Loader Version: 540.40.4~45 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 19 days 4:30 Graphics/Displays: AMD Radeon Pro 5500 XT: Chipset Model: AMD Radeon Pro 5500 XT Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0041 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XT-011 Option ROM Version: 113-D322A1XT-011 EFI Driver Version: 01.01.231 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) 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 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.7.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.2 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.5.dev202206100131 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: 1.1 ChimeraX-DistMonitor: 1.1.6 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.2 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: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6.2 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.20.4 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.4 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.12.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Editing fixed Tom Goddard all ChimeraX