id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4443 MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted shon.a.koren@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description Tried aligning using MatchMaker two chains (6zr2/D and 6ztq/D). I have lots of structures open and I've moved some of them, which I don't think chimera likes much. Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\shona\OneDrive\Desktop\6zr2.pdb format pdb No such file/path: C:\Users\shona\OneDrive\Desktop\6zr2.pdb > open 6zr2 format mmcif fromDatabase pdb 6zr2 title: Cryo-EM structure of respiratory complex I in the active state from Mus musculus at 3.1 A [more info...] Chain information for 6zr2 #1 --- Chain | Description A | NADH-ubiquinone oxidoreductase chain 3 B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial H | NADH-ubiquinone oxidoreductase chain 1 I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial J | NADH-ubiquinone oxidoreductase chain 6 K | NADH-ubiquinone oxidoreductase chain 4L L | NADH-ubiquinone oxidoreductase chain 5 M | NADH-ubiquinone oxidoreductase chain 4 N | NADH-ubiquinone oxidoreductase chain 2 O | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 T U | Acyl carrier protein, mitochondrial V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 X | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 Y | MCG5603 Z | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 a | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 b | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial d | NADH dehydrogenase [ubiquinone] 1 subunit C2 e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 f | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 g | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial h | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial i | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 j | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial k | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 l | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial m | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Non-standard residues in 6zr2 #1 --- 3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn- phosphatidylethanolamine) ATP — adenosine-5'-triphosphate CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy- butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate FES — FE2/S2 (inorganic) cluster FMN — flavin mononucleotide (riboflavin monophosphate) NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine) SF4 — iron/sulfur cluster ZN — zinc ion > select all 67042 atoms, 68744 bonds, 38 pseudobonds, 8216 residues, 3 models selected > hide sel atoms > set bgColor white > show sel cartoons > color sel lightgrey > set bgColor black > color /D red > color /D:314 pink > color /D:314 green > select clear > select all 67042 atoms, 68744 bonds, 38 pseudobonds, 8216 residues, 3 models selected > hide sel cartoons > select /D 3464 atoms, 3554 bonds, 430 residues, 1 model selected > show sel cartoons > select clear > select /D:314 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel ball Changed 6 atom styles > show sel target ab > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:132 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel lime > show sel target ab > style sel ball Changed 6 atom styles > color sel lime > show sel target ab > style sel ball Changed 6 atom styles > color /D tan > color /D:314 298 113 lightgreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color /D:314 :298 :113 lightgreen > color /D:314 :293 :113 lightgreen > color /D:298 tan > select clear > select /D:293@CA 1 atom, 1 residue, 1 model selected > color sel lime > select up 18 atoms, 15 bonds, 3 residues, 1 model selected > color sel lime > select clear > select ::name=""SF4"" 48 atoms, 72 bonds, 6 residues, 1 model selected > show sel target ab > surface sel > color (#!1 & sel) byhetero > select clear > select up 40 atoms, 60 bonds, 5 residues, 4 models selected > surface hidePatches (#!1 & sel) > hide (#!1 & sel) target a > select up 58 atoms, 75 bonds, 8 residues, 4 models selected > surface (#!1 & sel) > hide (#!1 & sel) target a > surface (#!1 & sel) > color (#!1 & sel) lime > select clear > select /D:293 6 atoms, 5 bonds, 1 residue, 1 model selected > select /D:113 6 atoms, 5 bonds, 1 residue, 1 model selected > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > surface (#!1 & sel) > select clear > select /D:113 6 atoms, 5 bonds, 1 residue, 1 model selected > show (#!1 & sel) target ab > surface hidePatches (#!1 & sel) > style (#!1 & sel) sphere Changed 6 atom styles > select /D:314 6 atoms, 5 bonds, 1 residue, 1 model selected > show (#!1 & sel) target ab > style (#!1 & sel) sphere Changed 12 atom styles > select clear > set bgColor white > select /D:293@CB 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > set bgColor black > ui tool show H-Bonds > select up 12 atoms, 10 bonds, 2 residues, 2 models selected > select up 18 atoms, 15 bonds, 3 residues, 2 models selected > hbonds sel color #ffffff 8 hydrogen bonds found > color /D:299-315 pink > color /D:299-315 red > color /D:314 lime > select clear > select clear > select clear > select clear > select #1.8 8 pseudobonds, 1 model selected No visible atoms, bonds, or surfaces selected > color sel blue > select clear > set bgColor white > select /D:140 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:139 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /D:314@SG 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 12 atoms, 10 bonds, 2 residues, 2 models selected > select up 18 atoms, 15 bonds, 3 residues, 2 models selected > ui tool show Contacts > contacts sel overlapCutoff -15.0 interModel false select true > makePseudobonds false 19329 contacts > contacts sel overlapCutoff -15.0 resSeparation 5 interModel false select > true makePseudobonds false 1976983 contacts > contacts sel overlapCutoff -4.0 resSeparation 5 interModel false select true > makePseudobonds false 216710 contacts > contacts sel resSeparation 5 interModel false select true makePseudobonds > false 7128 contacts > select /D:314 :293 :113 18 atoms, 15 bonds, 3 residues, 1 model selected > contacts sel resSeparation 5 interModel false select true makePseudobonds > false 19 contacts > select /D:314 :293 :113 18 atoms, 15 bonds, 3 residues, 1 model selected Illegal contacts 'color' attribute value (Color([1.0, 0.6666667, 0.0, 1.0])), leaving attribute unchanged Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])), leaving attribute unchanged Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])), leaving attribute unchanged Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])), leaving attribute unchanged > select clear > select /D:293@CA 1 atom, 1 residue, 1 model selected > select /D:314 :293 :113 18 atoms, 15 bonds, 3 residues, 1 model selected > ui tool show Contacts > contacts sel resSeparation 5 interModel false select true makePseudobonds > false 19 contacts > select /D:314 :293 :113 18 atoms, 15 bonds, 3 residues, 1 model selected > contacts sel resSeparation 5 interModel false select true 19 contacts > select clear > set bgColor black > set bgColor white > color (#!1 & sel) red > select clear > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > lighting soft > lighting full > lighting simple > lighting soft > ui mousemode right clip > select /D:160 :59 purple Expected a keyword > color /D:160 :59 purple > color /D:108 :190 :85 :105 cyan > select /D:108 190 85 105 160 59 Expected a keyword > select /D:108 :190 :85 :105 :160 :59 64 atoms, 61 bonds, 6 residues, 1 model selected > show (#!1 & sel) target ab > style (#!1 & sel) ball Changed 64 atom styles > select clear > set bgColor black > set bgColor white > select up 29 atoms, 28 bonds, 4 residues, 2 models selected > select up 3464 atoms, 3554 bonds, 430 residues, 2 models selected > select clear > graphics silhouettes false > graphics silhouettes true > open 6Q9E Summary of feedback from opening 6Q9E fetched from pdb --- warning | Unable to fetch template for 'U10': might have incorrect bonds note | Fetching compressed mmCIF 6q9e from http://files.rcsb.org/download/6q9e.cif 6q9e title: Complex III2 focused refinement from Ovine respiratory supercomplex I+III2 [more info...] Chain information for 6q9e #2 --- Chain | Description a1 a3 | Ubiquinol-cytochrome c reductase core protein 1 a2 a4 | Ubiquinol-cytochrome c reductase core protein 2 b1 b2 | Cytochrome b c1 c2 | Cytochrome c1 d1 d2 | Cytochrome b-c1 complex subunit 7 f1 f2 | Cytochrome b-c1 complex subunit Rieske, mitochondrial h1 h2 | Cytochrome b-c1 complex subunit 6 i1 i2 | Ubiquinol-cytochrome c reductase, complex III subunit X q1 q2 | Ubiquinol-cytochrome c reductase complex III subunit VII x1 x2 | Cytochrome b-c1 complex subunit Rieske, mitochondrial Non-standard residues in 6q9e #2 --- 3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn- phosphatidylethanolamine) CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) FES — FE2/S2 (inorganic) cluster HEC — heme C HEM — protoporphyrin IX containing Fe (HEME) U10 — ubiquinone-10 (Coenzyme Q10) > select #2/h2:29@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 154 atoms, 153 bonds, 19 residues, 1 model selected > select up 532 atoms, 540 bonds, 65 residues, 1 model selected > select up 31997 atoms, 32773 bonds, 4008 residues, 1 model selected > hide sel atoms > select ::name=""U10"" 76 atoms, 76 bonds, 3 residues, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel resSeparation 5 interModel false reveal true 100 contacts > contacts sel overlapCutoff 1.0 resSeparation 5 interModel false reveal true No contacts > contacts sel overlapCutoff -10.0 interModel false reveal true 30021 contacts > contacts sel overlapCutoff -10.0 interModel false select true reveal true 30021 contacts > hide sel atoms > show sel cartoons > hide sel atoms > select #2/U10 Nothing selected > select #2:U10 76 atoms, 76 bonds, 3 residues, 1 model selected > show sel atoms > hide #2.3 models > select #2 31997 atoms, 32773 bonds, 30068 pseudobonds, 4008 residues, 4 models selected > ui mousemode right ""translate selected models"" > show cartoons #2 Expected ',' or a keyword > show #2 cartoons > select clear > open Missing or invalid ""fileNames"" argument: Expected a file name > open C:\Users\shona\OneDrive\Desktop/U10.cif > open C:\Users\shona\OneDrive\Desktop/U10.cif name U10 > open C:/Users/shona/OneDrive/Desktop/U10.cif > hide #2 cartoons > hide #2 surfaces > hide #2 atoms > show #2:U10 > select #2/b1:406@C1 1 atom, 1 residue, 1 model selected > select up 28 atoms, 28 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > surface sel > surface style #2 mesh > select #1/D:412 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 84 atoms, 83 bonds, 12 residues, 2 models selected > select up 3464 atoms, 3554 bonds, 430 residues, 2 models selected > select up 67042 atoms, 68744 bonds, 8216 residues, 2 models selected > ui mousemode right ""translate selected models"" > select #2/b1:406@C1M 1 atom, 1 residue, 1 model selected > select up 28 atoms, 28 bonds, 1 residue, 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right clip > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected atoms"" > open 6ztq Summary of feedback from opening 6ztq fetched from pdb --- warning | Unable to fetch template for 'HQH': might have incorrect bonds note | Fetching compressed mmCIF 6ztq from http://files.rcsb.org/download/6ztq.cif 6ztq title: Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A at 3.0 A [more info...] Chain information for 6ztq #3 --- Chain | Description A | NADH-ubiquinone oxidoreductase chain 3 B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial H | NADH-ubiquinone oxidoreductase chain 1 I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial J | NADH-ubiquinone oxidoreductase chain 6 K | NADH-ubiquinone oxidoreductase chain 4L L | NADH-ubiquinone oxidoreductase chain 5 M | NADH-ubiquinone oxidoreductase chain 4 N | NADH-ubiquinone oxidoreductase chain 2 O | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 T U | Acyl carrier protein, mitochondrial V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 X | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 Y | MCG5603 Z | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 a | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 b | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial d | NADH dehydrogenase [ubiquinone] 1 subunit C2 e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 f | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 g | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial h | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial i | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 j | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial k | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 l | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial m | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Non-standard residues in 6ztq #3 --- 3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn- phosphatidylethanolamine) ATP — adenosine-5'-triphosphate CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy- butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate FES — FE2/S2 (inorganic) cluster FMN — flavin mononucleotide (riboflavin monophosphate) HQH — Piericidin A NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine) SF4 — iron/sulfur cluster ZN — zinc ion > select #3 67072 atoms, 68773 bonds, 38 pseudobonds, 8217 residues, 3 models selected > ui mousemode right ""translate selected models"" > hide sel atoms > show sel cartoons > select clear > color #3 lightgrey > color #3/D red > hide #3 cartoons > show #3:D cartoons > show #3:D cartoons > select #3/D 3545 atoms, 3634 bonds, 432 residues, 1 model selected > cartoon sel > color sel tan > show #3:HGH atoms > show #3:HGH > select ::name=""HQH"" 30 atoms, 30 bonds, 1 residue, 1 model selected > show sel target ab > select ::name=""SF4"" 96 atoms, 144 bonds, 12 residues, 2 models selected > select #3:SF4 48 atoms, 72 bonds, 6 residues, 1 model selected > show sel surfaces > ui tool show Matchmaker > matchmaker #1/D to #3/D pairing ss Parameters --- Chain pairing | ss 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 6ztq, chain D (#3) with 6zr2, chain D (#1), sequence alignment score = 2333.1 RMSD between 429 pruned atom pairs is 0.238 angstroms; (across all 430 pairs: 0.267) Traceback (most recent call last): File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > hide #!3 models > hide #!2 models > show #!3 models > hide #3 Traceback (most recent call last): File ""D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""D:\ChimeraX 1.1\bin\lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > save ""C:/Users/shona/OneDrive/Desktop/bugged session.cxs"" OpenGL version: 3.3.0 NVIDIA 445.87 OpenGL renderer: GeForce GTX 1050/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Inspiron 5577 OS: Microsoft Windows 10 Pro (Build 19041) Memory: 17,035,116,544 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 WMI: 1.5.1 File attachment: bugged session.cxs }}} [attachment:""bugged session.cxs""] " defect closed normal Structure Comparison duplicate all ChimeraX