id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7674 "Report sqm.out; try to make quotes ""reusable""" Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Failures in adding charges are currently really difficult for even the moderately savvy user to debug, for a few reasons: - when SQM fails, the relevant error messages are written to sqm.out rather than stdout/stderr. Since sqm.out is deleted along with the temporary directory, that's all lost. - in the logged command (i.e.: ""Running ANTECHAMBER command: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2 -fi mol2 -o /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.out.mol2 -fo mol2 -c bcc -nc -5 -j 5 -s 2 -dr n"") the quotes around 'AM1' are not the same unicode symbol as the quotes expected by antechamber - so if I copy/paste/modify the command to the shell, the result is an inscrutable error message: Fortran runtime error: Cannot match namelist object name am1 ... which goes away if I delete and re-type the quotes on the command line. I think it would be much better if the ChimeraX code could capture and report the sqm.out contents (if they exist) on failure. Log: Startup Messages --- note | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7pqd Summary of feedback from opening 7pqd fetched from pdb --- notes | Fetching compressed mmCIF 7pqd from http://files.rcsb.org/download/7pqd.cif Fetching CCD BCL from http://ligand-expo.rcsb.org/reports/B/BCL/BCL.cif Fetching CCD SP2 from http://ligand-expo.rcsb.org/reports/S/SP2/SP2.cif Fetching CCD 3PE from http://ligand-expo.rcsb.org/reports/3/3PE/3PE.cif Fetching CCD CD4 from http://ligand-expo.rcsb.org/reports/C/CD4/CD4.cif Fetching CCD UQ1 from http://ligand-expo.rcsb.org/reports/U/UQ1/UQ1.cif Fetching CCD U10 from http://ligand-expo.rcsb.org/reports/U/U10/U10.cif Fetching CCD BPH from http://ligand-expo.rcsb.org/reports/B/BPH/BPH.cif Fetching CCD SQD from http://ligand-expo.rcsb.org/reports/S/SQD/SQD.cif Fetching CCD LMT from http://ligand-expo.rcsb.org/reports/L/LMT/LMT.cif Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif 7pqd title: Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation [more info...] Chain information for 7pqd #1 --- Chain | Description | UniProt AA AB AC AD AE AF AG AH AI AJ AK AL AM AN aa ab ac ad ae af ag ah ai aj ak al am an | LH1-alpha | BA BB BC BD BE BF BG BH BI BJ BK BL BM BN ba bb bc bd be bf bg bh bi bj bk bl bm bn | LH1-beta | H h | RC-H | L l | RC-L | M m | Reaction center protein M chain | RCEM_RHOS4 UA UB ua ub | PufZ | UU uu | PufY | X x | PufX | Non-standard residues in 7pqd #1 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) BCL — bacteriochlorophyll A BPH — bacteriopheophytin A CD4 — (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (tetramyristoyl-cardiolipin) FE — Fe (III) ion LMT — dodecyl-β-D-maltoside SP2 — 3,4-dihydrospheroidene SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol (sulfoquinovosyldiacylglycerol) U10 — ubiquinone-10 (Coenzyme Q10) UQ1 — ubiquinone-1 > usage vol volume [volumes] [style style] [change change] [show] [hide] [toggle] [close close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness a number] [transparency a number] [appearance appearance] [nameAppearance a text string] [nameForget nameForget] [step map step] [region map region] [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3 floats] [voxelSize 1 or 3 floats] [planes planes x|y|z[,[,[,[,]]]]] [dumpHeader true or false] [pickable true or false] [symmetry symmetry] [center center point] [centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a coordinate-system] [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a number] [showOutlineBox true or false] [outlineBoxRgb a color] [limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode] [colormapOnGpu true or false] [colormapSize an integer] [colormapExtendLeft true or false] [colormapExtendRight true or false] [backingColor backingColor] [blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false] [minimalTextureMemory true or false] [maximumIntensityProjection true or false] [linearInterpolation true or false] [dimTransparency true or false] [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting true or false] [twoSidedLighting true or false] [flipNormals true or false] [subdivideSurface true or false] [subdivisionLevels an integer] [surfaceSmoothing true or false] [smoothingIterations an integer] [smoothingFactor a number] [squareMesh true or false] [capFaces true or false] [boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector] [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount an integer] [imageMode imageMode] [calculateSurfaces true or false] — set volume model parameters, display style and colors style: one of image, mesh, solid, or surface change: one of image or surface close: one of image or surface level: some numbers, repeatable rmsLevel: some numbers, repeatable sdLevel: some numbers, repeatable encloseVolume: some numbers fastEncloseVolume: some numbers color: a color, repeatable appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin, Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs, CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone, Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II, Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow Bone nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin, Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs, CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone, Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II, Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow Bone colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16, la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8, rgba12, rgba16, rgba4, or rgba8 backingColor: a color or none projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto planeSpacing: one of max, mean, or min or a number orthoplanes: one of off, xy, xyz, xz, or yz positionPlanes: some integers imageMode: one of box faces, full region, orthoplanes, or tilted slab Subcommands are: * volume add * volume bin * volume boxes * volume channels * volume copy * volume cover * volume erase * volume falloff * volume flatten * volume flip * volume fourier * volume gaussian * volume laplacian * volume localCorrelation * volume mask * volume maximum * volume median * volume minimum * volume morph * volume multiply * volume new * volume octant * volume ~octant * volume onesmask * volume permuteAxes * volume resample * volume ridges * volume scale * volume settings * volume splitbyzone * volume subtract * volume threshold * volume tile * volume unbend * volume unroll * volume unzone * volume zone > usage mol molmap atoms resolution [gridSpacing gridSpacing] [edgePadding a number] [onGrid a density map specifier] [cutoffRange a number] [sigmaFactor a number] [balls true or false] [symmetry symmetry] [center center point] [axis an axis vector] [coordinateSystem a coordinate-system] [displayThreshold a number] [replace true or false] [showDialog true or false] — Compute a map by placing Gaussians at atom positions resolution: a number > 0 gridSpacing: a number > 0 > molmap #1 3 Opened 7pqd map 3 as #2, grid size 152,233,113, pixel 1, shown at level 0.11, step 1, values float32 > hide #!1 models > volume invert \2 Expected a density maps specifier or a keyword > volume invert #2 Expected a density maps specifier or a keyword > volume multiply #2 -1 Expected a keyword > volume multiply -1 #2 Missing or invalid ""volumes"" argument: invalid density maps specifier > usage vol mult volume multiply volumes [onGrid a density maps specifier] [boundingGrid true or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3 floats] [valueType numeric value type] [hideMaps true or false] [subregion map region] [step map step] [modelId modelId] [inPlace true or false] [scaleFactors scaleFactors] — Multiply maps pointwise modelId: a model id scaleFactors: some numbers > volume scale #2 factor -1 Opened 7pqd map 3 scaled as #3, grid size 152,233,113, pixel 1, shown at step 1, values float32 > volume #3 level -0.8116 > volume #3 level -0.7766 > ui tool show ""Side View"" > close #3 > ui tool show ""Side View"" > lighting soft > close #2 > show #!1 models > molmap #1 res 3 Missing or invalid ""resolution"" argument: Expected a number > molmap #1 3 Opened 7pqd map 3 as #2, grid size 152,233,113, pixel 1, shown at level 0.11, step 1, values float32 > color #2 near 1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2 near #1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #2 fromatoms #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color zone #2 near #1 > hide #!1 models > usage molmap molmap atoms resolution [gridSpacing gridSpacing] [edgePadding a number] [onGrid a density map specifier] [cutoffRange a number] [sigmaFactor a number] [balls true or false] [symmetry symmetry] [center center point] [axis an axis vector] [coordinateSystem a coordinate-system] [displayThreshold a number] [replace true or false] [showDialog true or false] — Compute a map by placing Gaussians at atom positions resolution: a number > 0 gridSpacing: a number > 0 > close #2 > molmap #1 6 Opened 7pqd map 6 as #2, grid size 85,126,66, pixel 2, shown at level 0.109, step 1, values float32 > color zone #2 near #1 > color zone #2 near #1 range 5 Expected a keyword > color zone #2 near #1 distance 5 > show #!1 models > hide #!2 models > cartoon > hide protein > molmap #1&(protein|:BCL,SP2,HEM,HEC) 5 Opened 7pqd map 5 as #3, grid size 99,147,75, pixel 1.67, shown at level 0.104, step 1, values float32 > close #2 > close #1,3 > open 5xth Summary of feedback from opening 5xth fetched from pdb --- notes | Fetching compressed mmCIF 5xth from http://files.rcsb.org/download/5xth.cif Fetching CCD PLX from http://ligand-expo.rcsb.org/reports/P/PLX/PLX.cif Fetching CCD 8Q1 from http://ligand-expo.rcsb.org/reports/8/8Q1/8Q1.cif Fetching CCD NDP from http://ligand-expo.rcsb.org/reports/N/NDP/NDP.cif Fetching CCD CDL from http://ligand-expo.rcsb.org/reports/C/CDL/CDL.cif Fetching CCD PEE from http://ligand-expo.rcsb.org/reports/P/PEE/PEE.cif Fetching CCD CU from http://ligand-expo.rcsb.org/reports/C/CU/CU.cif Fetching CCD HEA from http://ligand-expo.rcsb.org/reports/H/HEA/HEA.cif Fetching CCD HEC from http://ligand-expo.rcsb.org/reports/H/HEC/HEC.cif 5xth title: Cryo-EM structure of human respiratory supercomplex I1III2IV1 [more info...] Chain information for 5xth #1 --- Chain | Description | UniProt 0 | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_BOVIN 1 | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_BOVIN 2 | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_BOVIN 3 | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_BOVIN 4 | Cytochrome c oxidase subunit 6B1 | CX6B1_BOVIN 5 | Cytochrome c oxidase subunit 6C | COX6C_BOVIN 6 | Cytochrome c oxidase subunit 7A1, mitochondrial | CX7A1_BOVIN 7 | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_BOVIN 8 | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_BOVIN 9 | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_BOVIN A | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial | NDUV1_HUMAN AA AN | Cytochrome b-c1 complex subunit 8 | QCR8_HUMAN AB AO | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_HUMAN AC AP | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_HUMAN AD AQ | Cytochrome b-c1 complex subunit 9 | QCR9_HUMAN AE AR | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_HUMAN AF AS | Cytochrome b-c1 complex subunit 7 | QCR7_HUMAN AG AT | Cytochrome b-c1 complex subunit 10 | QCR10_HUMAN AH AU | Cytochrome c1, heme protein, mitochondrial | CY1_HUMAN AJ AV | Cytochrome b | CYB_HUMAN AK AW | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_HUMAN AL AY | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_HUMAN B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | NDUS8_HUMAN C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | NDUS7_HUMAN E | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | NDUA6_HUMAN F | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_HUMAN G X | Acyl carrier protein, mitochondrial | ACPM_HUMAN H | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | NDUA5_HUMAN I | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 | NDUA7_HUMAN J | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial | NDUA9_HUMAN K | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | NDUV3_HUMAN L | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | NDUS4_HUMAN M | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial | NDUS1_HUMAN N | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 | NDUAC_HUMAN O | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial | NDUV2_HUMAN P | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial | NDUS3_HUMAN Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | NDUS2_HUMAN S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | NDUA1_HUMAN T | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | NDUS6_HUMAN U | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 | NDUA3_HUMAN V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | NDUAB_HUMAN W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | NDUAD_HUMAN Y | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial | NDUB2_HUMAN Z | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 | NDUB3_HUMAN a | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial | NDUB5_HUMAN b | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 | NDUB6_HUMAN c | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial | NDUB8_HUMAN d | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | NDUBA_HUMAN e | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial | NDUBB_HUMAN f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | NDUC1_HUMAN g | NADH dehydrogenase [ubiquinone] 1 subunit C2 | NDUC2_HUMAN h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | NDUS5_HUMAN i | NADH-ubiquinone oxidoreductase chain 2 | Q4GRX1_HUMAN j | NADH-ubiquinone oxidoreductase chain 3 | B9EE38_HUMAN k | NADH-ubiquinone oxidoreductase chain 4L | V9JN72_HUMAN l | NADH-ubiquinone oxidoreductase chain 5 | X5BVZ3_HUMAN m | NADH-ubiquinone oxidoreductase chain 6 | Q8HAX7_HUMAN n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 | NDUB1_HUMAN o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 | NDUB4_HUMAN p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 | NDUB9_HUMAN r | NADH-ubiquinone oxidoreductase chain 4 | B2XJG5_HUMAN s | NADH-ubiquinone oxidoreductase chain 1 | H9PGF0_HUMAN u | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 | NDUA8_HUMAN v | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 | NDUB7_HUMAN w | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial | NDUAA_HUMAN x | Cytochrome c oxidase subunit 1 | COX1_BOVIN y | Cytochrome c oxidase subunit 2 | COX2_BOVIN z | Cytochrome c oxidase subunit 3 | COX3_BOVIN Non-standard residues in 5xth #1 --- 8Q1 — S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta- alanyl}amino)ethyl] dodecanethioate (S-dodecanoyl-4'-phosphopantetheine) CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) CU — copper (II) ion FES — FE2/S2 (inorganic) cluster FMN — flavin mononucleotide (riboflavin monophosphate) HEA — heme-A HEC — heme C HEM — protoporphyrin IX containing Fe (HEME) MG — magnesium ion NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) PLX — (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol SF4 — iron/sulfur cluster ZN — zinc ion > molmap #1&(protein) 5 Opened 5xth map 5 as #2, grid size 145,188,152, pixel 1.67, shown at level 0.101, step 1, values float32 > hide #!1 models > show #!1 models > cartoon > hide > hide #!2 models > show #!2 models > hide #!2 models > show > style stick Changed 115642 atom styles > lighting simple > close #1-2 > open 6t0b Summary of feedback from opening 6t0b fetched from pdb --- notes | Fetching compressed mmCIF 6t0b from http://files.rcsb.org/download/6t0b.cif Fetching CCD PEF from http://ligand-expo.rcsb.org/reports/P/PEF/PEF.cif Fetching CCD PCF from http://ligand-expo.rcsb.org/reports/P/PCF/PCF.cif Fetching CCD CUA from http://ligand-expo.rcsb.org/reports/C/CUA/CUA.cif 6t0b title: The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae [more info...] Chain information for 6t0b #1 --- Chain | Description | UniProt A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_YEAST B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_YEAST C N | Cytochrome b | CYB_YEAST D O | Cytochrome c1, heme protein, mitochondrial | CY1_YEAST E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_YEAST F Q | Cytochrome b-c1 complex subunit 6 | QCR6_YEAST G R | Cytochrome b-c1 complex subunit 7 | QCR7_YEAST H S | Cytochrome b-c1 complex subunit 8 | QCR8_YEAST I T | Cytochrome b-c1 complex subunit 9 | QCR9_YEAST J U | Cytochrome b-c1 complex subunit 10 | QCR10_YEAST a n | Cytochrome c oxidase subunit 1 | COX1_YEAST b o | Cytochrome c oxidase subunit 2 | COX2_YEAST c p | Cytochrome c oxidase subunit 3 | COX3_YEAST d q | Cytochrome c oxidase subunit 4, mitochondrial | COX4_YEAST e r | Cytochrome c oxidase polypeptide 5B, mitochondrial | COX5B_YEAST f s | Cytochrome c oxidase subunit 6, mitochondrial | COX6_YEAST g t | Cytochrome c oxidase subunit 7 | COX7_YEAST h u | Cytochrome c oxidase polypeptide VIII, mitochondrial | COX8_YEAST i v | Cytochrome c oxidase subunit 7A | COX9_YEAST j w | Cytochrome c oxidase subunit 6B | COX12_YEAST k x | Cytochrome c oxidase subunit 6A, mitochondrial | COX13_YEAST l y | Cox26 | YD19A_YEAST m z | Respiratory supercomplex factor 2, mitochondrial | RCF2_YEAST Non-standard residues in 6t0b #1 --- CA — calcium ion CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) CU — copper (II) ion CUA — dinuclear copper ion FES — FE2/S2 (inorganic) cluster HEA — heme-A HEC — heme C HEM — protoporphyrin IX containing Fe (HEME) MG — magnesium ion PCF — 1,2-diacyl-Sn-glycero-3-phoshocholine PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine (3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol) ZN — zinc ion > open 10340 fromDatabase emdb Summary of feedback from opening 10340 fetched from emdb --- note | Fetching compressed map 10340 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10340/map/emd_10340.map.gz Opened emdb 10340 as #2, grid size 448,448,448, pixel 1.09, shown at level 0.203, step 2, values float32 > volume #2 color #b2ffb226 > volume #2 step 1 > volume gaussian #2 bfactor 150 Opened emdb 10340 gaussian as #3, grid size 448,448,448, pixel 1.09, shown at step 1, values float32 > volume #3 color #e5bf9923 > volume #3 color #e5bf9924 > molmap #1&protein 6 Opened 6t0b map 6 as #4, grid size 75,102,162, pixel 2, shown at level 0.101, step 1, values float32 > hide #!1 models > select clear > show #!1 models > coulombic #1&protein The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /g ALA 60 OXT /e LYS 151 OXT /t ALA 60 OXT /c VAL 269 OXT /p VAL 269 OXT /r LYS 151 OXT Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIS+TYR (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.in.mol2 -fi mol2 -o /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIS+TYR) `` (HIS+TYR) `Welcome to antechamber 20.0: molecular input file processor.` (HIS+TYR) `` (HIS+TYR) `Info: Finished reading file (/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.in.mol2); atoms read (63), bonds read (64).` (HIS+TYR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIS+TYR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIS+TYR) `` (HIS+TYR) `` (HIS+TYR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HIS+TYR) `Info: Total number of electrons: 244; net charge: 0` (HIS+TYR) `` (HIS+TYR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HIS+TYR) `` (HIS+TYR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HIS+TYR) `` (HIS+TYR) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HIS+TYR) `` Charges for residue HIS+TYR determined Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69, maximum 12.75 Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57, maximum 9.66 Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34, maximum 13.75 Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12, maximum 26.17 Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41, maximum 15.32 Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07, maximum 6.06 Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98, maximum 10.07 Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67, maximum 11.34 Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56, maximum 19.51 Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48, maximum 11.81 Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78, maximum 11.40 Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65, maximum 9.34 Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27, maximum 14.16 Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18, maximum 22.82 Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67, maximum 15.86 Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18, maximum 6.42 Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01, maximum 8.56 Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72, maximum 12.05 Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52, maximum 14.49 Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50, maximum 10.22 Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12, maximum 14.50 Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63, maximum 9.06 Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32, maximum 9.43 Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79, maximum 8.25 Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35, maximum 8.80 Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54, maximum 5.74 Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54, maximum 18.83 Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85, maximum 14.99 Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40, maximum 11.38 Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70, maximum 8.57 Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49, maximum 11.03 Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32, maximum 7.92 Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70, maximum 10.31 Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07, maximum 13.36 Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61, maximum 8.69 Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65, maximum 9.81 Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80, maximum 11.90 Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40, maximum 9.19 Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52, maximum 7.54 Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58, maximum 19.92 Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68, maximum 13.20 Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57, maximum 12.66 Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91, maximum 8.16 Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44, maximum 9.03 Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32, maximum 8.49 Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62, maximum 11.63 > ~cartoon #1 > show #1&|protein Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #1&~protein > set bgColor white > color #1:CDL,PEF green > usage clip clip [near near] [far far] [front front] [back back] [position center point] [axis an axis vector] [coordinateSystem a coordinate-system] — set clip planes near: off or a number far: off or a number front: off or a number back: off or a number clip list — List active clip planes clip model models [clipping] — Turn off clipping for individual models. clipping: true or false clip off — Turn off all clip planes > clip model #3 false > camera ortho > clip near offset 1 Invalid ""near"" argument: Expected 'off' or a number > clip near 1 [Repeated 7 time(s)] > clip near 10 [Repeated 4 time(s)] > clip near -50 > usage clip cap clip [near near] [far far] [front front] [back back] [position center point] [axis an axis vector] [coordinateSystem a coordinate-system] — set clip planes near: off or a number far: off or a number front: off or a number back: off or a number clip list — List active clip planes clip model models [clipping] — Turn off clipping for individual models. clipping: true or false clip off — Turn off all clip planes > usage clip clip [near near] [far far] [front front] [back back] [position center point] [axis an axis vector] [coordinateSystem a coordinate-system] — set clip planes near: off or a number far: off or a number front: off or a number back: off or a number clip list — List active clip planes clip model models [clipping] — Turn off clipping for individual models. clipping: true or false clip off — Turn off all clip planes > usage cap ""cap"" is not a command name > usage surf surface [atoms] [enclose an atoms specifier] [include an atoms specifier] [probeRadius a number] [gridSpacing a number] [resolution a number] [level a number] [color a color] [transparency a number] [visiblePatches an integer] [sharpBoundaries true or false] [nthread an integer] [replace true or false] [update true or false] — create molecular surface Subcommands are: * surface cap * surface check * surface close * surface dust * surface hidePatches * surface showall * surface showPatches * surface splitbycolor * surface squaremesh * surface style * surface undust * surface unzone * surface zone > usage surf cap surface cap [enable] [offset a number] [subdivision a number] [mesh true or false] — Enable or disable clipping surface caps enable: true or false > surface color lightgrey > coulombic #1&protein Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69, maximum 12.75 Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57, maximum 9.66 Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34, maximum 13.75 Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12, maximum 26.17 Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41, maximum 15.32 Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07, maximum 6.06 Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98, maximum 10.07 Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67, maximum 11.34 Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56, maximum 19.51 Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48, maximum 11.81 Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78, maximum 11.40 Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65, maximum 9.34 Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27, maximum 14.16 Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18, maximum 22.82 Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67, maximum 15.86 Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18, maximum 6.42 Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01, maximum 8.56 Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72, maximum 12.05 Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52, maximum 14.49 Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50, maximum 10.22 Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12, maximum 14.50 Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63, maximum 9.06 Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32, maximum 9.43 Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79, maximum 8.25 Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35, maximum 8.80 Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54, maximum 5.74 Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54, maximum 18.83 Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85, maximum 14.99 Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40, maximum 11.38 Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70, maximum 8.57 Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49, maximum 11.03 Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32, maximum 7.92 Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70, maximum 10.31 Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07, maximum 13.36 Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61, maximum 8.69 Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65, maximum 9.81 Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80, maximum 11.90 Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40, maximum 9.19 Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52, maximum 7.54 Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58, maximum 19.92 Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68, maximum 13.20 Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57, maximum 12.66 Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91, maximum 8.16 Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44, maximum 9.03 Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32, maximum 8.49 Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62, maximum 11.63 > clip near 50 [Repeated 1 time(s)] > clip near -50 [Repeated 1 time(s)] > clip near 10 [Repeated 9 time(s)] > clip near -20 > clip near -200 > surface color lightgrey > coulombic #1&protein Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69, maximum 12.75 Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57, maximum 9.66 Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34, maximum 13.75 Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12, maximum 26.17 Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41, maximum 15.32 Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07, maximum 6.06 Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98, maximum 10.07 Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67, maximum 11.34 Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56, maximum 19.51 Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48, maximum 11.81 Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78, maximum 11.40 Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65, maximum 9.34 Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27, maximum 14.16 Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18, maximum 22.82 Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67, maximum 15.86 Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18, maximum 6.42 Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01, maximum 8.56 Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72, maximum 12.05 Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52, maximum 14.49 Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50, maximum 10.22 Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12, maximum 14.50 Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63, maximum 9.06 Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32, maximum 9.43 Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79, maximum 8.25 Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35, maximum 8.80 Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54, maximum 5.74 Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54, maximum 18.83 Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85, maximum 14.99 Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40, maximum 11.38 Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70, maximum 8.57 Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49, maximum 11.03 Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32, maximum 7.92 Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70, maximum 10.31 Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07, maximum 13.36 Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61, maximum 8.69 Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65, maximum 9.81 Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80, maximum 11.90 Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40, maximum 9.19 Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52, maximum 7.54 Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58, maximum 19.92 Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68, maximum 13.20 Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57, maximum 12.66 Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91, maximum 8.16 Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44, maximum 9.03 Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32, maximum 8.49 Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62, maximum 11.63 > clip near 20 [Repeated 7 time(s)] > clip near -100 > close #1.28#1.2-27,29-47 > coulombic #1&protein Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69, maximum 12.75 Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57, maximum 9.66 Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34, maximum 13.75 Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12, maximum 26.17 Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41, maximum 15.32 Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07, maximum 6.06 Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98, maximum 10.07 Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67, maximum 11.34 Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56, maximum 19.51 Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48, maximum 11.81 Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78, maximum 11.40 Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65, maximum 9.34 Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27, maximum 14.16 Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18, maximum 22.82 Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67, maximum 15.86 Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18, maximum 6.42 Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01, maximum 8.56 Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72, maximum 12.05 Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52, maximum 14.49 Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50, maximum 10.22 Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12, maximum 14.50 Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63, maximum 9.06 Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32, maximum 9.43 Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79, maximum 8.25 Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35, maximum 8.80 Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54, maximum 5.74 Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54, maximum 18.83 Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85, maximum 14.99 Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40, maximum 11.38 Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70, maximum 8.57 Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49, maximum 11.03 Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32, maximum 7.92 Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70, maximum 10.31 Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07, maximum 13.36 Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61, maximum 8.69 Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65, maximum 9.81 Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80, maximum 11.90 Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40, maximum 9.19 Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52, maximum 7.54 Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58, maximum 19.92 Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68, maximum 13.20 Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57, maximum 12.66 Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91, maximum 8.16 Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44, maximum 9.03 Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32, maximum 8.49 Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62, maximum 11.63 > surface color lightgrey > coulombic #1&protein Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69, maximum 12.75 Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57, maximum 9.66 Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34, maximum 13.75 Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12, maximum 26.17 Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41, maximum 15.32 Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07, maximum 6.06 Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98, maximum 10.07 Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67, maximum 11.34 Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56, maximum 19.51 Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48, maximum 11.81 Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78, maximum 11.40 Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65, maximum 9.34 Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27, maximum 14.16 Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18, maximum 22.82 Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67, maximum 15.86 Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18, maximum 6.42 Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01, maximum 8.56 Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72, maximum 12.05 Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52, maximum 14.49 Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50, maximum 10.22 Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12, maximum 14.50 Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63, maximum 9.06 Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32, maximum 9.43 Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79, maximum 8.25 Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35, maximum 8.80 Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54, maximum 5.74 Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54, maximum 18.83 Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85, maximum 14.99 Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40, maximum 11.38 Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70, maximum 8.57 Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49, maximum 11.03 Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32, maximum 7.92 Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70, maximum 10.31 Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07, maximum 13.36 Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61, maximum 8.69 Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65, maximum 9.81 Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80, maximum 11.90 Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40, maximum 9.19 Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52, maximum 7.54 Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58, maximum 19.92 Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68, maximum 13.20 Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57, maximum 12.66 Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91, maximum 8.16 Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44, maximum 9.03 Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32, maximum 8.49 Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62, maximum 11.63 > clip near 20 [Repeated 8 time(s)] > clip #3 false Expected a keyword > usage clip clip [near near] [far far] [front front] [back back] [position center point] [axis an axis vector] [coordinateSystem a coordinate-system] — set clip planes near: off or a number far: off or a number front: off or a number back: off or a number clip list — List active clip planes clip model models [clipping] — Turn off clipping for individual models. clipping: true or false clip off — Turn off all clip planes > clip model #3 false > color #3 #3febe324 models [Repeated 2 time(s)] > select :CDL,PEF 1455 atoms, 1421 bonds, 34 residues, 1 model selected > style sel sphere Changed 1455 atom styles > select clear > movie record > usage perframe perframe command [ranges ranges] [frames an integer] [interval an integer] [format a text string] [zeroPadWidth an integer] [showCommands true or false] — Run a command before each graphics frame is drawn command: a text string ranges: a range, repeatable perframe stop — Stop all perframe commands > perframe ""clip near 1"" frames 250 > movie stop > movie encode /Users/tcroll/Desktop/6t0b_tunnels.mp4 Movie saved to /Users/tcroll/Desktop/6t0b_tunnels.mp4 > clip near -250 > movie record > movie stop > usage movie record movie record [directory name of a folder to save/write; a name of 'browse' will bring up a file browser] [pattern a text string] [format format] [size size] [supersample an integer] [limit an integer] — Start saving frames of a movie to image files format: one of JPEG, PNG, or PPM size: some integers > windowsize window size 1344 761 > movie record > perframe ""clip near 0.25"" frames 800 > movie stop > pwd Current working directory is: /Users/tcroll/Desktop > movie encode 6t0b_flythrough.mp4 Movie saved to 6t0b_flythrough.mp4 > close #2-4#1.2-47 > close > isolde demo crystal_intro > set selectionWidth 4 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description | UniProt A | predicted microcompartment protein | A5N734_CLOK5 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description | UniProt 1.2/A | predicted microcompartment protein | A5N734_CLOK5 WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing ""(dataset) FOBS, SIGFOBS"". Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,34,34, pixel 0.723, shown at level 0.0949, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,34,34, pixel 0.723, shown at level -0.057,0.057, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,34,34, pixel 0.723, shown at level 0.346, step 1, values float32 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB standards. Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,34,34, pixel 0.723, shown at level 0.305, step 1, values float32 Loaded crystallographic demo: PDB ID 3io0 Populating font family aliases took 214 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > IEP Unknown command: alphafold IEP > isolde add ligand IEP place_ligand() was called with use_md_template=True, but no suitable template was found. This command has been ignored. > close #1.1 Deleting Crystallographic maps(3io0-sf.mtz) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_29 Deleting (LIVE) MDFF potential > delete ~:IEP > delete sel [Repeated 3 time(s)] > save /Users/tcroll/Desktop/IEP.pdb #1 > isolde parameterise sel Running ANTECHAMBER command: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.in.mol2 -fi mol2 -o /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.out.mol2 -fo mol2 -c bcc -nc -5 -j 5 -s 2 -dr n (IEP) `` (IEP) `Welcome to antechamber 20.0: molecular input file processor.` (IEP) `` (IEP) `Info: Finished reading file (/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.in.mol2); atoms read (149), bonds read (149).` (IEP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (IEP) `` (IEP) `` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (IEP) `Info: Total number of electrons: 564; net charge: -5` (IEP) `` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (IEP) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (IEP) `Cannot properly run ""/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue IEP Check reply log for details > save iep.mol2 #1 > show > usage bondrot ""bondrot"" is not a command name > usage rotate ""rotate"" is not a command name > ui mousemode right ""bond rotation"" > torsion /A:1000@C59,C58,C57,C56 -84.06 > torsion /A:1000@C59,C58,C57,C56 21.72 > torsion /A:1000@C62,C61,C60,C59 -70.26 > torsion /A:1000@C62,C61,C60,C59 -14.03 > torsion /A:1000@C59,C58,C57,C56 6.39 > torsion /A:1000@C30,C29,O28,P25 -52.61 > torsion /A:1000@C30,C29,O28,P25 -64.56 > torsion /A:1000@H74,O47,C30,C29 -61.19 > torsion /A:1000@C29,O28,P25,O24 157.50 > torsion /A:1000@P37,O36,C33,C32 122.89 > save iep.mol2 #1 > torsion /A:1000@C30,C29,O28,P25 -155.19 > torsion /A:1000@C15,C16,C17,C18 102.52 > torsion /A:1000@C60,C59,C58,C57 160.98 > torsion /A:1000@C58,C57,C56,C55 134.76 > torsion /A:1000@C63,C62,C61,C60 102.67 > torsion /A:1000@C56,C55,C54,C53 1.93 > torsion /A:1000@C57,C56,C55,C54 141.08 > save iep.mol2 #1 > coulombic #1 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue IEP (net charge -5) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2 -fi mol2 -o /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.out.mol2 -fo mol2 -c bcc -nc -5 -j 5 -s 2 -dr n (IEP) `` (IEP) `Welcome to antechamber 20.0: molecular input file processor.` (IEP) `` (IEP) `Info: Finished reading file (/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2); atoms read (149), bonds read (149).` (IEP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (IEP) `` (IEP) `` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (IEP) `Info: Total number of electrons: 564; net charge: -5` (IEP) `` (IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (IEP) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (IEP) `Cannot properly run ""/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue IEP Check reply log for details OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple 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: MacBook Pro Model Identifier: MacBookPro18,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 37 days 3:06 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina 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 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: 1.39.1 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: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0.dev0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1.5 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: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4 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-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 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: 1.18.3 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 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 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 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 all ChimeraX