id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17542 Measure center: Array argument has non-numeric values zg2234@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-x86_64-i386-64bit ChimeraX Version: 1.10.dev202504260127 (2025-04-26 01:27:24 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10.dev202504260127 (2025-04-26) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/ZhenGong/Desktop/ECD.cxs Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level 0.0653, step 1, values float32 Opened J1738_deepEMhancer.mrc as #4, grid size 256,256,256, pixel 1.06, shown at level 0.175, step 1, values float32 Opened 4ay9 map 10 resampled as #3, grid size 256,256,256, pixel 1.06, shown at level 0.0653, step 1, values float32 Log from Mon Apr 28 11:39:10 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ZhenGong/Desktop/ECD.cxs format session Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level 0.0653, step 1, values float32 Log from Sun Apr 27 21:13:50 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9.dev202408210848 (2024-08-21) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4a9y Summary of feedback from opening 4a9y fetched from pdb --- notes | Fetching compressed mmCIF 4a9y from http://files.rcsb.org/download/4a9y.cif https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/AQZ/AQZ.cif Fetching CCD AQZ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/AQZ/AQZ.cif 4a9y title: P38Α map kinase bound to CMPD 8 [more info...] Chain information for 4a9y #1 --- Chain | Description | UniProt A | MITOGEN-ACTIVATED PROTEIN KINASE 14 | MK14_HUMAN 2-360 Non-standard residues in 4a9y #1 --- AQZ — N-(3-{[7-methoxy-6-(2-pyrrolidin-1-ylethoxy)quinazolin-4-yl]amino}-4-methylphenyl)-2-morpholin-4-ylisonicotinamide > open 4ay9 Summary of feedback from opening 4ay9 fetched from pdb --- notes | Fetching compressed mmCIF 4ay9 from http://files.rcsb.org/download/4ay9.cif https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TYS/TYS.cif Fetching CCD TYS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TYS/TYS.cif 4ay9 title: Structure of follicle-stimulating hormone in complex with the entire ectodomain of its receptor [more info...] Chain information for 4ay9 #2 --- Chain | Description | UniProt A D G | GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE | Q96QJ4_HUMAN 1-92 B E H | FOLLITROPIN SUBUNIT BETA | FSHB_HUMAN 1-111 X Y Z | FOLLICLE-STIMULATING HORMONE RECEPTOR | FSHR_HUMAN 17-366 Non-standard residues in 4ay9 #2 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 4ay9 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly 3| software_defined_assembly > close #1 > ui mousemode right zoom > hide cartoons > hide atoms > show cartoons > delete /Y-Z > delete /C-F > delete /G-H > ui mousemode right zoom > save /Users/ZhenGong/Desktop/ECD.cxs > molmap #2 10 Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level 0.0653, step 1, values float32 > molmap #2 20 Opened 4ay9 map 20 as #1, grid size 31,27,27, pixel 6.67, shown at level 0.0327, step 1, values float32 > molmap #2 7 Opened 4ay9 map 7 as #1, grid size 55,43,43, pixel 2.33, shown at level 0.0852, step 1, values float32 > molmap #2 10 Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level 0.0653, step 1, values float32 > save /Users/ZhenGong/Desktop/ECD.cxs ——— End of log from Sun Apr 27 21:13:50 2025 ——— opened ChimeraX session > vop pad #1 size 44,44,44 > volume pad #1 size 44,44,44 Expected a density maps specifier or a keyword > vop new size 44 Opened new as #3, grid size 44,44,44, pixel 1, shown at step 1, values float32 > hide #!1 models > hide #!2 models > volume #3 level -0.5276 > close #3 > show #!1 models > info usage vop Expected a models specifier or a keyword > usage vop pad vop [optional] — alias of ""volume $*"" optional: the rest of line 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] [calculateSurfaces true or false] [boxFaces true or false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode imageMode] [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] [initialColors initialColors] [showOutlineBox true or false] [outlineBoxRgb a color] [limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft true or false] [colormapExtendRight true or false] [blendOnGpu true or false] [projectionMode projectionMode] [rayStep a number] [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] [positionPlanes positionPlanes] [tiltedSlabAxis an axis vector] [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount an integer] [backingColor backingColor] — 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 orthoplanes: one of off, xy, xyz, xz, or yz imageMode: one of box faces, full region, orthoplanes, or tilted slab initialColors: some colors 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 projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays planeSpacing: one of max, mean, or min or a number positionPlanes: 3-tuple of integers backingColor: a color or none Subcommands are: * volume add * volume bin * volume boxes * volume channels * volume copy * volume cover * volume defaultvalues * 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 sharpen * volume splitbyzone * volume subtract * volume threshold * volume tile * volume unbend * volume unroll * volume unzone * volume zone > hide #!1 models > show #!1 models > select #1 2 models selected > select #2 4100 atoms, 4142 bonds, 1 pseudobond, 569 residues, 2 models selected > molmap sel 20 onGrid #mymap Invalid ""onGrid"" argument: invalid density map specifier > molmap sel 20 onGrid #1 Opened 4ay9 map 20 as #3, grid size 44,36,35, pixel 3.33, shown at level 0.0323, step 1, values float32 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > open /Users/ZhenGong/Documents/Xray/Phenix/F74/J1738_deepEMhancer.mrc Opened J1738_deepEMhancer.mrc as #4, grid size 256,256,256, pixel 1.06, shown at level 8.2e-05, step 1, values float32 > close #3 > volume #4 level 0.1755 > select subtract #2 Nothing selected > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,19.739,0,1,0,4.8842,0,0,1,-113.69 > view matrix models #4,1,0,0,-47.325,0,1,0,-144.66,0,0,1,-124.61 > view matrix models #4,1,0,0,-115.63,0,1,0,-117.49,0,0,1,-130.23 > view matrix models #4,1,0,0,-121,0,1,0,-126.36,0,0,1,-134.11 > view matrix models #4,1,0,0,-121.61,0,1,0,-126.42,0,0,1,-133.56 > view matrix models #4,1,0,0,-125.54,0,1,0,-122.54,0,0,1,-137.61 > vop resample #1 ongrid #4 Opened 4ay9 map 10 resampled as #3, grid size 256,256,256, pixel 1.06, shown at step 1, values float32 > vop center #3 [Repeated 1 time(s)] > save /Users/ZhenGong/Desktop/4ay9_10A.mrc models #4 > save /Users/ZhenGong/Desktop/ECD.cxs ——— End of log from Mon Apr 28 11:39:10 2025 ——— > view name session-start opened ChimeraX session > hide #!3 models > molmap #2 5 Opened 4ay9 map 5 as #5, grid size 69,53,52, pixel 1.67, shown at level 0.0995, step 1, values float32 > show #!4 models > molmap #2 5 onGrid #4 Opened 4ay9 map 5 as #5, grid size 256,256,256, pixel 1.06, shown at level 0.0987, step 1, values float32 > hide #!4 models > center #5 Unknown command: center #5 > toolshed show > view #5 > save /Users/ZhenGong/Desktop/ECD_complex_5A.mrc models #5 > save /Users/ZhenGong/Desktop/ECD.cxs > hide #!5 models > combine #2 > delete #6/A-B > rename #6 4ay9_ECD > molmap #6 5 onGrid #5 Opened 4ay9_ECD map 5 as #7, grid size 256,256,256, pixel 1.06, shown at level 0.0942, step 1, values float32 > save /Users/ZhenGong/Desktop/ECD.cxs No map chosen to save > save /Users/ZhenGong/Desktop/4ay9_ECD_5A.mrc models #7 > hide #!6 models > hide #!7 models > show #!6 models > hide #!6 models > combine #2 > delete #8/R > select #8 4100 atoms, 4142 bonds, 1 pseudobond, 569 residues, 3 models selected > delete #8/X > rename #8 4ay9_hFSH > molmap #8 5 onGrid #7 Opened 4ay9_hFSH map 5 as #9, grid size 256,256,256, pixel 1.06, shown at level 0.0912, step 1, values float32 > save /Users/ZhenGong/Desktop/4ay9_hFSH_5A.mrc models #9 > save /Users/ZhenGong/Desktop/ECD.cxs > open 8neb Fetching url http://files.rcsb.org/download/8neb.cif failed: HTTP Error 404: Not Found > open 8enb Summary of feedback from opening 8enb fetched from pdb --- note | Fetching compressed mmCIF 8enb from http://files.rcsb.org/download/8enb.cif 8enb title: Crystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 2 [more info...] Chain information for 8enb #10 --- Chain | Description | UniProt A C | Bursicon | A0T3A2_CAEEL 1-92 B D | Cys_knot domain-containing protein | A7DT38_CAEEL 1-106 8enb mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > hide #!9 models > hide #!8 models > delete #10/C-D > close #10 > open /Users/ZhenGong/Documents/AlphaFold/Wei/hA2B5/hA2B5.pdb Chain information for hA2B5.pdb #10 --- Chain | Description A | No description available B | No description available Computing secondary structure > molmap #10 5 onGrid #9 Opened hA2B5.pdb map 5 as #11, grid size 256,256,256, pixel 1.06, shown at level 0.097, step 1, values float32 > view #10 > save /Users/ZhenGong/Desktop/ECD.cxs > save /Users/ZhenGong/Desktop/hA2B5_5A.mrc models #11 > hide #10 models > hide #!11 models > open > /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_00_00122_volume_sharp.mrc Opened cryosparc_P2_J346_class_00_00122_volume_sharp.mrc as #12, grid size 200,200,200, pixel 1.14, shown at level 0.0567, step 1, values float32 > view #12 > volume #12 level 0.1283 > volume #12 level 0.1641 > show #!2 models > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,-74.169,0,1,0,-51.33,0,0,1,-65.126 > view matrix models #8,1,0,0,-77.261,0,1,0,-62.989,0,0,1,-78.78 > select add #12 1596 atoms, 1611 bonds, 233 residues, 4 models selected > view matrix models > #8,1,0,0,-178.27,0,1,0,-148.83,0,0,1,-201.2,#12,1,0,0,-101.01,0,1,0,-85.845,0,0,1,-122.42 > volume #12 color #b2ffff81 > view matrix models > #8,1,0,0,-173.44,0,1,0,-165.29,0,0,1,-193.57,#12,1,0,0,-96.177,0,1,0,-102.3,0,0,1,-114.79 > fitmap #2 inMap #12 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms average map value = 0.2383, steps = 84 shifted from previous position = 6.95 rotated from previous position = 1.51 degrees atoms outside contour = 1604, contour level = 0.16415 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99974818 0.00481500 0.02191777 102.61289223 -0.00512003 0.99989053 0.01388221 100.60400404 -0.02184853 -0.01399094 0.99966339 117.04283034 Axis -0.52759164 0.82842202 -0.18805323 Axis point 5492.76226159 0.00000000 -4791.79812976 Rotation angle (degrees) 1.51367030 Shift along axis 7.19458600 > select subtract #12 1596 atoms, 1611 bonds, 233 residues, 1 model selected > save /Users/ZhenGong/Desktop/ECD.cxs > ui mousemode right zoom > hide #!12 models > open > /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_03_00122_volume_sharp.mrc Opened cryosparc_P2_J346_class_03_00122_volume_sharp.mrc as #13, grid size 200,200,200, pixel 1.14, shown at level 0.0555, step 1, values float32 > view #12 No displayed objects specified. > view #13 > volume #13 level 0.1232 > volume #13 color #b2b2ff85 > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,-197.97,0,1,0,-198.66,0,0,1,-222.2 > view matrix models #8,1,0,0,-202.21,0,1,0,-201.1,0,0,1,-225.8 > select add #13 1596 atoms, 1611 bonds, 233 residues, 3 models selected > view matrix models > #8,1,0,0,-298.23,0,1,0,-310.68,0,0,1,-329.3,#13,1,0,0,-96.02,0,1,0,-109.57,0,0,1,-103.51 > view matrix models > #8,1,0,0,-292.84,0,1,0,-304.62,0,0,1,-338.93,#13,1,0,0,-90.624,0,1,0,-103.51,0,0,1,-113.13 > hide #!13 models > show #!13 models > select add #13 1596 atoms, 1611 bonds, 233 residues, 4 models selected > select subtract #13 1596 atoms, 1611 bonds, 233 residues, 1 model selected > show #!12 models > hide #!13 models > hide #!12 models > show #!13 models > fitmap #2 inMap #13 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms average map value = 0.1985, steps = 72 shifted from previous position = 7.7 rotated from previous position = 0.337 degrees atoms outside contour = 1983, contour level = 0.12318 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.99982384 0.00723047 0.01732050 103.87432226 -0.00742308 0.99991104 0.01108226 99.12190251 -0.01723883 -0.01120888 0.99978857 117.47480336 Axis -0.51059242 0.79160300 -0.33564874 Axis point 6609.57652282 0.00000000 -5517.18586549 Rotation angle (degrees) 1.25079193 Shift along axis -14.00251472 > ui mousemode right zoom > save /Users/ZhenGong/Desktop/ECD.cxs > hide #!13 models > show #!12 models > hide #!12 models > open > /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_04_00122_volume_sharp.mrc Opened cryosparc_P2_J346_class_04_00122_volume_sharp.mrc as #14, grid size 200,200,200, pixel 1.14, shown at level 0.0585, step 1, values float32 > hide #!2 models > select add #14 1596 atoms, 1611 bonds, 233 residues, 3 models selected > view #4 No displayed objects specified. > view #14 > volume #14 level 0.1727 > volume #14 color #ffb2ff8a > show #!2 models > ui mousemode right ""translate selected models"" > view matrix models > #8,1,0,0,-363.61,0,1,0,-389.51,0,0,1,-448.23,#14,1,0,0,-70.767,0,1,0,-84.89,0,0,1,-109.31 > ui mousemode right zoom > ui mousemode right translate > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.29473,0.52925,0.79563,-657.36,0.54139,0.59361,-0.59542,-170.92,-0.78742,0.60624,-0.11158,124.4,#14,0.29473,0.52925,0.79563,-140.17,0.54139,0.59361,-0.59542,-33.359,-0.78742,0.60624,-0.11158,40.67 > view matrix models > #8,0.03312,0.98496,-0.16958,-300.47,-0.97957,-0.001683,-0.20109,502.18,-0.19835,0.17278,0.96478,-423.16,#14,0.03312,0.98496,-0.16958,-48.209,-0.97957,-0.001683,-0.20109,146.66,-0.19835,0.17278,0.96478,-101.62 > view matrix models > #8,0.23082,0.30128,0.92518,-597.64,0.40787,0.83332,-0.37313,-315.85,-0.88338,0.46348,0.069463,138.91,#14,0.23082,0.30128,0.92518,-124.7,0.40787,0.83332,-0.37313,-69.032,-0.88338,0.46348,0.069463,44.948 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.23082,0.30128,0.92518,-598.67,0.40787,0.83332,-0.37313,-329.77,-0.88338,0.46348,0.069463,143.91,#14,0.23082,0.30128,0.92518,-125.73,0.40787,0.83332,-0.37313,-82.952,-0.88338,0.46348,0.069463,49.951 > view matrix models > #8,0.23082,0.30128,0.92518,-601.14,0.40787,0.83332,-0.37313,-328.77,-0.88338,0.46348,0.069463,143.5,#14,0.23082,0.30128,0.92518,-128.21,0.40787,0.83332,-0.37313,-81.947,-0.88338,0.46348,0.069463,49.535 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.31025,0.38609,0.86872,-641.91,0.3703,0.79256,-0.48449,-246.61,-0.87557,0.472,0.10293,121.72,#14,0.31025,0.38609,0.86872,-139.02,0.3703,0.79256,-0.48449,-60.955,-0.87557,0.472,0.10293,43.984 > view matrix models > #8,0.26202,0.904,0.33782,-592.8,-0.092454,0.37196,-0.92363,309.26,-0.96062,0.21078,0.18104,226.78,#14,0.26202,0.904,0.33782,-126.2,-0.092454,0.37196,-0.92363,82.443,-0.96062,0.21078,0.18104,71.038 > view matrix models > #8,0.22369,0.95123,0.21243,-539.82,-0.28013,0.2715,-0.92077,424.08,-0.93354,0.14646,0.3272,175.85,#14,0.22369,0.95123,0.21243,-112.55,-0.28013,0.2715,-0.92077,112.67,-0.93354,0.14646,0.3272,57.982 > view matrix models > #8,0.21458,0.94715,0.23847,-546.31,-0.26187,0.29101,-0.92018,408.55,-0.94095,0.135,0.31047,191.07,#14,0.21458,0.94715,0.23847,-114.14,-0.26187,0.29101,-0.92018,108.63,-0.94095,0.135,0.31047,61.874 > view matrix models > #8,0.22055,0.94002,0.26022,-555.67,-0.22581,0.30875,-0.92395,388.58,-0.94887,0.14502,0.28037,203.82,#14,0.22055,0.94002,0.26022,-116.54,-0.22581,0.30875,-0.92395,103.35,-0.94887,0.14502,0.28037,65.148 > view matrix models > #8,0.22162,0.93269,0.28456,-564.14,-0.18902,0.32737,-0.9258,367.09,-0.95664,0.15139,0.24884,218.63,#14,0.22162,0.93269,0.28456,-118.69,-0.18902,0.32737,-0.9258,97.685,-0.95664,0.15139,0.24884,68.942 > view matrix models > #8,0.16823,0.9003,0.40144,-582.56,-0.17645,0.42817,-0.8863,303.09,-0.96983,0.078263,0.23089,261.84,#14,0.16823,0.9003,0.40144,-122.99,-0.17645,0.42817,-0.8863,81.455,-0.96983,0.078263,0.23089,79.93 > fitmap #2 inMap #14 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_04_00122_volume_sharp.mrc (#14) using 4100 atoms average map value = 0.1594, steps = 244 shifted from previous position = 7.53 rotated from previous position = 41.6 degrees atoms outside contour = 2733, contour level = 0.17271 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_04_00122_volume_sharp.mrc (#14) coordinates: Matrix rotation and translation 0.19274257 0.43478583 -0.87966561 103.04460535 0.57988377 0.67271390 0.45955503 84.78455024 0.79157130 -0.59867963 -0.12246464 108.51232456 Axis -0.53354093 -0.84260450 0.07315550 Axis point -36.42614255 0.00000000 78.70707277 Rotation angle (degrees) 97.38315762 Shift along axis -118.48008459 > hide #!14 models > show #!13 models > show #!14 models > hide #!14 models > show #!14 models > hide #!13 models > save /Users/ZhenGong/Desktop/ECD.cxs > hide #!14 models > show #!13 models > fitmap #2 inMap #13 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms average map value = 0.1985, steps = 164 shifted from previous position = 7.54 rotated from previous position = 41.6 degrees atoms outside contour = 1983, contour level = 0.12318 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.99981506 0.00752044 0.01769989 103.86426667 -0.00771132 0.99991258 0.01074060 99.12079799 -0.01761756 -0.01087511 0.99978565 117.46972529 Axis -0.48993081 0.80048759 -0.34523532 Axis point 6497.22223353 0.00000000 -5465.37210870 Rotation angle (degrees) 1.26404518 Shift along axis -12.09603394 > hide #!13 models > show #!12 models > fitmap #2 inMap #12 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms average map value = 0.2383, steps = 76 shifted from previous position = 7.7 rotated from previous position = 0.349 degrees atoms outside contour = 1603, contour level = 0.16415 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99973869 0.00506581 0.02229116 102.60786136 -0.00537772 0.99988816 0.01395504 100.60598318 -0.02221797 -0.01407126 0.99965412 117.04727616 Axis -0.52263837 0.83001243 -0.19475243 Axis point 5403.47171036 0.00000000 -4705.77970571 Rotation angle (degrees) 1.53641727 Shift along axis 7.08216925 > view name 1 > view list Named views: 1, session-start > view 1 > turn x 90 > turn x -90 > turn x 90 > view 1 > turn x 90 > turn x -90 > turn y 90 > save /Users/ZhenGong/Desktop/ECD.cxs > view 1 > hide #!12 models > show #!14 models > hide #!14 models > show #!13 models > fitmap #2 inMap #13 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms average map value = 0.1985, steps = 72 shifted from previous position = 7.71 rotated from previous position = 0.351 degrees atoms outside contour = 1983, contour level = 0.12318 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.99982220 0.00727842 0.01739495 103.87288257 -0.00746975 0.99991204 0.01095957 99.11815390 -0.01731365 -0.01108755 0.99978863 117.47409245 Axis -0.50469823 0.79454245 -0.33761219 Axis point 6592.44871797 0.00000000 -5517.25306246 Rotation angle (degrees) 1.25154726 Shift along axis -13.33156469 > volume #13 level 0.09416 > volume #13 level 0.1111 > hide #!13 models > hide #!2 models > open > /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_01_00122_volume_sharp.mrc Opened cryosparc_P2_J346_class_01_00122_volume_sharp.mrc as #15, grid size 200,200,200, pixel 1.14, shown at level 0.164, step 1, values float32 > view #15 > volume #15 level 0.107 > volume #15 level 0.1191 > volume #15 level 0.2191 > close #15 > open > /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_02_00122_volume_sharp.mrc Opened cryosparc_P2_J346_class_02_00122_volume_sharp.mrc as #15, grid size 200,200,200, pixel 1.14, shown at level 0.112, step 1, values float32 > volume #15 level 0.07776 > close #15 > open /Users/ZhenGong/Downloads/cryosparc_P2_J349_002_volume_map_sharp.mrc Opened cryosparc_P2_J349_002_volume_map_sharp.mrc as #15, grid size 100,100,100, pixel 2.28, shown at level 0.206, step 1, values float32 > volume #15 level 1.347 > close #15 > open > /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_00_00102_volume_sharp.mrc Opened cryosparc_P2_J362_class_00_00102_volume_sharp.mrc as #15, grid size 200,200,200, pixel 1.14, shown at level 0.0583, step 1, values float32 > volume #15 level 0.172 > volume #15 color #99bfe580 > show #!2 models > ui mousemode right zoom > show #!12 models > hide #!15 models > open > /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_01_00102_volume_sharp.mrc Opened cryosparc_P2_J362_class_01_00102_volume_sharp.mrc as #16, grid size 200,200,200, pixel 1.14, shown at level 0.0568, step 1, values float32 > volume #16 level 0.1553 > volume #16 level 0.1295 > open > /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_02_00102_volume_sharp.mrc Opened cryosparc_P2_J362_class_02_00102_volume_sharp.mrc as #17, grid size 200,200,200, pixel 1.14, shown at level 0.0594, step 1, values float32 > volume #17 level 0.2871 > hide #!12 models > show #!14 models > hide #!2 models > close #15-17 > hide #!14 models > open /Users/ZhenGong/Downloads/cryosparc_P2_J364_001_volume_map_sharp.mrc Opened cryosparc_P2_J364_001_volume_map_sharp.mrc as #15, grid size 200,200,200, pixel 1.14, shown at level 0.0616, step 1, values float32 > volume #15 level 0.1897 > volume #15 color #ffffb281 > hide #!15 models > show #!15 models > show #!12 models > show #!2 models > fitmap #2 inMap #12 Fit molecule 4ay9 (#2) to map cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms average map value = 0.2383, steps = 76 shifted from previous position = 7.69 rotated from previous position = 0.334 degrees atoms outside contour = 1604, contour level = 0.16415 Position of 4ay9 (#2) relative to cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99975159 0.00467759 0.02179171 102.62473300 -0.00497948 0.99989210 0.01382002 100.61260709 -0.02172471 -0.01392509 0.99966701 117.06077010 Axis -0.52843236 0.82881218 -0.18392829 Axis point 5527.00296467 0.00000000 -4831.31561060 Rotation angle (degrees) 1.50431772 Shift along axis 7.62793659 > select add #15 1596 atoms, 1611 bonds, 233 residues, 5 models selected > ui mousemode right ""translate selected models"" > view matrix models > #8,0.16823,0.9003,0.40144,-715.84,-0.17645,0.42817,-0.8863,237.92,-0.96983,0.078263,0.23089,115.17,#14,0.16823,0.9003,0.40144,-256.27,-0.17645,0.42817,-0.8863,16.282,-0.96983,0.078263,0.23089,-66.735,#15,1,0,0,-133.28,0,1,0,-65.173,0,0,1,-146.67 > ui mousemode right ""rotate selected models"" [Repeated 1 time(s)] > view matrix models > #8,0.32637,0.35025,-0.87796,63.168,-0.8984,-0.17382,-0.40331,581.59,-0.29387,0.92039,0.25794,-555.47,#14,0.32637,0.35025,-0.87796,-32.131,-0.8984,-0.17382,-0.40331,128.86,-0.29387,0.92039,0.25794,-273.74,#15,0.017786,0.87052,-0.49182,-61.541,-0.46953,0.44155,0.76457,-25.967,0.88274,0.21733,0.41659,-216.18 > view matrix models > #8,-0.51885,-0.58937,-0.61922,719.56,-0.85224,0.41335,0.32067,-49.69,0.066964,0.69411,-0.71675,-138.53,#14,-0.51885,-0.58937,-0.61922,178.22,-0.85224,0.41335,0.32067,-64.659,0.066964,0.69411,-0.71675,-150.41,#15,-0.86648,0.38802,0.3141,14.937,0.35751,0.043151,0.93291,-98.771,0.34844,0.92064,-0.17611,-168.47 > view matrix models > #8,-0.32055,-0.57609,0.75191,88.069,-0.01003,0.79581,0.60546,-626.37,-0.94718,0.18654,-0.26088,252.23,#14,-0.32055,-0.57609,0.75191,73.552,-0.01003,0.79581,0.60546,-181.68,-0.94718,0.18654,-0.26088,-56.734,#15,-0.27074,-0.85652,0.4394,74.9,0.95784,-0.19411,0.2118,-64.995,-0.096124,0.47822,0.87296,-177.29 > view matrix models > #8,-0.064846,0.42349,0.90358,-594.05,-0.2186,0.87746,-0.42694,-183,-0.97366,-0.22521,0.035677,361.7,#14,-0.064846,0.42349,0.90358,-177.79,-0.2186,0.87746,-0.42694,-124.42,-0.97366,-0.22521,0.035677,20.068,#15,0.7331,-0.60807,0.30466,-62.447,0.58181,0.79267,0.1821,-131.99,-0.35223,0.043755,0.93489,-101.54 > view matrix models > #8,-0.078833,0.39593,0.91489,-579.56,-0.31022,0.86244,-0.39996,-158.6,-0.94739,-0.31535,0.054836,394.95,#14,-0.078833,0.39593,0.91489,-171.95,-0.31022,0.86244,-0.39996,-122.29,-0.94739,-0.31535,0.054836,40.047,#15,0.71047,-0.62744,0.31868,-58.937,0.56371,0.77849,0.27601,-138.43,-0.42127,-0.016455,0.90679,-82.904 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.078833,0.39593,0.91489,-554.94,-0.31022,0.86244,-0.39996,-127.3,-0.94739,-0.31535,0.054836,421.48,#14,-0.078833,0.39593,0.91489,-147.34,-0.31022,0.86244,-0.39996,-90.99,-0.94739,-0.31535,0.054836,66.571,#15,0.71047,-0.62744,0.31868,-34.323,0.56371,0.77849,0.27601,-107.13,-0.42127,-0.016455,0.90679,-56.38 > view matrix models > #8,-0.078833,0.39593,0.91489,-557,-0.31022,0.86244,-0.39996,-108.53,-0.94739,-0.31535,0.054836,436.76,#14,-0.078833,0.39593,0.91489,-149.4,-0.31022,0.86244,-0.39996,-72.216,-0.94739,-0.31535,0.054836,81.854,#15,0.71047,-0.62744,0.31868,-36.384,0.56371,0.77849,0.27601,-88.359,-0.42127,-0.016455,0.90679,-41.096 > view matrix models > #8,-0.078833,0.39593,0.91489,-531.8,-0.31022,0.86244,-0.39996,-117.78,-0.94739,-0.31535,0.054836,430.13,#14,-0.078833,0.39593,0.91489,-124.2,-0.31022,0.86244,-0.39996,-81.468,-0.94739,-0.31535,0.054836,75.227,#15,0.71047,-0.62744,0.31868,-11.184,0.56371,0.77849,0.27601,-97.612,-0.42127,-0.016455,0.90679,-47.724 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.20314,-0.97914,-0.0030863,630.97,0.75023,-0.15767,0.64211,-309.42,-0.6292,0.12812,0.76661,-199.23,#14,-0.20314,-0.97914,-0.0030863,272.17,0.75023,-0.15767,0.64211,79.872,-0.6292,0.12812,0.76661,-84.626,#15,-0.91694,-0.38066,0.11967,180.84,0.24202,-0.76899,-0.59167,219.57,0.31725,-0.51357,0.79725,-67.498 > view matrix models > #8,0.91187,-0.31884,0.25851,-168.6,-0.077046,0.48564,0.87075,-506.3,-0.40318,-0.81393,0.41828,388.85,#14,0.91187,-0.31884,0.25851,88.919,-0.077046,0.48564,0.87075,-85.805,-0.40318,-0.81393,0.41828,164.61,#15,-0.029877,-0.52654,-0.84962,196.04,0.77382,-0.55022,0.31378,29.105,-0.6327,-0.64808,0.42389,105.71 > view matrix models > #8,0.83603,-0.52249,0.16749,2.2315,-0.099248,0.15622,0.98272,-366.78,-0.53963,-0.83821,0.078745,582.71,#14,0.83603,-0.52249,0.16749,144.66,-0.099248,0.15622,0.98272,-15.182,-0.53963,-0.83821,0.078745,196.04,#15,-0.26252,-0.51968,-0.81303,219.69,0.51845,-0.78659,0.33538,85.847,-0.81381,-0.33347,0.47593,85.076 > view matrix models > #8,0.5928,-0.62649,-0.50606,408.96,-0.26033,-0.74371,0.61573,321.66,-0.76211,-0.23326,-0.60397,601.71,#14,0.5928,-0.62649,-0.50606,220.2,-0.26033,-0.74371,0.61573,227.57,-0.76211,-0.23326,-0.60397,102.78,#15,-0.66746,0.07568,-0.74079,191.15,-0.46618,-0.81822,0.33644,209.99,-0.58067,0.5699,0.58141,-61.529 > view matrix models > #8,0.81647,-0.51438,0.26228,-35.399,-0.35291,-0.085043,0.93178,-138.93,-0.45699,-0.85333,-0.25097,702.14,#14,0.81647,-0.51438,0.26228,135.9,-0.35291,-0.085043,0.93178,47.629,-0.45699,-0.85333,-0.25097,223.32,#15,-0.22046,-0.59678,-0.77153,219.06,0.23812,-0.79999,0.55074,98.057,-0.94588,-0.062303,0.31847,86.602 > view matrix models > #8,0.74405,0.1043,0.65993,-513.91,-0.65702,0.29354,0.69438,-156.05,-0.12129,-0.95024,0.28693,432.9,#14,0.74405,0.1043,0.65993,-40.581,-0.65702,0.29354,0.69438,-23.689,-0.12129,-0.95024,0.28693,205.17,#15,0.48399,-0.67153,-0.56107,118.49,0.4325,-0.37381,0.82049,-5.6294,-0.76072,-0.63977,0.10951,154.97 > view matrix models > #8,0.55988,-0.66475,0.49461,27.181,0.22084,0.69507,0.68418,-632.17,-0.7986,-0.27382,0.53596,164.86,#14,0.55988,-0.66475,0.49461,156.28,0.22084,0.69507,0.68418,-123.88,-0.7986,-0.27382,0.53596,29.241,#15,-0.30573,-0.8218,-0.48081,224.05,0.93759,-0.34775,-0.0018113,19.903,-0.16571,-0.45136,0.87682,-24.459 > view matrix models > #8,-0.88228,-0.46104,0.095024,511.71,0.11831,-0.021802,0.99274,-339.11,-0.45562,0.88711,0.073782,-378.03,#14,-0.88228,-0.46104,0.095024,145.11,0.11831,-0.021802,0.99274,25.365,-0.45562,0.88711,0.073782,-216.21,#15,-0.52535,-0.12594,0.84152,23.498,0.3988,-0.91008,0.11276,139.53,0.75164,0.39484,0.52833,-198.16 > view matrix models > #8,-0.73675,-0.26693,0.62124,145.9,-0.074213,0.94515,0.31809,-529.12,-0.67208,0.18825,-0.71615,391.98,#14,-0.73675,-0.26693,0.62124,59.397,-0.074213,0.94515,0.31809,-155.13,-0.67208,0.18825,-0.71615,9.7887,#15,-0.11486,-0.5349,0.83707,21.933,0.96613,0.13586,0.21939,-64.912,-0.23108,0.83392,0.50118,-126.62 > view matrix models > #8,0.64841,0.52666,0.54973,-669.48,-0.22268,0.82172,-0.52458,-70.427,-0.728,0.21773,0.65009,-170.41,#14,0.64841,0.52666,0.54973,-132.86,-0.22268,0.82172,-0.52458,-63.122,-0.728,0.21773,0.65009,-96.936,#15,0.80391,-0.37614,-0.4607,33.476,0.49175,0.85607,0.15916,-85.094,0.33452,-0.3545,0.87317,-96.71 > view matrix models > #8,0.41635,0.83806,0.35256,-688.19,-0.82853,0.19004,0.5267,20.51,0.37441,-0.5114,0.77349,-154.12,#14,0.41635,0.83806,0.35256,-191.49,-0.82853,0.19004,0.5267,14.288,0.37441,-0.5114,0.77349,61.897,#15,0.96608,-0.027108,-0.2568,-49.935,0.24316,-0.23925,0.94002,-11.454,-0.086921,-0.97058,-0.22454,148.21 > view matrix models > #8,0.8959,-0.43716,-0.07905,39.585,0.11649,0.059464,0.99141,-382.18,-0.4287,-0.89742,0.1042,571.28,#14,0.8959,-0.43716,-0.07905,141.98,0.11649,0.059464,0.99141,6.0604,-0.4287,-0.89742,0.1042,207.69,#15,-0.2746,-0.2752,-0.92134,204.27,0.47113,-0.87379,0.12058,125.54,-0.83823,-0.40095,0.36959,107.71 > view matrix models > #8,0.87573,-0.48214,-0.025457,47.966,0.090966,0.11298,0.98942,-402.83,-0.47416,-0.86878,0.1428,553.38,#14,0.87573,-0.48214,-0.025457,148.92,0.090966,0.11298,0.98942,-6.4331,-0.47416,-0.86878,0.1428,198.28,#15,-0.29697,-0.3384,-0.89291,211.33,0.51422,-0.8446,0.14907,113.69,-0.8046,-0.41489,0.42483,99.163 > view matrix models > #8,0.87526,-0.48277,-0.029145,49.972,0.028738,-0.0082424,0.99955,-322.54,-0.4828,-0.87571,0.0066597,615.83,#14,0.87526,-0.48277,-0.029145,149.34,0.028738,-0.0082424,0.99955,22.14,-0.4828,-0.87571,0.0066597,209.95,#15,-0.2991,-0.33532,-0.89336,211.28,0.39868,-0.89451,0.20227,127.87,-0.86695,-0.29566,0.40123,95.339 > view matrix models > #8,0.97989,0.074004,-0.18533,-219.5,0.17687,0.10803,0.97829,-421.19,0.092418,-0.99139,0.092763,471.48,#14,0.97989,0.074004,-0.18533,27.176,0.17687,0.10803,0.97829,-4.9246,0.092418,-0.99139,0.092763,227.99,#15,0.15707,0.023043,-0.98732,123.53,0.51973,-0.85202,0.062798,123.38,-0.83976,-0.52301,-0.1458,178.97 > view matrix models > #8,0.50574,-0.63651,-0.58231,471.82,0.53927,-0.29361,0.78929,-233.21,-0.67337,-0.7132,0.19476,506.88,#14,0.50574,-0.63651,-0.58231,228.67,0.53927,-0.29361,0.78929,102.78,-0.67337,-0.7132,0.19476,158.45,#15,-0.72174,0.15434,-0.67474,181.26,0.14323,-0.92042,-0.36374,224.44,-0.67719,-0.35917,0.6422,53.093 > view matrix models > #8,0.80185,-0.59727,-0.017691,129.4,0.16843,0.19752,0.96572,-462.14,-0.5733,-0.77734,0.25898,485.4,#14,0.80185,-0.59727,-0.017691,176.27,0.16843,0.19752,0.96572,-25.335,-0.5733,-0.77734,0.25898,168.5,#15,-0.40993,-0.38154,-0.82848,223.16,0.59384,-0.80107,0.075081,106.95,-0.69232,-0.46121,0.55496,76.565 > hide #!15 models > open /Users/ZhenGong/Downloads/cryosparc_P2_J366_001_volume_map_sharp.mrc Opened cryosparc_P2_J366_001_volume_map_sharp.mrc as #16, grid size 200,200,200, pixel 1.14, shown at level 0.0514, step 1, values float32 > volume #16 level 0.2307 > select add #16 1596 atoms, 1611 bonds, 233 residues, 8 models selected > select subtract #15 1596 atoms, 1611 bonds, 233 residues, 6 models selected > select subtract #14 1596 atoms, 1611 bonds, 233 residues, 4 models selected > view matrix models > #8,0.2216,0.90268,0.36886,-499.25,-0.49441,-0.22204,0.84039,-35.103,0.84051,-0.36859,0.39709,-164.44,#16,-0.36799,0.57184,-0.7332,168.53,-0.27869,0.68445,0.67369,-9.7395,0.88708,0.45224,-0.092505,-25.325 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.2216,0.90268,0.36886,-656.15,-0.49441,-0.22204,0.84039,-95.86,0.84051,-0.36859,0.39709,-220.01,#16,-0.36799,0.57184,-0.7332,11.627,-0.27869,0.68445,0.67369,-70.497,0.88708,0.45224,-0.092505,-80.898 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.89831,0.43647,0.050287,-515.41,-0.2281,0.36549,0.90243,-446.31,0.3755,-0.82214,0.42789,90.647,#16,0.45873,0.28608,-0.84126,-34.208,-0.41716,0.90527,0.080373,-12.989,0.78456,0.31408,0.53462,-125.23 > show #!13 models > hide #!12 models > hide #!16 models > open /Users/ZhenGong/Downloads/cryosparc_P2_J368_001_volume_map_sharp.mrc Opened cryosparc_P2_J368_001_volume_map_sharp.mrc as #17, grid size 200,200,200, pixel 1.14, shown at level 0.0476, step 1, values float32 > volume #17 level 0.2292 > select subtract #16 1596 atoms, 1611 bonds, 233 residues, 1 model selected > select add #17 1596 atoms, 1611 bonds, 233 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #8,0.89831,0.43647,0.050287,-659.79,-0.2281,0.36549,0.90243,-504.87,0.3755,-0.82214,0.42789,36.012,#17,1,0,0,-144.39,0,1,0,-58.559,0,0,1,-54.635 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.38302,-0.91918,-0.091629,265.68,0.49435,0.12017,0.86092,-692.76,-0.78033,-0.37505,0.50043,308.37,#17,-0.061727,-0.50601,0.86032,-69.955,0.53983,0.70808,0.4552,-139.77,-0.83951,0.49252,0.22945,74.702 > view matrix models > #8,0.68726,-0.63692,0.34928,-238.4,-0.71711,-0.51822,0.46604,353.59,-0.11583,-0.57076,-0.8129,814.76,#17,0.35695,-0.074355,0.93116,-172.02,-0.84694,0.39474,0.35619,60.958,-0.39405,-0.91578,0.077925,195.87 > view matrix models > #8,0.61874,-0.42854,0.65842,-470.87,0.0063428,-0.83536,-0.54966,727.34,0.78557,0.34427,-0.51415,-167.22,#17,0.40189,0.29642,0.86638,-209.97,-0.38655,-0.8028,0.45397,128.66,0.8301,-0.51735,-0.20805,48.583 > hide #!17 models > show #!15 models > hide #!13 models > view matrix models > #8,0.61874,-0.42854,0.65842,-470.87,0.0063428,-0.83536,-0.54966,727.34,0.78557,0.34427,-0.51415,-167.22,#17,0.40189,0.29642,0.86638,-209.97,-0.38655,-0.8028,0.45397,128.66,0.8301,-0.51735,-0.20805,48.583 > ui mousemode right ""translate selected models"" > select add #15 1596 atoms, 1611 bonds, 233 residues, 5 models selected > select subtract #17 1596 atoms, 1611 bonds, 233 residues, 3 models selected > view matrix models > #8,0.61874,-0.42854,0.65842,-473.3,0.0063428,-0.83536,-0.54966,660.58,0.78557,0.34427,-0.51415,-204.43,#15,-0.40993,-0.38154,-0.82848,220.72,0.59384,-0.80107,0.075081,40.19,-0.69232,-0.46121,0.55496,39.35 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.46041,-0.70209,0.54322,-233.83,0.21779,-0.5039,-0.83585,616.19,0.86057,0.50315,-0.079091,-556.03,#15,-0.10373,-0.51944,-0.84818,201.66,0.30959,-0.82728,0.46878,34.778,-0.94519,-0.21397,0.24663,75.078 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.46041,-0.70209,0.54322,-255.43,0.21779,-0.5039,-0.83585,623.12,0.86057,0.50315,-0.079091,-538.68,#15,-0.10373,-0.51944,-0.84818,180.05,0.30959,-0.82728,0.46878,41.708,-0.94519,-0.21397,0.24663,92.432 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.3963,-0.76797,0.50316,-178.96,0.13298,-0.49424,-0.8591,670.78,0.90844,0.40737,-0.093742,-515.66,#15,-0.0064043,-0.54223,-0.8402,169.95,0.3771,-0.7795,0.50018,24.36,-0.92615,-0.31364,0.20947,105.93 > view matrix models > #8,0.64279,-0.60998,0.46341,-322.03,-0.68524,-0.18743,0.70378,-15.977,-0.34244,-0.76993,-0.53846,735.22,#15,-0.28077,-0.60145,-0.74795,200.36,0.47946,0.58719,-0.65216,-22.505,0.83143,-0.54172,0.12351,-72.89 > view matrix models > #8,-0.27125,0.093691,0.95794,-474.66,-0.36878,-0.92942,-0.013523,547.04,0.88906,-0.35694,0.28666,-452.44,#15,-0.067304,0.63514,-0.76946,30.865,0.81528,-0.40956,-0.40937,27.152,-0.57515,-0.65488,-0.49025,180.13 > view matrix models > #8,-0.54317,-0.83405,0.096537,502.06,0.76792,-0.447,0.45879,-413.68,-0.3395,0.32333,0.88329,-518.95,#15,0.87396,-0.19314,-0.44597,-22.324,-0.47004,-0.5691,-0.67467,232.48,-0.1235,0.79926,-0.58816,-35.76 > view matrix models > #8,-0.36458,-0.92648,0.093331,459.44,0.74818,-0.23179,0.62169,-581.73,-0.55436,0.29648,0.77768,-351.34,#15,0.78462,-0.36457,-0.50146,14.919,-0.61379,-0.34272,-0.7112,227.41,0.087426,0.86581,-0.49267,-79.925 > hide #!2 models > view matrix models > #8,0.57819,0.26833,0.77052,-801.14,-0.76661,0.50194,0.40046,-53.245,-0.2793,-0.82222,0.49592,108.64,#15,-0.79407,0.16033,-0.5863,155.65,0.23177,0.97157,-0.048217,-103.91,0.5619,-0.17418,-0.80866,19.308 > view matrix models > #8,-0.7143,0.67338,0.19063,-34.966,-0.58668,-0.72466,0.36149,343.36,0.38156,0.14637,0.91268,-788.73,#15,0.1449,0.9661,0.21366,-142.24,0.78369,0.019767,-0.62084,3.6802,-0.60402,0.2574,-0.75426,105.19 > view matrix models > #8,-0.69143,0.71446,0.10711,-10.289,-0.69409,-0.61582,-0.37284,789.27,-0.20042,-0.33214,0.92169,-361.31,#15,0.12387,0.94439,0.30461,-147.11,0.98463,-0.15506,0.080352,-77.431,0.12312,0.28997,-0.94908,33.765 > select subtract #8 2 models selected > show #!1 models > hide #!15 models > hide #!1 models > show #!2 models > show #!12 models > hide #!12 models > hide #!2 models > open 7vd8 Summary of feedback from opening 7vd8 fetched from pdb --- notes | Fetching compressed mmCIF 7vd8 from http://files.rcsb.org/download/7vd8.cif Fetching CCD NA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 7vd8 title: 1.96 A structure of human apoferritin obtained from Talos Arctica microscope [more info...] Chain information for 7vd8 #18 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain | FRIH_HUMAN 5-176 Non-standard residues in 7vd8 #18 --- NA — sodium ion ZN — zinc ion 1248 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > show #!2 models > close #18 > open 8fm3 Summary of feedback from opening 8fm3 fetched from pdb --- notes | Fetching compressed mmCIF 8fm3 from http://files.rcsb.org/download/8fm3.cif Fetching CCD Y26 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/Y26/Y26.cif 8fm3 title: HIV-1 gp120 complex with CJF-III-288 [more info...] Chain information for 8fm3 #18 --- Chain | Description A B C D | Envelope glycoprotein gp120 Non-standard residues in 8fm3 #18 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Y26 — propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate 8fm3 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > hide #!2 models > delete #18/B-D > show #!2 models > close #18 > open 9DU3 Summary of feedback from opening 9DU3 fetched from pdb --- notes | Fetching compressed mmCIF 9du3 from http://files.rcsb.org/download/9du3.cif Fetching CCD A1BCX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/A1BCX/A1BCX.cif 9du3 title: SARS-CoV-2 Mpro in complex with compound 1 [more info...] Chain information for 9du3 #18 --- Chain | Description | UniProt A | 3C-like proteinase nsp5 | R1AB_SARS2 1-306 Non-standard residues in 9du3 #18 --- A1BCX — N-[(2S)-3-cyclopropyl-1-({(2R)-1-hydroxy-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide 9du3 mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide #!2 models > color #18 #29ffafff > show #!2 models > hide #!2 models > close #18 > open 15c8 Summary of feedback from opening 15c8 fetched from pdb --- note | Fetching compressed mmCIF 15c8 from http://files.rcsb.org/download/15c8.cif 15c8 title: Catalytic antibody 5C8, free fab [more info...] Chain information for 15c8 #18 --- Chain | Description | UniProt H | IGG 5C8 FAB (HEAVY CHAIN) | IGH1M_MOUSE 2-226 L | IGG 5C8 FAB (LIGHT CHAIN) | KAC_MOUSE 2-212 > show #!2 models > hide #!2 models > molmap #18 5 onGrid #11 Opened 15c8 map 5 as #19, grid size 256,256,256, pixel 1.06, shown at level 0.102, step 1, values float32 No map chosen to save > save /Users/ZhenGong/Desktop/15C8_5A.mrc models #19 > close #19 > close #18 > open 16GS Summary of feedback from opening 16GS fetched from pdb --- notes | Fetching compressed mmCIF 16gs from http://files.rcsb.org/download/16gs.cif Fetching CCD MES from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/MES/MES.cif Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif 16gs title: Glutathione S-transferase P1-1 apo form 3 [more info...] Chain information for 16gs #18 --- Chain | Description | UniProt A B | GLUTATHIONE S-TRANSFERASE | GSTP1_HUMAN 1-209 Non-standard residues in 16gs #18 --- MES — 2-(N-morpholino)-ethanesulfonic acid SO4 — sulfate ion > show #!13 models > hide #!13 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > molmap #18 5 onGrid #11 Opened 16gs map 5 as #19, grid size 256,256,256, pixel 1.06, shown at level 0.113, step 1, values float32 > save /Users/ZhenGong/Desktop/16GS_5A.mrc models #19 > view #18 > view #19 > hide #18 models > save /Users/ZhenGong/Desktop/16GS_5A.mrc models #19 > open 15c8 15c8 title: Catalytic antibody 5C8, free fab [more info...] Chain information for 15c8 #20 --- Chain | Description | UniProt H | IGG 5C8 FAB (HEAVY CHAIN) | IGH1M_MOUSE 2-226 L | IGG 5C8 FAB (LIGHT CHAIN) | KAC_MOUSE 2-212 > view #20 > hide #!19 models > molmap #20 5 onGrid #11 Opened 15c8 map 5 as #21, grid size 256,256,256, pixel 1.06, shown at level 0.102, step 1, values float32 > hide #20 models > view #21 > save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21 > center #21 Unknown command: center #21 > crosslinks Missing or invalid ""pbonds"" argument: empty atom specifier > ui tool show ""Map Coordinates"" > view #21 > save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21 > ui mousemode right zoom > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!13 models > hide #!13 models > view #21 > hide #!19 models > save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21 > center Unknown command: center > measure center #19 Center of mass grid index for 16GS_5A.mrc = (136.53, 127.02, 146.29) Center of mass xyz scene coordinates for 16GS_5A.mrc = (19.18, 12.10, 17.45) > measure center #21 Center of mass grid index for 15C8_5A.mrc = (173.43, 123.03, 179.26) Center of mass xyz scene coordinates for 15C8_5A.mrc = (58.30, 7.87, 52.40) Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/std_commands/measure_center.py"", line 72, in measure_center areas = vertex_areas(surf.vertices, surf.triangles) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: Array argument has non-numeric values TypeError: Array argument has non-numeric values File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/std_commands/measure_center.py"", line 72, in measure_center areas = vertex_areas(surf.vertices, surf.triangles) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > measure center #21 Center of mass grid index for 15C8_5A.mrc = (173.43, 123.03, 179.26) Center of mass xyz scene coordinates for 15C8_5A.mrc = (58.30, 7.87, 52.40) Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/std_commands/measure_center.py"", line 72, in measure_center areas = vertex_areas(surf.vertices, surf.triangles) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: Array argument has non-numeric values TypeError: Array argument has non-numeric values File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/std_commands/measure_center.py"", line 72, in measure_center areas = vertex_areas(surf.vertices, surf.triangles) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 INTEL-23.0.26 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0) OS Loader Version: 583~900 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 7 days, 20 hours, 5 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL2407WFPHC: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: GM50481P3ENS Mirror: Off Online: Yes Rotation: Supported Adapter Type: Analog VGA or Analog Over DVI-I Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.16 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.6 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504260127 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.9 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.57.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.6 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.14 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.7 pluggy: 1.5.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Analysis fixed all ChimeraX