id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20504 ChimeraX bug report submission ermanno.uboldi@… "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020100ec40 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, 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""ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=6.5G written=126.3M(2%) resident=4727K(0%) swapped_out=121.7M(2%) unallocated=6.4G(98%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 2480K 53 ColorSync 208K 13 CoreAnimation 3520K 180 CoreGraphics 144K 8 CoreServices 624K 2 CoreUI image data 5984K 60 Dispatch continuations 64.0M 1 Foundation 48K 2 Kernel Alloc Once 48K 2 MALLOC 5.3G 680 MALLOC guard page 3712K 4 Mach message 64K 2 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 56.7M 45 Stack 203.5M 45 VM_ALLOCATE 543.2M 539 VM_ALLOCATE (reserved) 384.0M 4 reserved VM address space (unallocated) __AUTH 5936K 654 __AUTH_CONST 90.0M 1046 __CTF 824 1 __DATA 46.9M 1259 __DATA_CONST 61.2M 1296 __DATA_DIRTY 8813K 903 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 634.5M 248 __OBJC_RO 78.4M 1 __OBJC_RW 2570K 1 __TEXT 1.5G 1315 __TEXT (graphics) 4560K 5 __TPRO_CONST 128K 2 dyld private memory 14.4M 114 mapped file 836.5M 119 page table in kernel 4727K 1 shared memory 3248K 29 =========== ======= ======= TOTAL 9.8G 8645 TOTAL, minus reserved VM space 9.4G 8645 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""932a93e8a50bcd05aac9f622376d9cf5b2df3941"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""6813dc6e1e50e5344eb573e9"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000021 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/eruboldi/Downloads/cryosparc_P2_J117_005_volume_map_sharp.mrc Opened cryosparc_P2_J117_005_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 0.573, shown at level 0.0195, step 2, values float32 > volume #1 level 0.09875 > surface dust #1 size 5.73 > open /Users/eruboldi/Downloads/cryosparc_P2_J118_004_volume_map_sharp(2).mrc Opened cryosparc_P2_J118_004_volume_map_sharp(2).mrc as #2, grid size 512,512,512, pixel 0.573, shown at level 0.0181, step 2, values float32 > volume #2 step 1 > volume #1 step 1 > volume #2 level 0.06514 > hide #!1 models > open /Users/eruboldi/Downloads/cryosparc_P2_J119_012_volume_map_sharp(1).mrc Opened cryosparc_P2_J119_012_volume_map_sharp(1).mrc as #3, grid size 512,512,512, pixel 0.573, shown at level 0.0218, step 2, values float32 > volume #3 level 0.05708 > volume #3 step 1 > hide #!2 models > open /Users/eruboldi/Downloads/cryosparc_P2_J112_mask.mrc Opened cryosparc_P2_J112_mask.mrc as #4, grid size 256,256,256, pixel 1.15, shown at level 5e-05, step 1, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_pocket_zone.mrc Opened cryosparc_P2_pocket_zone.mrc as #5, grid size 256,256,256, pixel 1.15, shown at level 0.000153, step 1, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_pocket_zone.mrc Opened cryosparc_P2_pocket_zone.mrc as #6, grid size 256,256,256, pixel 1.15, shown at level 0.000153, step 1, values float32 > close #6 > hide #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!4 models > hide #!5 models > ui tool show ""Map Coordinates"" > show #!2 models > hide #!2 models > hide #!3 models > ui mousemode right pivot > show #!1 models > ui mousemode right ""map eraser"" > select add #6 1 model selected > measure center #6 Center of area of surface eraser sphere #6 = (166.08, 151.77, 139.14) > measure center #6 Center of area of surface eraser sphere #6 = (166.92, 149.37, 144.61) > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > open /Users/eruboldi/Downloads/cryosparc_P2_J41_mask.mrc Opened cryosparc_P2_J41_mask.mrc as #7, grid size 256,256,256, pixel 1.15, shown at level 5e-05, step 1, values float32 > hide #!7 models > show #!7 models > volume #7 level 0.005545 > hide #!7 models > open /Users/eruboldi/Downloads/cryosparc_P2_J49_005_volume_map_sharp.mrc Opened cryosparc_P2_J49_005_volume_map_sharp.mrc as #8, grid size 512,512,512, pixel 0.573, shown at level 0.0183, step 2, values float32 > volume #8 level 0.1004 > close #8 > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/scGPI8_model.cif"" Chain information for scGPI8_model.cif #8 --- Chain | Description A | . Computing secondary structure > ui mousemode right select > select /A:264 8 atoms, 7 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,157.49,0,1,0,26.968,0,0,1,87.466 > view matrix models #8,1,0,0,134.81,0,1,0,21.411,0,0,1,93.877 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.39917,0.092616,0.91219,110.56,-0.8717,-0.34679,-0.34624,15.889,0.28427,-0.93336,0.21916,105.05 > view matrix models > #8,0.66844,0.029165,-0.74319,137.79,-0.41707,-0.81265,-0.40701,22.019,-0.61582,0.58203,-0.53104,100.3 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.66844,0.029165,-0.74319,81.031,-0.41707,-0.81265,-0.40701,74.021,-0.61582,0.58203,-0.53104,142.08 > view matrix models > #8,0.66844,0.029165,-0.74319,176.2,-0.41707,-0.81265,-0.40701,109.79,-0.61582,0.58203,-0.53104,145.03 > view matrix models > #8,0.66844,0.029165,-0.74319,170.13,-0.41707,-0.81265,-0.40701,145.1,-0.61582,0.58203,-0.53104,154.12 > view matrix models > #8,0.66844,0.029165,-0.74319,169.08,-0.41707,-0.81265,-0.40701,143.32,-0.61582,0.58203,-0.53104,156.84 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.71668,0.083033,-0.69244,169.12,-0.3634,-0.80298,-0.47241,144.52,-0.59524,0.5902,-0.5453,157.2 > view matrix models > #8,0.69884,0.12238,-0.70473,169,-0.31357,-0.83312,-0.45563,144.96,-0.64288,0.53939,-0.54384,156.69 > view matrix models > #8,0.72161,0.10655,-0.68405,169.08,-0.33667,-0.80937,-0.48123,144.91,-0.60492,0.57756,-0.54818,157.12 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.72161,0.10655,-0.68405,168.56,-0.33667,-0.80937,-0.48123,145.76,-0.60492,0.57756,-0.54818,159.03 > fitmap #8 inMap #1 Fit molecule scGPI8_model.cif (#8) to map cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms average map value = 0.02028, steps = 296 shifted from previous position = 5.64 rotated from previous position = 7.13 degrees atoms outside contour = 5147, contour level = 0.098752 Position of scGPI8_model.cif (#8) relative to cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.71779636 0.21765195 -0.66135923 165.63719187 -0.23155425 -0.82118933 -0.52156565 149.74454187 -0.65662092 0.52751846 -0.53904847 161.93839117 Axis 0.91926437 -0.00415196 -0.39361883 Axis point 0.00000000 41.75342475 142.01205706 Rotation angle (degrees) 145.20717960 Shift along axis 87.90063538 > view matrix models > #8,0.7178,0.21765,-0.66136,165.66,-0.23155,-0.82119,-0.52157,155.98,-0.65662,0.52752,-0.53905,155.99 > fitmap #8 inMap #1 Fit molecule scGPI8_model.cif (#8) to map cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms average map value = 0.02302, steps = 152 shifted from previous position = 3.76 rotated from previous position = 5.69 degrees atoms outside contour = 5134, contour level = 0.098752 Position of scGPI8_model.cif (#8) relative to cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.74196785 0.23510976 -0.62785916 163.47744822 -0.26000535 -0.76229400 -0.59270995 156.35121066 -0.61796516 0.60301847 -0.50446784 152.71826487 Axis 0.92389946 -0.00764476 -0.38255894 Axis point 0.00000000 41.55591256 141.41207239 Rotation angle (degrees) 139.67596948 Shift along axis 91.41772192 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.46974,0.36786,-0.80251,161.86,-0.61097,-0.52071,-0.59631,152.19,-0.63723,0.77042,-0.01985,147.94 > ui tool show ""Side View"" > view matrix models > #8,0.71071,0.2295,-0.665,163.47,-0.50958,-0.48375,-0.71156,154.35,-0.485,0.84458,-0.22686,151.48 > fitmap #8 inMap #1 Fit molecule scGPI8_model.cif (#8) to map cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms average map value = 0.06134, steps = 112 shifted from previous position = 2.45 rotated from previous position = 5.83 degrees atoms outside contour = 4111, contour level = 0.098752 Position of scGPI8_model.cif (#8) relative to cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.77375979 0.22909923 -0.59060083 163.73360311 -0.45927231 -0.43925139 -0.77209272 156.75909933 -0.43630808 0.86866091 -0.23465612 151.75385877 Axis 0.91868396 -0.08639096 -0.38543014 Axis point -0.00000000 25.08904811 165.03396707 Rotation angle (degrees) 116.74842283 Shift along axis 78.38635533 > select add #8 5770 atoms, 5908 bonds, 743 residues, 1 model selected > select subtract #8 Nothing selected > select add #8 5770 atoms, 5908 bonds, 743 residues, 1 model selected > volume zone #1 nearAtoms sel newMap true Opened cryosparc_P2_J117_005_volume_map_sharp.mrc zone as #9, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > view matrix models > #8,0.22212,-0.67397,-0.70457,159.33,-0.97502,-0.15487,-0.15923,145.08,-0.0018018,0.72234,-0.69153,160.97 > ui mousemode right translate > select subtract #8 Nothing selected > ui mousemode right select > select clear > ui mousemode right translate > volume #9 level 0.1271 > volume #9 level 0.1172 > molmap #9 4.5 No atoms specified > ui mousemode right select Drag select of eraser sphere, 68 of 1000 triangles, 403 residues, 9 cryosparc_P2_J117_005_volume_map_sharp.mrc zone > select subtract #9 3104 atoms, 403 residues, 2 models selected Drag select of eraser sphere, 455 residues, 9 cryosparc_P2_J117_005_volume_map_sharp.mrc zone > molmap sel 4.5 Opened scGPI8_model.cif map 4.5 as #10, grid size 57,59,59, pixel 1.5, shown at level 0.1, step 1, values float32 > molmap sel 10 Opened scGPI8_model.cif map 10 as #10, grid size 36,37,37, pixel 3.33, shown at level 0.0644, step 1, values float32 > select subtract #9 3520 atoms, 455 residues, 2 models selected > molmap sel 15 Opened scGPI8_model.cif map 15 as #10, grid size 30,31,31, pixel 5, shown at level 0.0465, step 1, values float32 > molmap sel 2- Missing or invalid ""resolution"" argument: Expected a number > molmap sel 20 Opened scGPI8_model.cif map 20 as #10, grid size 27,28,28, pixel 6.67, shown at level 0.0343, step 1, values float32 > rename #10 mask_TMDs > volume #10 level 0.06766 > hide #!9 models > select add #8 5770 atoms, 5908 bonds, 743 residues, 2 models selected > select subtract #8 1 model selected > volume #10 color #b2ffff9d > volume #10 level 0.04401 > volume #10 level 0.045 > save ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" > models #10 > close #6 > resample #10 512 Unknown command: resample #10 512 > volume resample #10 512 Expected a keyword > volume resample #10 onGrid #1 Opened mask_TMDs.mrc resampled as #6, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > save ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" > models #10 > save ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" > models #6 > close #11 > volume #6 color #b2b2ff89 > open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask.mrc Opened cryosparc_P2_J126_mask.mrc as #11, grid size 512,512,512, pixel 0.573, shown at level 0.39, step 2, values float32 > hide #!11 models > open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask(1).mrc Opened cryosparc_P2_J126_mask(1).mrc as #12, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > show #!11 models > hide #!11 models > volume #12 step 1 > volume #11 step 1 > volume #12 color #ffb2b285 > volume #11 color #ffb2ff83 > hide #!12 models > show #!12 models > hide #!11 models > show #!11 models > hide #!11 models > open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask(2).mrc Opened cryosparc_P2_J126_mask(2).mrc as #13, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > close #13 > show #!11 models > hide #!11 models > close #11 > open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc > /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp.mrc > /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc > /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp.mrc > /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp.mrc > /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp.mrc Opened cryosparc_P2_J130_map_sharp.mrc as #11.1, grid size 512,512,512, pixel 0.573, shown at level 0.0158, step 2, values float32 Opened cryosparc_P2_J134_map_sharp.mrc as #11.2, grid size 512,512,512, pixel 0.573, shown at level 0.0156, step 2, values float32 Opened cryosparc_P2_J133_map_sharp.mrc as #11.3, grid size 512,512,512, pixel 0.573, shown at level 0.0164, step 2, values float32 Opened cryosparc_P2_J132_map_sharp.mrc as #11.4, grid size 512,512,512, pixel 0.573, shown at level 0.0157, step 2, values float32 Opened cryosparc_P2_J131_map_sharp.mrc as #11.5, grid size 512,512,512, pixel 0.573, shown at level 0.0192, step 2, values float32 Opened cryosparc_P2_J135_map_sharp.mrc as #11.6, grid size 512,512,512, pixel 0.573, shown at level 0.015, step 2, values float32 > volume #11.5 step 1 > volume #11.4 step 1 > volume #11.2 step 1 > volume #11.1 step 1 > close #12 > hide #!11.6 models > hide #!11.5 models > hide #!11.4 models > hide #!11.3 models > hide #!11.2 models > volume #11.1 level 0.02752 > hide #!6 models > volume #11.2 level 0.03347 > volume #11.3 level 0.05914 > hide #8 models > volume #11.4 level 0.03018 > volume #11.5 level 0.1208 > volume #11.3 level 0.07859 > volume #11.5 level 0.1111 > close #11 > open /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp(1).mrc Opened cryosparc_P2_J134_map_sharp(1).mrc as #11, grid size 512,512,512, pixel 0.573, shown at level 0.0169, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp(1).mrc Opened cryosparc_P2_J135_map_sharp(1).mrc as #12, grid size 512,512,512, pixel 0.573, shown at level 0.0175, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(1).mrc Opened cryosparc_P2_J132_map_sharp(1).mrc as #13, grid size 512,512,512, pixel 0.573, shown at level 0.0159, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(1).mrc Opened cryosparc_P2_J131_map_sharp(1).mrc as #14, grid size 512,512,512, pixel 0.573, shown at level 0.0156, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp(1).mrc Opened cryosparc_P2_J130_map_sharp(1).mrc as #15, grid size 512,512,512, pixel 0.573, shown at level 0.0152, step 2, values float32 > volume #15 step 1 > volume #14 step 1 > volume #13 step 1 > volume #11 step 1 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > open /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc Opened cryosparc_P2_J133_map_sharp.mrc as #16, grid size 512,512,512, pixel 0.573, shown at level 0.0164, step 2, values float32 > volume #16 step 1 > volume #16 level 0.05701 > volume #15 level 0.04022 > volume #12 level 0.04298 > select clear > ui mousemode right translate > volume #11 level 0.05933 > volume #13 level 0.05099 > volume #11 level 0.08054 > volume #11 level 0.06781 > volume #12 level 0.04722 > surface dust #12 size 5.73 > volume #14 level 0.0492 > volume #15 level 0.04738 > volume #16 level 0.07733 > show #!11 models > show #!13 models > close #11-16 > open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp(1).mrc Opened cryosparc_P2_J130_map_sharp(1).mrc as #11, grid size 512,512,512, pixel 0.573, shown at level 0.0152, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(1).mrc Opened cryosparc_P2_J132_map_sharp(1).mrc as #12, grid size 512,512,512, pixel 0.573, shown at level 0.0159, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(1).mrc Opened cryosparc_P2_J131_map_sharp(1).mrc as #13, grid size 512,512,512, pixel 0.573, shown at level 0.0156, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc Opened cryosparc_P2_J133_map_sharp.mrc as #14, grid size 512,512,512, pixel 0.573, shown at level 0.0164, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp(1).mrc Opened cryosparc_P2_J134_map_sharp(1).mrc as #15, grid size 512,512,512, pixel 0.573, shown at level 0.0169, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp(1).mrc Opened cryosparc_P2_J135_map_sharp(1).mrc as #16, grid size 512,512,512, pixel 0.573, shown at level 0.0175, step 2, values float32 > volume #16 level 0.0345 > volume #15 level 0.04532 > volume #14 level 0.0747 > volume #13 level 0.05845 > volume #12 level 0.06065 > volume #11 level 0.03571 > volume #11 step 1 > volume #12 step 1 > volume #13 step 1 > volume #14 step 1 > volume #15 step 1 > volume #16 step 1 > hide #!16 models > hide #!15 models > hide #!14 models > show #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > show #8 models > hide #8 models > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #17 --- Chain | Description A | No description available > ui mousemode right select Drag select of 161 residues > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models #17,1,0,0,142.14,0,1,0,84.67,0,0,1,142.07 > view matrix models #17,1,0,0,153.13,0,1,0,66.462,0,0,1,107.32 > view matrix models #17,1,0,0,150.69,0,1,0,73.896,0,0,1,123 > ui mousemode right ""rotate selected models"" > view matrix models > #17,0.7091,0.5895,-0.38688,159.02,-0.7044,0.61686,-0.35115,76.227,0.031644,0.52152,0.85265,127.87 > ui mousemode right ""translate selected models"" > view matrix models > #17,0.7091,0.5895,-0.38688,155.41,-0.7044,0.61686,-0.35115,135.12,0.031644,0.52152,0.85265,158.08 > view matrix models > #17,0.7091,0.5895,-0.38688,142.81,-0.7044,0.61686,-0.35115,146.19,0.031644,0.52152,0.85265,146.87 > view matrix models > #17,0.7091,0.5895,-0.38688,162.26,-0.7044,0.61686,-0.35115,142.91,0.031644,0.52152,0.85265,142.3 > view matrix models > #17,0.7091,0.5895,-0.38688,158.96,-0.7044,0.61686,-0.35115,148.45,0.031644,0.52152,0.85265,133.95 > ui mousemode right ""rotate selected models"" > view matrix models > #17,0.86721,0.076857,-0.49197,159.41,-0.40389,0.68644,-0.60471,154.42,0.29123,0.72311,0.62633,139.8 > ui mousemode right ""translate selected models"" > view matrix models > #17,0.86721,0.076857,-0.49197,161.04,-0.40389,0.68644,-0.60471,150.26,0.29123,0.72311,0.62633,138.85 > view matrix models > #17,0.86721,0.076857,-0.49197,164.61,-0.40389,0.68644,-0.60471,153.12,0.29123,0.72311,0.62633,137.47 > fitmap #17 inMap #14 Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc (#14) using 3443 atoms average map value = 0.0322, steps = 104 shifted from previous position = 4.83 rotated from previous position = 9.24 degrees atoms outside contour = 2764, contour level = 0.0747 Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc (#14) coordinates: Matrix rotation and translation 0.87996734 -0.01021308 -0.47492438 161.34502821 -0.37959597 0.58595191 -0.71593803 152.81620256 0.28559478 0.81028147 0.51174170 143.32772345 Axis 0.87474587 -0.43588815 -0.21171015 Axis point 0.00000000 -32.33354734 259.04742590 Rotation angle (degrees) 60.73625898 Shift along axis 44.18119100 > view matrix models > #17,0.87997,-0.010213,-0.47492,167.94,-0.3796,0.58595,-0.71594,195.35,0.28559,0.81028,0.51174,181.69 > view matrix models > #17,0.87997,-0.010213,-0.47492,169.74,-0.3796,0.58595,-0.71594,108.14,0.28559,0.81028,0.51174,147.27 > ui mousemode right ""rotate selected models"" > view matrix models > #17,0.77614,-0.078854,-0.6256,171.83,-0.55134,0.39659,-0.73399,107.1,0.30599,0.9146,0.26434,152.26 > view matrix models > #17,-0.37438,0.15839,0.91365,140.62,-0.40471,-0.91442,-0.0073125,89.199,0.8343,-0.3725,0.40644,146.47 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.37438,0.15839,0.91365,118.88,-0.40471,-0.91442,-0.0073125,119.3,0.8343,-0.3725,0.40644,160.22 > view matrix models > #17,-0.37438,0.15839,0.91365,111.85,-0.40471,-0.91442,-0.0073125,132.58,0.8343,-0.3725,0.40644,149.17 > view matrix models > #17,-0.37438,0.15839,0.91365,118.67,-0.40471,-0.91442,-0.0073125,130.28,0.8343,-0.3725,0.40644,145.26 > view matrix models > #17,-0.37438,0.15839,0.91365,118.59,-0.40471,-0.91442,-0.0073125,132.96,0.8343,-0.3725,0.40644,148.08 > view matrix models > #17,-0.37438,0.15839,0.91365,120.27,-0.40471,-0.91442,-0.0073125,133.02,0.8343,-0.3725,0.40644,148.35 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.31644,0.12299,0.9406,119.85,-0.34499,-0.93858,0.0066597,132.88,0.88366,-0.32239,0.33944,149.94 > view matrix models > #17,-0.30831,0.21146,0.92749,120.47,-0.24454,-0.95983,0.13754,130.78,0.91932,-0.1844,0.34764,150.47 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.30831,0.21146,0.92749,118.41,-0.24454,-0.95983,0.13754,133.79,0.91932,-0.1844,0.34764,147.82 > fitmap #17 inMap #14 Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc (#14) using 3443 atoms average map value = 0.02918, steps = 96 shifted from previous position = 2.3 rotated from previous position = 4.18 degrees atoms outside contour = 2814, contour level = 0.0747 Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc (#14) coordinates: Matrix rotation and translation -0.30371940 0.28188313 0.91010792 119.70951532 -0.27198365 -0.94113421 0.20072690 130.55899966 0.91311522 -0.18656982 0.36250832 146.39703125 Axis -0.57304943 -0.00444965 -0.81950873 Axis point 22.44753544 63.68027872 0.00000000 Rotation angle (degrees) 160.24942846 Shift along axis -189.15405591 > view matrix models > #17,-0.30372,0.28188,0.91011,121.6,-0.27198,-0.94113,0.20073,134.92,0.91312,-0.18657,0.36251,150.43 > fitmap #17 inMap #14 Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc (#14) using 3443 atoms average map value = 0.03012, steps = 2000 shifted from previous position = 2.91 rotated from previous position = 6.92 degrees atoms outside contour = 2795, contour level = 0.0747 Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc (#14) coordinates: Matrix rotation and translation -0.28587070 0.19495150 0.93822804 120.89123326 -0.17562846 -0.97316168 0.14869765 137.42462625 0.94203640 -0.12227125 0.31243744 149.09858833 Axis -0.59022410 -0.00829537 -0.80719681 Axis point 15.72201488 67.43678169 0.00000000 Rotation angle (degrees) 166.72956931 Shift along axis -192.84481348 > view matrix models > #17,-0.28587,0.19495,0.93823,139.12,-0.17563,-0.97316,0.1487,118.41,0.94204,-0.12227,0.31244,147.12 > view matrix models > #17,-0.28587,0.19495,0.93823,139.32,-0.17563,-0.97316,0.1487,86.847,0.94204,-0.12227,0.31244,137.46 > view matrix models > #17,-0.28587,0.19495,0.93823,113,-0.17563,-0.97316,0.1487,93.591,0.94204,-0.12227,0.31244,147.1 > view matrix models > #17,-0.28587,0.19495,0.93823,99.122,-0.17563,-0.97316,0.1487,122.11,0.94204,-0.12227,0.31244,146.82 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.094315,-0.13063,0.98694,97.633,-0.72905,-0.66601,-0.15782,126.91,0.67793,-0.73441,-0.032419,149.72 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.094315,-0.13063,0.98694,120.11,-0.72905,-0.66601,-0.15782,128.35,0.67793,-0.73441,-0.032419,158.3 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.6247,0.067644,0.77793,122.79,-0.62188,-0.64559,-0.44326,134.01,0.47224,-0.76068,0.44537,148.76 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.6247,0.067644,0.77793,115.8,-0.62188,-0.64559,-0.44326,141.69,0.47224,-0.76068,0.44537,140.13 > view matrix models > #17,-0.6247,0.067644,0.77793,124.23,-0.62188,-0.64559,-0.44326,142.06,0.47224,-0.76068,0.44537,138.23 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.68677,-0.16302,0.70836,124.35,-0.47837,-0.63236,-0.60933,145.65,0.54727,-0.75732,0.35631,140.13 > view matrix models > #17,-0.66484,-0.1705,0.72727,124.06,-0.62419,-0.40803,-0.66626,147.06,0.41034,-0.89691,0.16485,142.57 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.66484,-0.1705,0.72727,123.75,-0.62419,-0.40803,-0.66626,147,0.41034,-0.89691,0.16485,146.7 > view matrix models > #17,-0.66484,-0.1705,0.72727,125.88,-0.62419,-0.40803,-0.66626,147.64,0.41034,-0.89691,0.16485,148.06 > view matrix models > #17,-0.66484,-0.1705,0.72727,122.2,-0.62419,-0.40803,-0.66626,142.31,0.41034,-0.89691,0.16485,139.22 > view matrix models > #17,-0.66484,-0.1705,0.72727,120.22,-0.62419,-0.40803,-0.66626,144.44,0.41034,-0.89691,0.16485,134.78 > view matrix models > #17,-0.66484,-0.1705,0.72727,131.28,-0.62419,-0.40803,-0.66626,126.22,0.41034,-0.89691,0.16485,93.657 > view matrix models > #17,-0.66484,-0.1705,0.72727,127.89,-0.62419,-0.40803,-0.66626,155.18,0.41034,-0.89691,0.16485,135.02 > view matrix models > #17,-0.66484,-0.1705,0.72727,131.96,-0.62419,-0.40803,-0.66626,153.58,0.41034,-0.89691,0.16485,142.61 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.52787,-0.12509,0.84007,130.58,-0.57146,-0.67941,-0.46025,148.94,0.62832,-0.72301,0.28716,141.86 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.52787,-0.12509,0.84007,129.09,-0.57146,-0.67941,-0.46025,150.21,0.62832,-0.72301,0.28716,138.84 > fitmap #17 inMap #14 Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc (#14) using 3443 atoms average map value = 0.08104, steps = 160 shifted from previous position = 4.56 rotated from previous position = 16.8 degrees atoms outside contour = 1744, contour level = 0.0747 Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc (#14) coordinates: Matrix rotation and translation -0.73804004 -0.17945467 0.65045592 128.55925345 -0.43846612 -0.60517067 -0.66446664 154.21643461 0.51287849 -0.77560587 0.36795540 139.89743742 Axis -0.35435943 0.43865571 -0.82583931 Axis point 43.58978446 109.70313086 0.00000000 Rotation angle (degrees) 170.97780258 Shift along axis -93.44106784 > surface dust #15 size 5.73 > ui mousemode right translate > volume #15 level 0.007121 > volume #15 level 0.06654 > volume #16 level 0.06109 > surface dust #16 size 5.73 > select add #17 3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected > select subtract #17 Nothing selected > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > surface dust #14 size 5.73 > hide #!14 models > show #!13 models > surface dust #13 size 5.73 > volume #13 level 0.06591 > open /Users/eruboldi/Downloads/cryosparc_P2_J93_003_volume_map_sharp(2).mrc Opened cryosparc_P2_J93_003_volume_map_sharp(2).mrc as #18, grid size 512,512,512, pixel 0.573, shown at level 0.0319, step 2, values float32 > volume #18 step 1 > volume #18 level 0.09101 > surface dust #13 size 5.73 > surface dust #18 size 5.73 > color #18 #ffb2b281 models > color #18 #ffb2b29f models > color #18 #ffb2b2c2 models > color #17 #c4b92aff > color #17 #fbed35ff > color #18 #3649f7c2 models > color #18 #3649f7b1 models > color #18 #3649f7b3 models > color #17 #fffb00ff > color #17 #fffc79ff > color #17 #fffb00ff > color #17 #acab39ff > color #17 #acab3aff > color #18 #e6f0edb3 models > color #18 #8c9290b3 models > surface dust #11 size 5.73 > surface dust #18 size 5.73 > volume #11 level 0.03571 > volume #11 level 0.05717 > hide #!17 models > select add #17 3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected > show #!17 models > volume zone #18 nearAtoms sel newMap true Opened cryosparc_P2_J93_003_volume_map_sharp(2).mrc zone as #19, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > rename #19 new_mask_part_sub > molmap #19 15 No atoms specified > volume #19 level 0.1103 > volume #19 level 0.07817 > volume gaussian #19 sDev 3 Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > color #20 #e5bf99cc models > color #20 #e5bf9995 models > color #20 #e5bf9982 models > volume gaussian #19 sDev 1 Opened new_mask_part_sub gaussian as #21, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > close #20 > volume gaussian #19 sDev 2 Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > close #20 > close #21 > volume gaussian #19 sDev 2 Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > volume gaussian #19 sDev 1.5 Opened new_mask_part_sub gaussian as #21, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > hide #!20 models > show #!20 models > hide #!20 models > hide #!21 models > show #!19 models > hide #!19 models > show #!19 models > show #!20 models > show #!21 models > hide #!21 models > hide #!20 models > close #21 > close #20 No map chosen to save > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/mask_after_loc_ref_part_subtr.mrc"" models #19 > volume #19 level 0.078 > volume #19 level 0.08 > open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask.mrc Opened cryosparc_P2_J138_mask.mrc as #20, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > volume #20 level 0.1091 > hide #!20 models > show #!20 models > hide #!19 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > close #19 > open ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/mask_after_loc_ref_part_subtr.mrc"" Opened mask_after_loc_ref_part_subtr.mrc as #19, grid size 512,512,512, pixel 0.573, shown at level 0.000229, step 2, values float32 > volume #15 level 0.07927 > volume #19 level 0.06016 > show #!18 models > volume #19 level 0.06615 > volume #19 step 1 > volume #19 level 0.08541 > open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc Opened cryosparc_P2_J130_map_sharp.mrc as #21, grid size 512,512,512, pixel 0.573, shown at level 0.0344, step 2, values float32 > volume #21 step 1 > volume #21 level 0.08033 > surface dust #18 size 5.73 > surface dust #20 size 5.73 > surface dust #19 size 5.73 > surface dust #21 size 5.73 > hide #!19 models > hide #!20 models > show #!20 models > hide #!21 models > hide #!20 models > show #!20 models > close #20 > show #!21 models > close #21 > open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc Opened cryosparc_P2_J130_map_sharp.mrc as #20, grid size 512,512,512, pixel 0.573, shown at level 0.0344, step 2, values float32 > volume #20 step 1 > volume #20 level 0.08033 > surface dust #18 size 5.73 > surface dust #20 size 5.73 > volume #20 level 0.08797 > hide #!18 models > show #!18 models > color #20 #ffb2b284 models > ui tool show ""Model Panel"" > ui tool show Log > select subtract #17 Nothing selected > color #18 #8c9290ff models > color #20 #ffb2b2ff models > hide #!20 models > show #!20 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!20 models > show #!20 models > lighting simple > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting flat > lighting simple > graphics silhouettes false > graphics silhouettes true > rename #20 -200 > open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp.mrc Opened cryosparc_P2_J131_map_sharp.mrc as #21, grid size 512,512,512, pixel 0.573, shown at level 0.0192, step 2, values float32 > open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp.mrc Opened cryosparc_P2_J132_map_sharp.mrc as #22, grid size 512,512,512, pixel 0.573, shown at level 0.0147, step 2, values float32 > volume #21 step 1 > volume #21 level 0.03556 > volume #22 step 1 > volume #22 level 0.04319 > volume #21 level 0.05737 > rename #21 -150, rename #22 -100 Expected a keyword > rename #21 -150 & rename #22 -100 Expected a keyword > ui tool show Log > rename #21 -150 > rename #22 -100 > hide #!18 models > cofr #17 > volume #22 level 0.05385 > hide #!21 models > volume #22 level 0.05385 > hide #!22 models > show #!21 models > volume #21 level 0.07919 > show #!20 models > volume #21 level 0.088 > volume #21 level 0.06074 > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > close #21 > close #22 > close #16 > close #12-13 > close #15 > close #11 > show #!14 models > volume #14 level 0.05179 > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > close #14 > open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(2).mrc Opened cryosparc_P2_J131_map_sharp(2).mrc as #11, grid size 512,512,512, pixel 0.573, shown at level 0.0453, step 2, values float32 > volume #11 step 1 > open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(2).mrc Opened cryosparc_P2_J132_map_sharp(2).mrc as #12, grid size 512,512,512, pixel 0.573, shown at level 0.0266, step 2, values float32 > volume #11 level 0.1081 > rename #11 -220 > rename #12 -180 > volume #12 level 0.06078 > surface dust #20 size 5.73 > surface dust #11 size 5.73 > surface dust #12 size 5.73 > open /Users/eruboldi/Downloads/cryosparc_P2_J41_mask(1).mrc Opened cryosparc_P2_J41_mask(1).mrc as #13, grid size 256,256,256, pixel 1.15, shown at level 5e-05, step 1, values float32 > hide #!13 models > show #!13 models > color #13 #b2b2b288 models > open ""/Users/eruboldi/Downloads/cryosparc_P2_Mask HRHAIR recon.mrc"" Opened cryosparc_P2_Mask HRHAIR recon.mrc as #14, grid size 256,256,256, pixel 1.15, shown at level 3.23e-05, step 1, values float32 > hide #!14 models > show #!14 models > hide #!13 models > hide #!11 models > show #!11 models > color #14 #ffffb297 models > hide #!11 models > close #14 > molmap #17 15 Opened ctGWT1_noGPF.pdb map 15 as #14, grid size 30,31,31, pixel 5, shown at level 0.0451, step 1, values float32 > color #14 #b2ffff9d models > open ""/Users/eruboldi/Downloads/cryosparc_P2_Mask HRHAIR recon.mrc"" Opened cryosparc_P2_Mask HRHAIR recon.mrc as #15, grid size 256,256,256, pixel 1.15, shown at level 3.23e-05, step 1, values float32 > show #!20 models > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" Opened mask_TMDs.mrc as #16, grid size 512,512,512, pixel 0.573, shown at level 0.00261, step 2, values float32 > close #16 > close #15 > close #20 > resample #14 ongrid #18 Unknown command: resample #14 ongrid #18 > volume resample #14 onGrid #18 Opened ctGWT1_noGPF.pdb map 15 resampled as #15, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > color #15 #ffb2b295 models > save ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" > models #15 > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"" Opened mask_TMDs.mrc as #16, grid size 512,512,512, pixel 0.573, shown at level 0.000331, step 2, values float32 > volume #16 level 0.04252 > volume #15 level 0.0425 > open /Volumes/mpb-1/eruboldi/cryosparc/CS-scgpi17-cu-10-mg- > ml/uploads/resampled_helices_mask.mrc Opened resampled_helices_mask.mrc as #20, grid size 256,256,256, pixel 1.15, shown at level 1.08e-05, step 1, values float32 > open /Volumes/mpb-1/eruboldi/cryosparc/CS-scgpi17-cu-10-mg- > ml/uploads/resampled_helices_mask.mrc Opened resampled_helices_mask.mrc as #21, grid size 256,256,256, pixel 1.15, shown at level 1.08e-05, step 1, values float32 > hide #!20 models > show #!20 models > close #21 > hide #!20 models > show #!20 models > hide #!17 models > hide #!16 models > show #!17 models > hide #!20 models > open /Users/eruboldi/Downloads/cryosparc_P2_mask_TMDs.mrc Opened cryosparc_P2_mask_TMDs.mrc as #21, grid size 512,512,512, pixel 0.573, shown at level 0.000331, step 2, values float32 > volume #21 level 0.04252 > close #20 > open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(1).mrc Opened cryosparc_P2_J138_mask(1).mrc as #20, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > hide #!21 models > volume #20 color #b2b2b27c > volume #20 step 1 > volume #21 level 0.08309 > volume #21 step 1 > volume #21 level 0.07821 > volume #21 color #cccc997f > volume #21 level 0.1018 > volume #21 level 0.05623 > volume #21 level 0.136 > volume #21 level 0.13 > rename #20 0.0425 > open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(2).mrc Opened cryosparc_P2_J138_mask(2).mrc as #22, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > color #22 #ffffb2b7 models > open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(4).mrc Opened cryosparc_P2_J138_mask(4).mrc as #23, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > color #23 #b2ffff92 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models Unsupported scale factor (0.000000) detected on Display1 > open /Users/eruboldi/Downloads/cryosparc_P2_J89_006_volume_map_sharp.mrc Opened cryosparc_P2_J89_006_volume_map_sharp.mrc as #24, grid size 512,512,512, pixel 0.573, shown at level 0.0204, step 2, values float32 > volume #24 step 1 > volume #24 level 0.05188 > hide #!22 models > hide #!21 models > volume #24 level 0.1148 > open /Users/eruboldi/Downloads/cryosparc_P2_J49_005_volume_map_sharp(1).mrc Opened cryosparc_P2_J49_005_volume_map_sharp(1).mrc as #25, grid size 512,512,512, pixel 0.573, shown at level 0.0183, step 2, values float32 > volume #25 step 1 > volume #25 level 0.09151 > surface dust #24 size 5.73 > surface dust #25 size 5.73 > hide #!25 models > show #!25 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > open /Users/eruboldi/Downloads/cryosparc_P2_J112_mask(1).mrc Opened cryosparc_P2_J112_mask(1).mrc as #26, grid size 256,256,256, pixel 1.15, shown at level 5e-05, step 1, values float32 > hide #!25 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > close #26 > open /Users/eruboldi/Downloads/cryosparc_P2_J139_003_volume_map_sharp.mrc Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #26, grid size 512,512,512, pixel 0.573, shown at level 0.0261, step 2, values float32 > volume #26 step 1 > volume #26 level 0.02609 > volume #26 level 0.05532 > volume #26 level 0.1503 > surface dust #26 size 5.73 > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.4.6 which is incompatible. scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.6 which is incompatible. \--- pip standard output: \--- \--- pyKVFinder module installed from PyPi repository. > kvfinder #8 31 cavities found for scGPI8_model.cif #8 scGPI8_model.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 8.1.2 | | 2901.31 | 2117.49 | 13432 | 18.09 | 5.38 8.1.14 | | 2148.98 | 1533.78 | 9949 | 8.16 | 2.56 8.1.3 | | 67.18 | 102.2 | 311 | 2.47 | 0.63 8.1.13 | | 65.66 | 76.82 | 304 | 3 | 1.02 8.1.11 | | 63.07 | 83.75 | 292 | 0 | 0 8.1.8 | | 47.95 | 62.18 | 222 | 2.55 | 1.16 8.1.17 | | 46.22 | 67.66 | 214 | 1.9 | 0.47 8.1.22 | | 45.58 | 74.53 | 211 | 0 | 0 8.1.5 | | 31.54 | 47.34 | 146 | 3.06 | 1.36 8.1.4 | | 31.32 | 52.92 | 145 | 0 | 0 8.1.28 | | 30.24 | 55.56 | 140 | 0 | 0 8.1.15 | | 29.81 | 34.16 | 138 | 1.8 | 0.6 8.1.9 | | 28.94 | 48.7 | 134 | 0 | 0 8.1.30 | | 21.17 | 39.07 | 98 | 0 | 0 8.1.10 | | 19.01 | 38.34 | 88 | 0 | 0 8.1.20 | | 17.06 | 17.03 | 79 | 0.85 | 0.25 8.1.21 | | 16.85 | 32.3 | 78 | 0 | 0 8.1.6 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.7 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.12 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.19 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.23 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.24 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.27 | | 12.31 | 29.54 | 57 | 0 | 0 8.1.25 | | 11.23 | 19.05 | 52 | 1.7 | 0.5 8.1.18 | | 10.15 | 17.89 | 47 | 1.2 | 0.32 8.1.1 | | 9.5 | 17.61 | 44 | 1.2 | 0.34 8.1.16 | | 9.29 | 15.01 | 43 | 0.85 | 0.29 8.1.26 | | 8.64 | 13.16 | 40 | 0.85 | 0.19 8.1.29 | | 8.42 | 16.15 | 39 | 1.34 | 0.48 8.1.31 | | 7.78 | 16.91 | 36 | 1.04 | 0.38 Populating font family aliases took 150 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > hide #!17 models > show #!17 models > ui tool show ""Find Cavities"" > kvfinder #17 16 cavities found for ctGWT1_noGPF.pdb #17 ctGWT1_noGPF.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 17.2.3 | | 2935.44 | 2126.31 | 13590 | 18.09 | 5.36 17.2.13 | | 412.78 | 309.39 | 1911 | 5.2 | 1.44 17.2.14 | | 67.18 | 72.72 | 311 | 3 | 1.04 17.2.12 | | 61.34 | 82.94 | 284 | 0 | 0 17.2.2 | | 42.55 | 72.32 | 197 | 3.06 | 0.81 17.2.8 | | 33.48 | 45.86 | 155 | 2.16 | 0.96 17.2.9 | | 30.24 | 48.47 | 140 | 0 | 0 17.2.5 | | 29.59 | 43.28 | 137 | 3.06 | 1.25 17.2.4 | | 28.3 | 49.03 | 131 | 0 | 0 17.2.10 | | 17.28 | 36.68 | 80 | 0 | 0 17.2.6 | | 14.04 | 25.09 | 65 | 1.2 | 0.25 17.2.7 | | 12.31 | 29.54 | 57 | 0 | 0 17.2.11 | | 12.31 | 29.54 | 57 | 0 | 0 17.2.16 | | 12.31 | 29.54 | 57 | 0 | 0 17.2.1 | | 9.29 | 17.04 | 43 | 1.2 | 0.35 17.2.15 | | 7.56 | 14.57 | 35 | 0.85 | 0.2 > hide #!26 models > mlp #17.2.1-16#!17 Map values for surface ""ctGWT1_noGPF.pdb_A SES surface"": minimum -26.61, mean -0.3621, maximum 24.49 To also show corresponding color key, enter the above mlp command and add key true > ui tool show ""Side View"" > hide #!17.2 models > hide #!17.3 models > show #17.3 models > hide #17.3 models > show #!26 models > open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(4).mrc Opened cryosparc_P2_J138_mask(4).mrc as #27, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > color #27 #99bfe57b models > hide #!27 models > open /Users/eruboldi/Downloads/cryosparc_P2_J141_004_volume_map_sharp.mrc Opened cryosparc_P2_J141_004_volume_map_sharp.mrc as #28, grid size 512,512,512, pixel 0.573, shown at level 0.0271, step 2, values float32 > volume #28 step 1 > volume #28 level 0.07878 > surface dust #26 size 5.73 > surface dust #28 size 5.73 > hide #!26 models > show #!26 models > hide #!28 models > show #!28 models > volume #28 level 0.1111 > hide #!26 models > show #!26 models > hide #!28 models > show #!28 models > hide #!28 models > volume #26 level 0.1211 > show #!28 models > hide #!28 models > show #!28 models > hide #!28 models > hide #!26 models > show #!28 models > show #!26 models > hide #!28 models > show #!28 models > hide #!26 models > open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask.mrc Opened cryosparc_P2_J126_mask.mrc as #29, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > show #!1 models > hide #!28 models > hide #!29 target m > show #!8 models > hide #!8 models > show #!8 models > hide #!17 models > surface dust #1 size 5.73 > volume #1 level 0.1195 > volume #1 level 0.1291 > hide #!8.1 models > show #!29 target m > color #29 #b2b2b28a models > open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size 512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32 > volume #30 step 1 > surface dust #1 size 5.73 > surface dust #29 size 5.73 > surface dust #30 size 5.73 > volume #30 level 0.04034 > hide #!29 models > volume #30 level 0.05735 > volume #30 level 0.06798 > hide #!1 models > volume #30 level 0.07435 > show #!29 models > hide #!29 models > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #31 --- Chain | Description A | No description available > rename #31 TMDs_Julian > mmaker #31 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scGPI8_model.cif, chain A (#8) with TMDs_Julian, chain A (#31), sequence alignment score = 3391.1 RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs: 0.000) > hide #!8 models > select add #31 3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected > hide #!30 models > show #!30 models > volume zone #30 nearAtoms sel newMap true Opened cryosparc_P2_J121_003_volume_map_sharp.mrc zone as #32, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > volume #32 level 0.09221 > show #!30 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!32 models > hide #!30 models > show #!32 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > show #!30 models > hide #!30 models > close #32 > show #!30 models > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 62 residues in model #31 to IUPAC-IUB standards. Chain information for TMDs_Julian #31.2 --- Chain | Description A | No description available > clipper associate #30 toModel #31 Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #31.1.1.1, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > isolde sim start #31.2/A Sim termination reason: None ISOLDE: stopped sim > addh #31.2 Summary of feedback from adding hydrogens to TMDs_Julian #31.2 --- notes | Termini for TMDs_Julian (#31.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: TMDs_Julian #31.2/A TYR 18, TMDs_Julian #31.2/A PRO 146, TMDs_Julian #31.2/A SER 666 Chain-final residues that are actual C termini: TMDs_Julian #31.2/A LEU 743 Chain-final residues that are not actual C termini: TMDs_Julian #31.2/A ALA 107, TMDs_Julian #31.2/A PHE 422 466 hydrogen bonds Adding 'H' to TMDs_Julian #31.2/A TYR 18 Adding 'H' to TMDs_Julian #31.2/A SER 666 3584 hydrogens added > isolde sim start #31.2/A ISOLDE: started sim > ui mousemode right translate > volume #31.1.1.1 level 0.09731 > hide #!31.1 models > show #!31.1 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 11 residues in model #31.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select add #31.2 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 16 models selected > select add #31.2 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 16 models selected > select add #31 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 23 models selected > select add #31 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 23 models selected > select subtract #31.1 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 18 models selected > select subtract #31.3 7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 17 models selected > hide #!31.1 models > hide #!31.2 models > show #!31.1 models > show #!31.2 models > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/J121_after_Isolde.mrc"" models #31.1.1.1 > close #31 > undo > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #30 --- Chain | Description A | No description available > open ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/J121_after_Isolde.mrc"" Opened J121_after_Isolde.mrc as #31, grid size 42,42,42, pixel 0.573, shown at level 0.203, step 1, values float32 > volume #31 level 0.05111 > close #31 > open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #31, grid size 512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32 > mmaker #30 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A (#30), sequence alignment score = 3391.1 RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs: 0.000) > volume #31 level 0.08558 > hide #!31 models > show #!31 target m > color #31 #ffb2ff80 models > color #30 #f39d37ff > color #30 #f8a138ff > surface dust #31 size 5.73 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 62 residues in model #30 to IUPAC-IUB standards. Chain information for ctGWT1_noGPF.pdb #30.2 --- Chain | Description A | No description available > clipper associate #31 toModel #30 Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30.1.1.1, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > clipper associate #28 toModel #30 Opened cryosparc_P2_J141_004_volume_map_sharp.mrc as #30.1.1.2, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > close #30 > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #28 --- Chain | Description A | No description available > open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size 512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32 > mmaker #28 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A (#28), sequence alignment score = 3391.1 RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs: 0.000) > color #28 #a27d15ff > color #28 #eab51eff > color #30 #ffb2b27d models > volume #30 level 0.03916 > surface dust #30 size 5.73 > volume #30 level 0.07347 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 62 residues in model #28 to IUPAC-IUB standards. Chain information for ctGWT1_noGPF.pdb #28.2 --- Chain | Description A | No description available > clipper associate #30 toModel #28 Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #28.1.1.1, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > close #28 > open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #28, grid size 512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32 > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #30 --- Chain | Description A | No description available > color #28 #b2ffb283 models > mmaker #30 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A (#30), sequence alignment score = 3391.1 RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs: 0.000) > color #30 #946b18ff > color #30 #fcb62aff > volume #28 step 1 > volume #28 level 0.05735 > surface dust #28 size 5.73 > color #28 #fa8be583 models > color #28 #ffb1f683 models > color #28 #ffc9f983 models > volume #28 level 0.1041 > volume #28 level 0.06373 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 62 residues in model #30 to IUPAC-IUB standards. Chain information for ctGWT1_noGPF.pdb #30.2 --- Chain | Description A | No description available > clipper associate #28 toModel #30 Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30.1.1.1, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > isolde sim start #30.2/A Sim termination reason: None ISOLDE: stopped sim > addh #30.2 Summary of feedback from adding hydrogens to ctGWT1_noGPF.pdb #30.2 --- notes | Termini for ctGWT1_noGPF.pdb (#30.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: ctGWT1_noGPF.pdb #30.2/A TYR 18, ctGWT1_noGPF.pdb #30.2/A PRO 146, ctGWT1_noGPF.pdb #30.2/A SER 666 Chain-final residues that are actual C termini: ctGWT1_noGPF.pdb #30.2/A LEU 743 Chain-final residues that are not actual C termini: ctGWT1_noGPF.pdb #30.2/A ALA 107, ctGWT1_noGPF.pdb #30.2/A PHE 422 466 hydrogen bonds Adding 'H' to ctGWT1_noGPF.pdb #30.2/A TYR 18 Adding 'H' to ctGWT1_noGPF.pdb #30.2/A SER 666 3584 hydrogens added > isolde sim start #30.2/A ISOLDE: started sim > ui mousemode right translate > volume #30.1.1.1 level 0.08194 > volume #30.1.1.1 level 0.06839 > cofr #30 > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/ctGWT1-noGFP_after_ISOLDE_J121.pdb"" models #30 > close #30 Sim termination reason: model deleted ISOLDE: model deleted during running simulation. > open ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/ctGWT1-noGFP_after_ISOLDE_J121.pdb"" Chain information for ctGWT1-noGFP_after_ISOLDE_J121.pdb #28 --- Chain | Description A | No description available > open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size 512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32 > view > ui tool show ""Side View"" > color #30 #e5bf9989 models > volume #30 level 0.0654 > hide #!30 models > show #!30 models > hide #!30 models > open ""/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"" Chain information for ctGWT1_noGPF.pdb #31 --- Chain | Description A | No description available > mmaker #31 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A (#31), sequence alignment score = 3391.1 RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs: 0.000) > show #!30 models > hide #!30 models > swapaa ALA #31:177 Missing or invalid ""residues"" argument: invalid residues specifier > swapaa ALA #31:177.A Missing or invalid ""residues"" argument: invalid residues specifier > swapaa A #31:177 Missing or invalid ""residues"" argument: invalid residues specifier > swapaa #31:177 ALA Using Dunbrack library Swapping ctGWT1_noGPF.pdb #31/A LYS 177 to ALA > swapaa #28:177 ALA Using Dunbrack library Swapping ctGWT1-noGFP_after_ISOLDE_J121.pdb #28/A LYS 177 to ALA > show #28:177, #31:177 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #28:177 > select #28:177 5 atoms, 4 bonds, 1 residue, 1 model selected > rmsd #28 #31 Missing required ""to"" argument > rmsd #28 to #31 Number of atoms from first atom spec (7010) differs from number in second (3439) > show H > delete H > rmsd #28 to #31 RMSD between 3439 atom pairs is 1.077 > rmsd #28:218-244 to #31:218-244 RMSD between 199 atom pairs is 1.221 > rmsd #28:690-708 to #31:690-708 RMSD between 139 atom pairs is 1.241 > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/ctGWT1_K177A-noGFP_after_ISOLDE_J121.pdb"" models #28 > relModel #30 > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/ctGWT1_K177A_noGPF.pdb"" models #31 relModel #30 > hide #!31 models > show #!30 models > show #!29 models > volume #30 level 0.06338 > open /Users/eruboldi/Downloads/cryosparc_P2_mask_TMDs(1).mrc Opened cryosparc_P2_mask_TMDs(1).mrc as #32, grid size 512,512,512, pixel 0.573, shown at level 0.00261, step 2, values float32 > volume #32 level 0.009252 > hide #!29 models > volume #32 level 0.009991 > volume #32 level 0.045 > color #32 #99bfe587 models > volume #32 level 0.07085 > show #!29 models > hide #!29 models > volume #32 level 0.07 > select add #28 3439 atoms, 3520 bonds, 2 pseudobonds, 445 residues, 3 models selected > select subtract #28 Nothing selected > open /Users/eruboldi/Downloads/cryosparc_P2_J146_003_volume_map_sharp.mrc Opened cryosparc_P2_J146_003_volume_map_sharp.mrc as #33, grid size 512,512,512, pixel 0.573, shown at level 0.0155, step 2, values float32 > volume #33 level 0.04583 > hide #!32 models > volume #33 level 0.07402 > surface dust #33 size 5.73 > cofr #28 > open /Users/eruboldi/Downloads/cryosparc_P2_J148_mask.mrc Opened cryosparc_P2_J148_mask.mrc as #34, grid size 512,512,512, pixel 0.573, shown at level 5e-05, step 2, values float32 > volume #33 step 1 > volume #34 step 1 > color #34 #b2b2b27e models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!28 models > show #!28 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!26 models > hide #!26 models > hide #!34 models > show #!34 models > show #!29 models > hide #!29 models > show #!29 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/scGPI17_Cu_Ermanno.cxs"" > save ""/Users/eruboldi/Desktop/GPI/chimeraX > sessions/ctGWT1/scGPI17_Cu_Julian.cxs"" includeMaps true > close #25 > close #1 > close #2-13 > show #!14 models > hide #!14 models > close #14 > show #!15 models > show #!16 models > close #15 > close #16 > show #!17 models > show #!19 models > show #!21 models > hide #!34 models > hide #!29 models > hide #!28 models > hide #!21 models > show #!21 models > hide #!19 models > show #!19 models > show #!18 models > close #18 > show #!20 models > hide #!21 models > show #!21 models > hide #!20 models > hide #!21 models > show #!21 models > show #!22 models > show #!23 models > close #22 > close #23 > close #20 > show #!24 models > show #!26 models > hide #!21 models > hide #!24 models > show #!24 models > hide #!24 models > hide #!19 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!26 models > show #!26 models > hide #!24 models > show #!28 models > hide #!28 models > close #28 > close #29 > close #30 > close #31 > close #32 > open ""/Users/eruboldi/Downloads/GlcNPI (1).pdb"" > select add #1 36 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,151.44,0,1,0,137.32,0,0,1,130.62 > view matrix models #1,1,0,0,172.48,0,1,0,145,0,0,1,133.52 > view matrix models #1,1,0,0,177.42,0,1,0,151.39,0,0,1,138.14 > view matrix models #1,1,0,0,177.43,0,1,0,152.25,0,0,1,119.35 > view matrix models #1,1,0,0,163.6,0,1,0,147.61,0,0,1,110.31 > ui mousemode right translate > ui tool show ""Side View"" > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,184.54,0,1,0,167.98,0,0,1,184.43 > open /Users/eruboldi/Downloads/cryosparc_P2_J146_003_volume_map_sharp(1).mrc Opened cryosparc_P2_J146_003_volume_map_sharp(1).mrc as #2, grid size 512,512,512, pixel 0.573, shown at level 0.0155, step 2, values float32 > hide #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.79262,-0.18585,0.5807,182.51,0.39175,0.57457,0.71861,168.98,-0.46721,0.79707,-0.38261,182.89 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.79262,-0.18585,0.5807,176.13,0.39175,0.57457,0.71861,164.42,-0.46721,0.79707,-0.38261,143.88 > view matrix models > #1,-0.79262,-0.18585,0.5807,166.7,0.39175,0.57457,0.71861,165.62,-0.46721,0.79707,-0.38261,152.79 > open /Users/eruboldi/Downloads/cryosparc_P2_J150_003_volume_map_sharp.mrc Opened cryosparc_P2_J150_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 0.573, shown at level 0.0158, step 2, values float32 > view matrix models > #1,-0.79262,-0.18585,0.5807,170.6,0.39175,0.57457,0.71861,158.65,-0.46721,0.79707,-0.38261,146.97 > hide #!3 models > view matrix models > #1,-0.79262,-0.18585,0.5807,182.73,0.39175,0.57457,0.71861,146.2,-0.46721,0.79707,-0.38261,148.33 > view matrix models > #1,-0.79262,-0.18585,0.5807,149.49,0.39175,0.57457,0.71861,125.15,-0.46721,0.79707,-0.38261,163.93 > view matrix models > #1,-0.79262,-0.18585,0.5807,149.02,0.39175,0.57457,0.71861,120.9,-0.46721,0.79707,-0.38261,154.97 > view matrix models > #1,-0.79262,-0.18585,0.5807,155.24,0.39175,0.57457,0.71861,124.67,-0.46721,0.79707,-0.38261,149.6 > view matrix models > #1,-0.79262,-0.18585,0.5807,152.17,0.39175,0.57457,0.71861,128.28,-0.46721,0.79707,-0.38261,152.54 > view matrix models > #1,-0.79262,-0.18585,0.5807,154.12,0.39175,0.57457,0.71861,129.04,-0.46721,0.79707,-0.38261,150.74 > view matrix models > #1,-0.79262,-0.18585,0.5807,153.57,0.39175,0.57457,0.71861,130.11,-0.46721,0.79707,-0.38261,151.56 > fitmap #1 inMap #26 Fit molecule GlcNPI (1).pdb (#1) to map cryosparc_P2_J139_003_volume_map_sharp.mrc (#26) using 36 atoms average map value = 0.1262, steps = 356 shifted from previous position = 3.66 rotated from previous position = 55.4 degrees atoms outside contour = 17, contour level = 0.12107 Position of GlcNPI (1).pdb (#1) relative to cryosparc_P2_J139_003_volume_map_sharp.mrc (#26) coordinates: Matrix rotation and translation -0.40645676 -0.89682846 0.17461850 155.66551378 0.19401174 0.10204180 0.97567767 132.96273726 -0.89283389 0.43044882 0.13251967 150.37079508 Axis -0.33641610 0.65863751 0.67306822 Axis point 99.04730815 69.41370304 0.00000000 Rotation angle (degrees) 125.86996479 Shift along axis 136.41566484 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Computing secondary structure > clipper associate #26 toModel #1 Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #1.1.1.1, grid size 512,512,512, pixel 0.573, shown at step 1, values float32 > isolde sim start #1.2/A Loading residue template for GPI from internal database Sim termination reason: None ISOLDE: stopped sim > addh #1.2 Summary of feedback from adding hydrogens to GlcNPI (1).pdb #1.2 --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 9 hydrogen bonds 30 hydrogens added > isolde sim start #1.2/A Sim termination reason: None ISOLDE: stopped sim > isolde sim start #1.2/A Sim termination reason: None ISOLDE: stopped sim Fetching CCD GPI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/GPI/GPI.cif > clipper spotlight #1.2 > clipper isolate #1.2.2/A maskRadius 4.0 focus false > isolde sim start #1.2/A Sim termination reason: None ISOLDE: stopped sim > isolde stepto #1.2/A > isolde sim start #1.2/A Sim termination reason: None ISOLDE: stopped sim > volume #1.1.1.1 level 0.1312 > close #1 > open /Users/eruboldi/Downloads/cryosparc_P2_J139_003_volume_map_sharp.mrc Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 0.573, shown at level 0.0261, step 2, values float32 > volume #1 step 1 > volume #3 step 1 > volume #2 step 1 > volume #1 level 0.1934 > volume #1 level 0.06975 > surface dust #1 size 5.73 > volume #1 level 0.1134 > hide #!1 models > show #!2 models > show #!3 models > volume #3 level 0.05586 > volume #2 level 0.0561 > hide #!3 models > hide #!17 models > volume #2 level 0.1215 > volume #2 level 0.06512 > volume #3 level 0.0514 > surface dust #2 size 5.73 > surface dust #3 size 5.73 > hide #!2 models > volume #3 level 0.067 > open ""/Users/eruboldi/Downloads/GlcNPI (1).pdb"" Must specify one map, got 0 > fitmap #1 inMap #3 Fit map cryosparc_P2_J139_003_volume_map_sharp.mrc in map cryosparc_P2_J150_003_volume_map_sharp.mrc using 121529 points correlation = 0.3597, correlation about mean = 0.1048, overlap = 940.5 steps = 112, shift = 2.81, angle = 7.29 degrees Position of cryosparc_P2_J139_003_volume_map_sharp.mrc (#1) relative to cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.99993782 0.01094420 -0.00214093 -2.32279855 -0.01112700 0.99192459 -0.12633999 19.70974441 0.00074095 0.12635595 0.99198469 -19.43107805 Axis 0.99614301 -0.01136052 -0.08700602 Axis point 0.00000000 163.59177387 145.47294829 Rotation angle (degrees) 7.28686300 Shift along axis -0.84713172 > select add #4 36 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-16.137,0,1,0,-3.5943,0,0,1,-90.621 Must specify one map, got 0 > fitmap #4 inMap #3 Fit molecule GlcNPI (1).pdb (#4) to map cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 36, contour level = 0.067 Position of GlcNPI (1).pdb (#4) relative to cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 -16.13710131 0.00000000 1.00000000 0.00000000 -3.59431574 0.00000000 0.00000000 1.00000000 -90.62087500 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis -90.62087500 > view matrix models #4,1,0,0,-46.737,0,1,0,-18.322,0,0,1,-196.93 > view matrix models #4,1,0,0,-50.746,0,1,0,-10.37,0,0,1,-235.09 > hide #!3 models > show #4 > hide #4 models > show #4 models > view matrix models #4,1,0,0,334.86,0,1,0,176.62,0,0,1,370.33 > view matrix models #4,1,0,0,241.14,0,1,0,130.68,0,0,1,224.78 > view matrix models #4,1,0,0,219.34,0,1,0,120.93,0,0,1,187.92 > view matrix models #4,1,0,0,201.32,0,1,0,111.95,0,0,1,160.36 > show #!3 models > view matrix models #4,1,0,0,169.72,0,1,0,93.483,0,0,1,120.88 > view matrix models #4,1,0,0,176.43,0,1,0,107.85,0,0,1,148.48 > view matrix models #4,1,0,0,174.74,0,1,0,128.54,0,0,1,147.18 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.24463,-0.95711,-0.15524,172.71,0.95859,-0.26281,0.10973,129.66,-0.14582,-0.12196,0.98176,146.94 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.24463,-0.95711,-0.15524,158.04,0.95859,-0.26281,0.10973,110.96,-0.14582,-0.12196,0.98176,150.23 > view matrix models > #4,-0.24463,-0.95711,-0.15524,157.14,0.95859,-0.26281,0.10973,131.27,-0.14582,-0.12196,0.98176,140.44 > view matrix models > #4,-0.24463,-0.95711,-0.15524,144.9,0.95859,-0.26281,0.10973,125.34,-0.14582,-0.12196,0.98176,147.63 > view matrix models > #4,-0.24463,-0.95711,-0.15524,142.19,0.95859,-0.26281,0.10973,125.44,-0.14582,-0.12196,0.98176,144.61 > view matrix models > #4,-0.24463,-0.95711,-0.15524,144.52,0.95859,-0.26281,0.10973,130.68,-0.14582,-0.12196,0.98176,146.53 > ui tool show ""Side View"" > view matrix models > #4,-0.24463,-0.95711,-0.15524,143.76,0.95859,-0.26281,0.10973,132.67,-0.14582,-0.12196,0.98176,142.37 > view matrix models > #4,-0.24463,-0.95711,-0.15524,137.8,0.95859,-0.26281,0.10973,131.05,-0.14582,-0.12196,0.98176,144.6 > view matrix models > #4,-0.24463,-0.95711,-0.15524,137.5,0.95859,-0.26281,0.10973,130.46,-0.14582,-0.12196,0.98176,146.77 > color #3 #b2ffff9c models > view matrix models > #4,-0.24463,-0.95711,-0.15524,137.82,0.95859,-0.26281,0.10973,130.93,-0.14582,-0.12196,0.98176,145.89 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.75914,0.29407,-0.58072,139.13,0.57924,0.10183,0.80877,131.03,0.29697,-0.95034,-0.093038,145.48 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.75914,0.29407,-0.58072,138.18,0.57924,0.10183,0.80877,129.63,0.29697,-0.95034,-0.093038,146.38 > fitmap #4 inMap #3 Fit molecule GlcNPI (1).pdb (#4) to map cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms average map value = 0.1488, steps = 188 shifted from previous position = 3.3 rotated from previous position = 63 degrees atoms outside contour = 11, contour level = 0.067 Position of GlcNPI (1).pdb (#4) relative to cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.79152332 -0.53345755 -0.29818430 138.23983655 0.60333437 0.60436263 0.52032053 126.43059174 -0.09735747 -0.59175068 0.80022038 145.23569780 Axis -0.69378145 -0.12528868 0.70920381 Axis point -36.03152662 261.84496038 0.00000000 Rotation angle (degrees) 53.26940734 Shift along axis -8.74684571 > view matrix models > #4,0.79152,-0.53346,-0.29818,139.79,0.60333,0.60436,0.52032,128.3,-0.097357,-0.59175,0.80022,143.63 > view matrix models > #4,0.79152,-0.53346,-0.29818,140.15,0.60333,0.60436,0.52032,128.54,-0.097357,-0.59175,0.80022,144.05 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.71056,-0.68075,-0.17799,140.1,0.66874,0.57468,0.47173,128.58,-0.21884,-0.45423,0.86359,143.96 > view matrix models > #4,-0.32514,0.034933,0.94502,139.71,0.7444,-0.60686,0.27855,128.28,0.58323,0.79404,0.17131,144.79 > view matrix models > #4,-0.20326,-0.44435,0.87249,139.72,0.97907,-0.10186,0.17621,128.63,0.010569,0.89004,0.45575,144.25 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.20326,-0.44435,0.87249,140.1,0.97907,-0.10186,0.17621,129.02,0.010569,0.89004,0.45575,147.14 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.69,0.57723,-0.4367,140.53,0.47331,0.096637,0.87558,128.92,0.54761,-0.81084,-0.20653,146.99 > fitmap #4 inMap #3 Fit molecule GlcNPI (1).pdb (#4) to map cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms average map value = 0.1008, steps = 116 shifted from previous position = 2.78 rotated from previous position = 8.74 degrees atoms outside contour = 14, contour level = 0.067 Position of GlcNPI (1).pdb (#4) relative to cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.58368143 0.64451198 -0.49388290 138.36249757 0.49279263 0.20224269 0.84631751 130.36763214 0.64534597 -0.73736166 -0.19956545 145.93899156 Axis -0.80933839 -0.58220230 -0.07753609 Axis point 0.00000000 80.77525529 59.13256761 Rotation angle (degrees) 101.93610009 Shift along axis -199.19795571 > hide #4 models > select subtract #4 Nothing selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Failed to send bug report. Error while sending follows: Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/bug_reporter/tool.py"", line 264, in submit errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10, ssl=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/webservices/post_form.py"", line 45, in post_multipart_formdata return r.status, r.msg, r.getheaders(), r.read() ^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 489, in read s = self._safe_read(self.length) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 640, in _safe_read raise IncompleteRead(data, amt-len(data)) http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected) OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16U000NJD/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 147 days, 17 hours, 40 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.22.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 2.4.6 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.2 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.15.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned