id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19012 Crash moving between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.0-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000030805b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030704f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000305037000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030402b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030301f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000302013000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000301007000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017fcd3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017ecc7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017bca3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ee3f0800 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, psutil._psutil_osx, psutil._psutil_posix, chimerax.mlp._mlp, chimerax.chem_group._chem_group, chimerax.atom_search.ast, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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All rights reserved. How to cite UCSF ChimeraX > open 6XIT 6xit title: Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with PIP2 [more info...] Chain information for 6xit #1 --- Chain | Description | UniProt A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380 Non-standard residues in 6xit #1 --- K — potassium ion PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) > rename #1 Kir3.2_docked > ui tool show Toolbar > set bgColor white > open 6XIS 6xis title: Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in apo form [more info...] Chain information for 6xis #2 --- Chain | Description | UniProt A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380 > rename #2 Kir3.1_extended > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > tile 2 models tiled > hide #!2.1 models > open 3JYC 3jyc title: Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2 at 3.1 Angstrom resolution [more info...] Chain information for 3jyc #3 --- Chain | Description A | Inward-rectifier K+ channel Kir2.2 Non-standard residues in 3jyc #3 --- K — potassium ion 3jyc mmCIF Assemblies --- 1| author_and_software_defined_assembly > open 3sPI 3spi title: Inward rectifier potassium channel Kir2.2 in complex with PIP2 [more info...] Chain information for 3spi #4 --- Chain | Description | UniProt A | Inward-rectifier K+ channel Kir2.2 | D2YW45_CHICK 36-378 Non-standard residues in 3spi #4 --- K — potassium ion PIO — [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy- cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha- phosphatidyl-d-myo-inositol 4,5-diphosphate) 3spi mmCIF Assemblies --- 1| author_and_software_defined_assembly > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > tile 4 models tiled > close #3 > close #4 > open /Users/omallen/Downloads/3SPI.pdb1 3SPI.pdb1 title: Inward rectifier potassium channel KIR2.2 In complex with PIP2 [more info...] Chain information for 3SPI.pdb1 --- Chain | Description 3.1/A | No description available 3.2/A 3.3/A 3.4/A | No description available > open /Users/omallen/Downloads/3JYC.pdb1 3JYC.pdb1 title: Crystal structure of the eukaryotic strong inward-rectifier K+ channel KIR2.2 At 3.1 angstrom resolution [more info...] Chain information for 3JYC.pdb1 --- Chain | Description 4.1/A | No description available 4.2/A 4.3/A 4.4/A | No description available > combine #3.1 #3.2 #3.3 #3.4 Remapping chain ID 'A' in 3SPI.pdb1 #3.2 to 'B' Remapping chain ID 'A' in 3SPI.pdb1 #3.3 to 'C' Remapping chain ID 'A' in 3SPI.pdb1 #3.4 to 'D' > rename #5 Kir2.2 > rename #5 Kir2.2_docked_3SPI > combine #4.1 #4.2 #4.3 #4.4 Remapping chain ID 'A' in 3JYC.pdb1 #4.2 to 'B' Remapping chain ID 'A' in 3JYC.pdb1 #4.3 to 'C' Remapping chain ID 'A' in 3JYC.pdb1 #4.4 to 'D' > close #4 > close #3 > rename #6 ""Kir2.2_Extended "" > tile 4 models tiled > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 36 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > tile columns 4 4 models tiled > hide #!1 models > hide #!2 models > view orient > ui tool show Matchmaker > matchmaker #!6 to #5 Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 1610.2 RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs: 10.379) > hide #1.1 models > hide #!6.2 models Drag select of 76 atoms, 71 bonds, 875 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 522.2 RMSD between 101 pruned atom pairs is 0.411 angstroms; (across all 104 pairs: 0.658) > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 522.2 RMSD between 101 pruned atom pairs is 0.411 angstroms; (across all 104 pairs: 0.658) > select clear Drag select of 1590 residues > show sel surfaces > hide sel cartoons > hide sel surfaces > undo > show sel surfaces Drag select of 28 atoms, 23 bonds, 757 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain D (#6), sequence alignment score = 484.6 RMSD between 95 pruned atom pairs is 0.336 angstroms; (across all 95 pairs: 0.336) > select clear > ~tile Drag select of 6 atoms, 4 bonds, 739 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 464.1 RMSD between 91 pruned atom pairs is 0.325 angstroms; (across all 91 pairs: 0.325) > matchmaker #!2 to #1 Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 1628 RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs: 6.565) > select clear > show #!1 models > show #!2 models > hide #!5 models > hide #!6 models > view orient > matchmaker #!2 to #1 Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 1628 RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs: 6.565) Drag select of 3 atoms, 793 residues > matchmaker #!2 to #1 Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 1628 RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs: 6.565) > matchmaker #!2 & sel to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2), sequence alignment score = 487.4 RMSD between 64 pruned atom pairs is 0.779 angstroms; (across all 97 pairs: 2.819) Drag select of 1 atoms, 1546 residues, 1 bonds > matchmaker #!2 & sel to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain B (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 923.3 RMSD between 173 pruned atom pairs is 0.825 angstroms; (across all 188 pairs: 1.087) > open /Users/omallen/Downloads/3SYA.pdb1 3SYA.pdb1 title: Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (KIR3.2) In complex with sodium and PIP2 [more info...] Chain information for 3SYA.pdb1 --- Chain | Description 3.1/A | No description available 3.2/A 3.3/A 3.4/A | No description available > combine #3.1 #3.2 #3.3 #3.4 Remapping chain ID 'A' in 3SYA.pdb1 #3.2 to 'B' Remapping chain ID 'A' in 3SYA.pdb1 #3.3 to 'C' Remapping chain ID 'A' in 3SYA.pdb1 #3.4 to 'D' > close #3 > rename #4 3SYA > view orient > matchmaker #!4 to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain B (#1) with 3SYA, chain A (#4), sequence alignment score = 982 RMSD between 200 pruned atom pairs is 0.486 angstroms; (across all 202 pairs: 0.604) > view orient > rename #4 Kir3.2_docked_Xtal_3SYA > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 20 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > hide #!2 models > open /Users/omallen/Downloads/3SYO.pdb1 3SYO.pdb1 title: Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (KIR3.2) In complex with sodium [more info...] Chain information for 3SYO.pdb1 --- Chain | Description 3.1/A | No description available 3.2/A 3.3/A 3.4/A | No description available > combine #3.1 #3.2 #3.3 #3.4 Remapping chain ID 'A' in 3SYO.pdb1 #3.2 to 'B' Remapping chain ID 'A' in 3SYO.pdb1 #3.3 to 'C' Remapping chain ID 'A' in 3SYO.pdb1 #3.4 to 'D' > combine #3.1 #3.2 #3.3 #3.4 Remapping chain ID 'A' in 3SYO.pdb1 #3.2 to 'B' Remapping chain ID 'A' in 3SYO.pdb1 #3.3 to 'C' Remapping chain ID 'A' in 3SYO.pdb1 #3.4 to 'D' > close #8 > rename #7 Kir3.2_extended_Xtal_3SYO > close #3 > matchmaker #!7 to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain B (#1) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 977.8 RMSD between 195 pruned atom pairs is 0.514 angstroms; (across all 197 pairs: 0.709) > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 24 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > show #!2 models > hide #!1 models > hide #!4 models > matchmaker #!7 to #2 & sel Computing secondary structure 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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 926.6 RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 190 pairs: 1.335) > matchmaker #!7 to #2 & sel Computing secondary structure 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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 926.6 RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 190 pairs: 1.335) > matchmaker #!7 to #2 Computing secondary structure 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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 1616.6 RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs: 5.735) > matchmaker #!7 to #2 Computing secondary structure 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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 1616.6 RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs: 5.735) > ui mousemode right ""move picked models"" > view matrix models > #2,-0.12905,0.99095,-0.03695,66.448,-0.23958,-0.067314,-0.96854,408.86,-0.96226,-0.11614,0.2461,327.52 > matchmaker #!7 to #2 Computing secondary structure 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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 1616.6 RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs: 5.735) > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"" > tile 2 models tiled > select add #7 21716 atoms, 9782 bonds, 9 pseudobonds, 2811 residues, 6 models selected > show sel & #!2,7 cartoons > select clear > show #!4 models > show #!1 models > tile 4 models tiled > ui tool show ""Color Actions"" > color bypolymer > color bychain > undo > lighting full > graphics silhouettes true > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting simple > graphics silhouettes false > lighting flat > color #7 #9437ffff > color #7 #ff8ad8ff > color #7 #ff2f92ff > color #7 #941751ff > color #7 #531b93ff > color #7 #931e6eff > color #7 #a4217bff > color #7 #6f4fa4ff > color #7 #ab7affff > color #7 #825dc1ff > hide #!7.2 models > hide #7.1 models > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Kirstructures.png"" width 2000 height 1256 > supersample 3 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"" > color #1 #537adbff > color #1 #5579dbff > select ligand 432 atoms, 432 bonds, 12 residues, 3 models selected > color (#!1,4 & sel) yellow > color (#!1,4 & sel) light gray > color (#!1,4 & sel) byhetero > select clear > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"" > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Kirstructures2.png"" width 2000 height 1256 > supersample 3 > hide #!4 models > hide #!2 models > hide #!1 models > hide #!7 models > show #!6 models > show #!5 models > tile 2 models tiled > color #5 #76e536ff > color #5 #42801eff > select ligand 432 atoms, 432 bonds, 12 residues, 3 models selected > color (#!5 & sel) light gray > color (#!5 & sel) byhetero > select clear > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/kir2_2strucs.png"" width 2000 height 1256 > supersample 3 > matchmaker #!6 to #5 Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 1610.2 RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs: 10.379) > ~tile > select add #5 10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected > hide sel cartoons > select #5/A:130-170 312 atoms, 318 bonds, 41 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #5/A:140-190 387 atoms, 392 bonds, 51 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #5/A:150-190 307 atoms, 310 bonds, 41 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #5/A:155-190 269 atoms, 272 bonds, 36 residues, 1 model selected > show sel cartoons > select add #6 10465 atoms, 10673 bonds, 10 pseudobonds, 1340 residues, 6 models selected > hide sel cartoons > hide sel atoms > undo > select add #5 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected > hide sel atoms > select subtract #6 10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 10 models selected > select subtract #5 4 models selected > select #/A:155-190 Expected an objects specifier or a keyword > select #5/A:155-190 269 atoms, 272 bonds, 36 residues, 1 model selected > show sel cartoons > select #6/A:155-190 269 atoms, 272 bonds, 36 residues, 1 model selected > show sel cartoons > select add #6 10196 atoms, 10401 bonds, 10 pseudobonds, 1304 residues, 5 models selected > select subtract #6 4 models selected > matchmaker #!6 to #5 Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 1610.2 RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs: 10.379) > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0030/cryosparc_P3_J5133_002_volume_map.mrc Opened cryosparc_P3_J5133_002_volume_map.mrc as #3, grid size 128,128,128, pixel 3.18, shown at level 0.0254, step 1, values float32 > hide #!5 models > hide #!6 models > view orient > volume #3 level 1.302 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0035to37/cryosparc_P3_J5300_005_volume_map_sharp.mrc Opened cryosparc_P3_J5300_005_volume_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.58, shown at level 0.317, step 1, values float32 > volume #8 level 1.919 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0035to37/Refine3D/job051/run_class001.mrc Opened run_class001.mrc as #9, grid size 256,256,256, pixel 1.58, shown at level 0.0134, step 1, values float32 > volume #9 level 0.06143 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 88, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 154, in status r.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PP/Cul2_VHL/crown_dimer_inEMmap-coot-0.pdb Summary of feedback from opening /Users/omallen/Library/CloudStorage/OneDrive- TheFrancisCrickInstitute/PP/Cul2_VHL/crown_dimer_inEMmap-coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 54 54 LEU 1 158 LEU 1 169 1 12 Start residue of secondary structure not found: HELIX 55 55 PRO 1 172 ARG 1 177 1 6 Start residue of secondary structure not found: HELIX 56 56 ARG 1 182 LEU 1 184 1 3 Start residue of secondary structure not found: HELIX 57 57 TYR 1 185 GLU 1 189 1 5 Start residue of secondary structure not found: HELIX 58 58 VAL 1 194 MET 1 211 1 18 69 messages similar to the above omitted crown_dimer_inEMmap-coot-0.pdb title: (NEDD8)-CRL2VHL-MZ1-BRD4BD2-ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-ub [more info...] Chain information for crown_dimer_inEMmap-coot-0.pdb #10 --- Chain | Description | UniProt 1 | No description available | B | von hippel-lindau disease tumor suppressor | VHL_HUMAN 54-213 C | elongin-B | ELOB_HUMAN 1-104 C1 | No description available | D | elongin-C | L7N190_MYOLU 16-112 D1 | No description available | E | CUL-2 | CUL2_HUMAN 1-745 E1 | No description available | R | RBX1 | R1 | No description available | Non-standard residues in crown_dimer_inEMmap-coot-0.pdb #10 --- ALAB — (alab) ARGB — (ARGB) ASNB — (ASNB) ASPB — (ASPB) CYSB — (cysb) GLNB — (GLNB) GLUB — (glub) GLYB — (glyb) HISB — (hisb) ILEB — (ileb) LEUB — (leub) LYSB — (lysb) METB — (metb) PHEB — (pheb) PROB — (prob) SERB — (serb) THRB — (THRB) TRPB — (TRPB) TYRB — (tyrb) VALB — (valb) ZN — zinc ion ZNR — (ZNR) > hide #!10 surfaces > hide #!10 atoms > show #!10 cartoons > select #10/E1:376 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #10/E1:465 27 atoms, 25 bonds, 2 residues, 1 model selected > select add #10/E1:466 34 atoms, 31 bonds, 3 residues, 1 model selected > select #10/1 2616 atoms, 2648 bonds, 1 pseudobond, 161 residues, 2 models selected > mlp sel Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_1 SES surface"": minimum 54.76, mean 170, maximum 266.4 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_1 SES surface"": minimum 1.016e+16, mean 7.225e+27, maximum 1.738e+29 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Could not come up with unique atom name in mega-residue LEUB+SERB+VALB+ARGB+LYSB+VALB+PROB+VALB+GLUB+GLNB+ASNB+LEUB+TYRB+CYSB+ARGB+ARGB+ARGB+GLUB+LEUB+LYSB+ASPB+LEUB+ILEB+THRB+VALB+TYRB+ARGB+VALB+SERB+PROB+LEUB+LEUB+TYRB+THRB+GLUB+ILEB+ASPB+ASNB+LEUB+ALAB+GLUB+PHEB+ASPB+ILEB+HISB+PROB+PROB+GLNB+ASNB+GLYB+VALB+ASPB+GLNB+VALB+LYSB+ASNB+ASPB+LEUB+LEUB+SERB+GLUB+PROB+ARGB+VALB+LEUB+PHEB+THRB+LEUB+GLNB+GLUB+GLUB+THRB+ARGB+GLNB+ILEB+ASNB+ALAB+VALB+HISB+LEUB+GLNB+LEUB+ARGB+GLYB+METB+ASPB+GLYB+HISB+ASPB+THRB+GLYB+ALAB+ASPB+ARGB+PHEB+LEUB+TRPB+LEUB+HISB+GLYB+ARGB+TYRB+SERB+HISB+ILEB+ARGB+ARGB+GLYB+THRB+GLYB+PROB+PROB+LEUB+THRB+PROB+TYRB+PROB+GLNB+PROB+GLUB+GLYB+ASPB+PHEB+ASNB+LEUB+TRPB+VALB+PROB+LEUB+VALB+VALB+ARGB+PROB+SERB+ARGB+ASNB+CYSB+PHEB+ILEB+VALB+GLNB+SERB+PROB+GLUB+ARGB+SERB+ASNB+VALB+SERB+ARGB+LEUB+VALB+PROB+ARGB+PROB+ARGB+GLYB+ALAB+GLUB+METB > hide sel surfaces > select #10/C1 1647 atoms, 1663 bonds, 104 residues, 1 model selected > select #10/E 10756 atoms, 10867 bonds, 658 residues, 1 model selected > mlp sel Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_E SES surface"": minimum -28.08, mean -2.865, maximum 27.9 To also show corresponding color key, enter the above mlp command and add key true > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true select true reveal true 1347 contacts > mlp sel Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_B SES surface"": minimum -25.31, mean -3.016, maximum 24.27 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_D SES surface"": minimum -26.49, mean -2.329, maximum 26.98 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_E SES surface"": minimum -28.08, mean -2.865, maximum 27.9 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_E1 SES surface"": minimum -27.95, mean -2.92, maximum 26.62 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_R SES surface"": minimum -25.86, mean -1.656, maximum 32.5 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_R1 SES surface"": minimum -25.04, mean -2.076, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_B SES surface"": minimum -25.31, mean -3.016, maximum 24.27 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_D SES surface"": minimum -26.49, mean -2.329, maximum 26.98 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_E SES surface"": minimum -28.08, mean -2.865, maximum 27.9 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_E1 SES surface"": minimum -27.95, mean -2.92, maximum 26.62 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_R SES surface"": minimum -25.86, mean -1.656, maximum 32.5 Map values for surface ""crown_dimer_inEMmap-coot-0.pdb_R1 SES surface"": minimum -25.04, mean -2.076, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > close #10 > close #11 > show #!9 models > open 5n4w 5n4w title: Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more info...] Chain information for 5n4w #10 --- Chain | Description | UniProt A | Cullin-2 | CUL2_HUMAN 1-745 B | Elongin-B | ELOB_HUMAN 1-104 C | Elongin-C | ELOC_HUMAN 17-112 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-102 V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213 Non-standard residues in 5n4w #10 --- ZN — zinc ion 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!10 atoms > show #!10 cartoons > view matrix models > #10,0.8737,-0.19688,0.44484,212.08,-0.41454,0.17717,0.89262,176.07,-0.25455,-0.96429,0.073175,279.19 > view matrix models > #10,0.56666,-0.48876,0.66333,222.85,-0.78337,-0.56913,0.24985,224.58,0.25541,-0.66121,-0.70539,181.2 > ui tool show ""Fit in Map"" > fitmap #10 inMap #9 Fit molecule 5n4w (#10) to map run_class001.mrc (#9) using 7719 atoms average map value = 0.04377, steps = 200 shifted from previous position = 23.4 rotated from previous position = 34.8 degrees atoms outside contour = 5857, contour level = 0.061429 Position of 5n4w (#10) relative to run_class001.mrc (#9) coordinates: Matrix rotation and translation 0.48211678 -0.02360497 0.87578891 222.37359187 -0.82792709 -0.33920712 0.44662654 233.07799226 0.28653123 -0.94041551 -0.18308064 222.99548022 Axis -0.81197692 0.34495251 -0.47085162 Axis point 0.00000000 207.50734557 -58.10861118 Rotation angle (degrees) 121.33798628 Shift along axis -205.15916825 > view matrix models > #10,0.48506,-0.021109,0.87423,221.64,-0.82538,-0.34133,0.44972,232.18,0.2889,-0.93971,-0.18299,222.33 > view matrix models > #10,0.70101,-0.21152,0.68106,214.93,-0.70743,-0.085524,0.70159,217.91,-0.090156,-0.97362,-0.20959,244.96 > fitmap #10 inMap #9 Fit molecule 5n4w (#10) to map run_class001.mrc (#9) using 7719 atoms average map value = 0.05398, steps = 116 shifted from previous position = 10.4 rotated from previous position = 17.3 degrees atoms outside contour = 4718, contour level = 0.061429 Position of 5n4w (#10) relative to run_class001.mrc (#9) coordinates: Matrix rotation and translation 0.68498024 0.04726472 0.72702690 208.49566223 -0.72845643 0.06138985 0.68233607 211.33126595 -0.01238165 -0.99699415 0.07648112 242.38189117 Axis -0.84297838 0.37116311 -0.38939105 Axis point 0.00000000 242.60128271 -80.27616259 Rotation angle (degrees) 95.08159838 Shift along axis -191.70030544 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/CRL2_VHL_dimer_9A.mrc Opened CRL2_VHL_dimer_9A.mrc as #11, grid size 256,256,256, pixel 1.61, shown at level 0.0168, step 1, values float32 > hide #!10 models > volume #11 level 0.06174 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/CRL2_VHL_monomer_relion_refine39.mrc Opened CRL2_VHL_monomer_relion_refine39.mrc as #12, grid size 256,256,256, pixel 1.61, shown at level 0.00361, step 1, values float32 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/3d_re_ext_noOG_mono/run_it025_class001.mrc Opened run_it025_class001.mrc as #13, grid size 256,256,256, pixel 1.61, shown at level 0.0109, step 1, values float32 > volume #13 level 0.02639 > close #13 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class001.mrc Opened run_it021_class001.mrc as #13, grid size 128,128,128, pixel 1.61, shown at level 0.0361, step 1, values float32 > view orient > close #12 > close #13 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class002.mrc Opened run_it021_class002.mrc as #12, grid size 128,128,128, pixel 1.61, shown at level 0.0349, step 1, values float32 > close #11 > close #12 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class003.mrc Opened run_it021_class003.mrc as #11, grid size 128,128,128, pixel 1.61, shown at level 0.0474, step 1, values float32 > close #11 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class004.mrc Opened run_it021_class004.mrc as #11, grid size 128,128,128, pixel 1.61, shown at level 0.0482, step 1, values float32 > close #11 > open /Volumes/lab- > enchevr/home/users/enchevr/cluster_processing/gJC0030/cryosparc_P3_J5133_002_volume_map.mrc Opened cryosparc_P3_J5133_002_volume_map.mrc as #11, grid size 128,128,128, pixel 3.18, shown at level 0.0254, step 1, values float32 > view orient > volume #11 level 1.316 > close #11 > close #8 > close #9 > close #3 > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/cryosparc_P256_J1166_008_volume_map_sharp.mrc Opened cryosparc_P256_J1166_008_volume_map_sharp.mrc as #3, grid size 440,440,440, pixel 0.65, shown at level 0.0436, step 2, values float32 > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb Chain information for apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #8 --- Chain | Description A B C D | No description available > view orient > volume #3 step 1 > volume #3 level 0.1282 > color #8 #ff80ccff > ui tool show ""Color Actions"" > color plum > undo > color #8 #ff00ccff > color #8 #990066ff > color #8 #ff99ccff > color #8 #cc6699ff > select add #8 17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected > ui tool show ""Color Actions"" > color sel plum > color sel orchid > color sel plum > select clear > select #8/A:95 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > view sel > color sel byhetero > volume #3 level -0.02149 > volume #3 level 0.01106 > volume #3 level 0.05012 > volume #3 color #b2b2b274 > delH Unknown command: delH > delete H > volume #3 level 0.0371 > surface dust #3 size 6.5 > select #8/A 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > select #8/A B C Expected a keyword > select #8/B 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > hide sel cartoons > select #8/C 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > hide sel cartoons > select #8/D 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > hide sel cartoons > select #8/A 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > ui tool show ""Surface Zone"" > surface zone #3 nearAtoms sel distance 3.9 > surface zone #3 nearAtoms sel distance 3.88 > surface zone #3 nearAtoms sel distance 31.83 > surface unzone #3 > select clear > ui tool show ""Side View"" > surface dust #3 size 6.5 > volume #3 color #b2b2b234 > select clear > graphics silhouettes false > graphics silhouettes true > volume #3 level 0.0375 > volume #3 level 0.036 > volume #3 level 0.035 > volume #3 level 0.034 > volume #3 style mesh > volume #3 style surface > volume #3 color #999999 > volume #3 color #99999931 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed In.png"" width 2000 height 1174 > supersample 3 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed In.cxs"" > view orient > select add #8 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel atoms > select #8/A:95 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub.cxs"" > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub.png"" width 2000 > height 1283 supersample 3 > select add #8 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > show sel cartoons > select #8/:95 Expected an objects specifier or a keyword > select #8:95 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select add #8 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > show sel surfaces > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 7716 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > style sel sphere Changed 8726 atom styles > show sel cartoons > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8724 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > ui tool show ""Color Actions"" > color sel plum > select ions 16 atoms, 16 residues, 5 models selected > color (#!8 & sel) purple > select clear > select #8:95 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > color (#!8 & sel) byhetero > select clear > volume #3 level 0.032 > volume #3 level 0.03 > volume #3 level 0.027 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_foursub.png"" width 2000 > height 1283 supersample 3 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_foursub.cxs"" > select add #8 8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #8/A 2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected > show sel cartoons > select #8/A:95 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > undo > select clear > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub_slab.cxs"" > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub_slab.png"" width > 2000 height 1283 supersample 3 > select #8/A:95 8 atoms, 7 bonds, 1 residue, 1 model selected > view sel > view matrix models #3,1,0,0,0.015224,0,1,0,0.059115,0,0,1,0.35771 > undo > ui mousemode right zoom > select clear > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed In2.png"" width 2000 height > 1283 supersample 3 > save ""/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper > work/Comms Biol/Revisions/Figures/Glyc_Zoomed In3.png"" width 2000 height > 1283 supersample 3 > volume #3 level 0.1783 > volume #3 level 0.1027 > volume #3 level 0.05942 > volume #3 level -0.01623 > volume #3 level 0.0324 > hide #!8 models > show #!8 models > hide #!8 models > open /Users/omallen/Downloads/cryosparc_P313_J756_003_volume_map.mrc Opened cryosparc_P313_J756_003_volume_map.mrc as #9, grid size 256,256,256, pixel 1.58, shown at level 0.144, step 1, values float32 > view orient > open 6SJ7 6sj7 title: Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam [more info...] Chain information for 6sj7 #11 --- Chain | Description | UniProt A | DDB1- and CUL4-associated factor 15 | DCA15_HUMAN 1-600 B | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 C | RNA binding protein 39 | Q7Z3L0_HUMAN 248-328 D | DET1- and DDB1-associated protein 1 | DDA1_HUMAN 2-102 Non-standard residues in 6sj7 #11 --- EF6 — N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide (Indisulam) > ui mousemode right ""move picked models"" > hide #!11.1 models > view matrix models > #11,0.71475,0.38388,-0.58461,174.52,-0.6763,0.59236,-0.43787,294.97,0.17821,0.70834,0.683,-5.6429 > view matrix models > #11,-0.88799,-0.11778,0.44453,291.14,0.18333,0.79585,0.57708,44.891,-0.42175,0.59393,-0.68511,266.26 > ui tool show ""Fit in Map"" > fitmap #11 inMap #9 Fit molecule 6sj7 (#11) to map cryosparc_P313_J756_003_volume_map.mrc (#9) using 10007 atoms average map value = 0.7233, steps = 296 shifted from previous position = 30.5 rotated from previous position = 24.8 degrees atoms outside contour = 854, contour level = 0.1437 Position of 6sj7 (#11) relative to cryosparc_P313_J756_003_volume_map.mrc (#9) coordinates: Matrix rotation and translation -0.96673591 0.19683731 0.16333023 269.52054256 0.25460354 0.80164449 0.54087259 39.00515569 -0.02446887 0.56446540 -0.82509399 250.87525081 Axis 0.11921943 0.94898804 0.29190484 Axis point 137.77969920 0.00000000 112.83953566 Rotation angle (degrees) 174.32146085 Shift along axis 142.37921000 > molmap #11 onGrid #9 Missing or invalid ""resolution"" argument: Expected a number > molmap #11 16 onGrid #9 Opened 6sj7 map 16 as #12, grid size 256,256,256, pixel 1.58, shown at level 0.0525, step 1, values float32 > fitmap #12 inMap #9 Fit map 6sj7 map 16 in map cryosparc_P313_J756_003_volume_map.mrc using 76622 points correlation = 0.8649, correlation about mean = 0.4178, overlap = 1.131e+04 steps = 84, shift = 0.687, angle = 1.38 degrees Position of 6sj7 map 16 (#12) relative to cryosparc_P313_J756_003_volume_map.mrc (#9) coordinates: Matrix rotation and translation 0.99988241 -0.00855465 0.01272709 -0.89910725 0.00831586 0.99979059 0.01869838 -6.06949391 -0.01288438 -0.01859035 0.99974416 7.37574193 Axis -0.77233455 0.53047192 0.34942652 Axis point -0.00000000 391.22616132 330.45659224 Rotation angle (degrees) 1.38327003 Shift along axis 0.05199530 > volume #9 level 0.3458 > volume #12 level 0.001839 > volume #12 level 0.01833 > view matrix models > #12,0.45373,-0.8057,-0.38076,376.39,0.80977,0.55114,-0.20129,-17.403,0.37203,-0.21699,0.9025,-4.0655 > view matrix models > #12,0.9108,-0.34067,-0.23321,145.67,0.31558,0.9387,-0.13873,-20.497,0.26617,0.05276,0.96248,-57.694 > ui tool show ""Segment Map"" Segmenting cryosparc_P313_J756_003_volume_map.mrc, density threshold 0.345814 Showing 14 region surfaces 78 watershed regions, grouped to 14 regions Showing cryosparc_P313_J756_003_volume_map.seg - 14 regions, 14 surfaces > select #13.1 1 model selected > select add #13.9 2 models selected > select add #13.14 3 models selected > select add #13.13 4 models selected > select add #13.6 5 models selected > select add #13.4 6 models selected > select subtract #13.4 5 models selected > select add #13.4 6 models selected > select add #13.12 7 models selected Deleted 7 regions > select clear > select #13.7 1 model selected Saving 7 regions to mrc file... Opened map_7_regions.mrc as #14, grid size 58,73,68, pixel 1.58, shown at step 1, values float32 Wrote map_7_regions.mrc > volume resample #14 onGrid #9 Opened map_7_regions.mrc resampled as #15, grid size 256,256,256, pixel 1.58, shown at step 1, values float32 > save /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/map_7_regions_resampled.mrc > models #15 > volume #15 level 1.292 > hide #!13 models > volume #15 level 0.4511 > hide #!9 models > volume #15 level 0.3517 > volume #15 level 0.3041 > show #!9 models > open /Users/omallen/Downloads/cryosparc_P313_J759_mask.mrc Opened cryosparc_P313_J759_mask.mrc as #16, grid size 256,256,256, pixel 1.58, shown at level 1, step 1, values float32 > volume #16 level 1 > volume #16 level 0.9588 > volume #16 level 1 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job062/run_class001.mrc Opened run_class001.mrc as #17, grid size 256,256,256, pixel 1.58, shown at level 0.0116, step 1, values float32 > hide #!9 models > hide #!11 models > volume #17 level 0.03334 > show #!11 models > ui tool show ""Fit in Map"" > fitmap #11 inMap #17 Fit molecule 6sj7 (#11) to map run_class001.mrc (#17) using 10007 atoms average map value = 0.0313, steps = 240 shifted from previous position = 13.8 rotated from previous position = 60.5 degrees atoms outside contour = 5698, contour level = 0.033338 Position of 6sj7 (#11) relative to run_class001.mrc (#17) coordinates: Matrix rotation and translation -0.64234097 -0.74479546 0.18077003 343.22633017 -0.34156107 0.48933352 0.80242679 103.36828308 -0.68610066 0.45368759 -0.56871210 300.11049324 Axis -0.34267907 0.85180689 0.39622730 Axis point 234.89367307 0.00000000 66.00875952 Rotation angle (degrees) 149.41325564 Shift along axis 89.34530485 > volume #17 color #b2ffb266 > select #11/C 619 atoms, 630 bonds, 79 residues, 1 model selected > color sel red > select clear > volume #17 level 0.002008 > volume #17 level 0.02459 > view matrix models > #11,-0.64234,-0.7448,0.18077,342.43,-0.34156,0.48933,0.80243,100.04,-0.6861,0.45369,-0.56871,294.55 > undo > view matrix models > #11,0.67268,0.71217,0.2008,9.4553,0.52746,-0.65184,0.54488,180.42,0.51893,-0.26061,-0.81412,278.95 > fitmap #11 inMap #17 Fit molecule 6sj7 (#11) to map run_class001.mrc (#17) using 10007 atoms average map value = 0.03151, steps = 384 shifted from previous position = 9.27 rotated from previous position = 39 degrees atoms outside contour = 3240, contour level = 0.024589 Position of 6sj7 (#11) relative to run_class001.mrc (#17) coordinates: Matrix rotation and translation 0.08979009 0.91122303 0.40200788 30.74415073 0.78350020 -0.31381773 0.53632627 101.75575288 0.61487005 0.26681647 -0.74212115 194.42736612 Axis -0.73553430 -0.58093407 -0.34857552 Axis point 0.00000000 47.67444457 88.99258705 Rotation angle (degrees) 169.44339584 Shift along axis -149.49938255 > volume #17 level 0.04068 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/MaskCreate/job063/mask.mrc Opened mask.mrc as #18, grid size 256,256,256, pixel 1.58, shown at level 0.928, step 1, values float32 > volume #18 level 1 > volume #17 level 0.01443 > volume #17 level 0.02459 > hide #!11 models > define axis Axis 'root #/axis' centered at [321.32502677 156.20559228 181.8597633 ] with direction [0.99374045 0.11090819 0.01339028], radius 72.5463, and length 437.392 > hide #19 models > close #19 > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb Chain information for apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19 --- Chain | Description A B C D | No description available > color #19 plum > open /Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/PIP/PIP.pdb Chain information for PIP.pdb #20 --- Chain | Description A B C D | No description available > color #20 tan > define axis #19/A:130-145 helix 1 Expected a keyword > define axis #19/A:130-145 name helix 1 Expected a keyword > define axis #19/A:130-145 name helix1 Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/helix1' centered at [126.91378569 147.26547845 163.11951946] with direction [ 0.33965673 0.2027149 -0.91844432], radius 3.42558, and length 27.9339 > define axis #19/A:146-165 name helix2 Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/helix2' centered at [140.42476112 150.98442922 138.96805527] with direction [ 0.48456634 0.1824387 -0.85551831], radius 3.69231, and length 35.5654 > define axis #20/B:146-165 name helix2 Axis 'PIP.pdb #20/helix2' centered at [135.32000615 138.29886849 126.33923009] with direction [ 0.20806586 -0.46569925 0.86013534], radius 3.85312, and length 35.4863 > define axis #20/B:130-145 name helix1 Axis 'PIP.pdb #20/helix1' centered at [128.30159345 150.84037494 102.23041697] with direction [-0.0989714 0.3819789 -0.91885624], radius 3.40584, and length 28.3154 > view orient > dssp Computing secondary structure > view matrix models > #20,0.49764,0.82476,0.26857,-81.95,0.86684,-0.48384,-0.12034,103.34,0.030698,0.29269,-0.95571,205.51 > ui tool show Matchmaker > matchmaker #!20 to #19 Computing secondary structure 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 apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb, chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9 RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs: 1.165) > view matrix models > #20.2,1,-1.0949e-15,6.9389e-18,1.2194,2.9406e-16,1,-5.5511e-17,0.0046535,-1.5613e-17,-1.7347e-18,1,0.51765 > undo > view matrix models > #20,0.91434,-0.40301,0.039457,66.558,-0.40269,-0.91519,-0.016148,334.98,0.042618,-0.001124,-0.99909,258.88 > matchmaker #!20 to #19 Computing secondary structure 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 apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb, chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9 RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs: 1.165) > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 7796 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select #19.2 1 model selected > select #19.3 1 model selected > select #19.2 1 model selected > close #19.2 > select #19.3 1 model selected > ~select #19.3 Nothing selected > select #19.3 1 model selected > close #19.3 > define axis #19/B:130-145 name helix1 Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/helix1' centered at [138.72323696 126.92555733 163.04858197] with direction [-0.2043703 0.34036144 -0.91781636], radius 3.42999, and length 27.7661 > define axis #19/B:146-165 name helix2 Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/helix2' centered at [134.99428095 140.43821806 138.84666192] with direction [-0.18361269 0.48631942 -0.8542715 ], radius 3.69519, and length 35.3353 > select add #19 17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 4 models selected > select add #20 35123 atoms, 35599 bonds, 12 pseudobonds, 2358 residues, 8 models selected > hide sel cartoons > hide sel atoms > select clear > angle helix1 helix2 Missing or invalid ""objects"" argument: invalid objects specifier Choose exactly one axis or plane in table Either three or four atoms must be selected! > select #19.2 1 model selected > select #19.3 1 model selected > select #20.2 1 model selected > select #20.3 1 model selected > close #19.2-3#20.2-3 > select add #19 17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected > select add #20 35123 atoms, 35599 bonds, 12 pseudobonds, 2358 residues, 4 models selected > show sel cartoons > hide sel cartoons > select #19/A:130-165 538 atoms, 541 bonds, 36 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #19/A:130-162 503 atoms, 505 bonds, 33 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #19/A:135-162 446 atoms, 447 bonds, 28 residues, 1 model selected > show sel cartoons > select #20/A:135-162 446 atoms, 447 bonds, 28 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #20/B:135-162 446 atoms, 447 bonds, 28 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #20/C:135-162 446 atoms, 447 bonds, 28 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #20/D:135-162 446 atoms, 447 bonds, 28 residues, 1 model selected > show sel cartoons > select clear > lighting flat > lighting full > lighting soft > select #19/A:160 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #20/D:160 38 atoms, 36 bonds, 2 residues, 2 models selected > show sel cartoons > show sel atoms > hide sel atoms > show sel atoms > color sel byhetero > hide sel atoms > select #20/D:161 10 atoms, 9 bonds, 1 residue, 1 model selected > select #20/D:160 19 atoms, 18 bonds, 1 residue, 1 model selected > select #20/D:160 @CA 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > style sel ball Changed 1 atom style > show sel surfaces > show sel atoms > hide sel surfaces > select #20/D:160 @CA and sel #19/A:160 @CA Expected a keyword > select #20/D:160 @CA, sel #19/A:160 @CA 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #20/D:160@CA #19/A:160@CA Distance between PIP.pdb #20/D ILE 160 CA and apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A ILE 160 CA: 3.274Å > select #20/D:161 @CA, sel #19/A:161 @CA 2 atoms, 2 residues, 2 models selected > distance #19/A:161@CA #20/D:161@CA Distance between apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A ALA 161 CA and PIP.pdb #20/D ALA 161 CA: 3.956Å > select #20/D:162 @CA, sel #19/A:162 @CA 2 atoms, 2 residues, 2 models selected > distance #19/A:162@CA #20/D:162@CA Distance between apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A ARG 162 CA and PIP.pdb #20/D ARG 162 CA: 2.964Å > select #20/D:159 @CA, sel #19/A:159 @CA 2 atoms, 2 residues, 2 models selected > distance #19/A:159@CA #20/D:159@CA Distance between apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A LYS 159 CA and PIP.pdb #20/D LYS 159 CA: 1.843Å > ~distance #19/A:162@CA #20/D:162@CA > ~distance #19/A:159@CA #20/D:159@CA > distance style color black > select clear > select #20/D:153 @CA, sel #19/A:153 @CA 2 atoms, 2 residues, 2 models selected > distance #19/A:153@CA #20/D:153@CA Distance between apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A THR 153 CA and PIP.pdb #20/D THR 153 CA: 0.730Å > show sel atoms > select up 28 atoms, 26 bonds, 2 residues, 3 models selected > show sel atoms > hide sel atoms > select #20/D:157 @CA, sel #19/A:157 @CA 2 atoms, 2 residues, 2 models selected > distance #19/A:157@CA #20/D:157@CA Distance between apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A VAL 157 CA and PIP.pdb #20/D VAL 157 CA: 1.298Å > ~distance #19/A:157@CA #20/D:157@CA > ~distance #19/A:153@CA #20/D:153@CA > select clear > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > SilhouetteWidth 1 Unknown command: SilhouetteWidth 1 > silhouetteWidth 1 Unknown command: silhouetteWidth 1 > set silhouetteWidth 1 > color #19 orchid > color #19 plum > distance style decimalPlaces 2 > distance style decimalPlaces 1 > distance style dashes 10 > distance style dashes 11 > distance style dashes 10 > distance style dashes 9 > distance style dashes 8 > distance style dashes 7 > distance style dashes 8 > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting simple > lighting soft > ui tool show ""Color Actions"" > color plum > undo > color orchid > undo > hide #21.1 models > ui tool show ""Side View"" > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Tm2_distance.png"" width 2000 height 1372 supersample 3 > distance style radius 0.05 > color #19 #d2a4d3ff > color #19 #c197c2ff > select add #19 17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected > ui tool show ""Color Actions"" > color sel plum > color sel violet > color sel thistle > color sel pale violet red > color sel medium purple > color sel purple > color sel dark magenta > color sel dark orchid > color sel medium violet red > color sel medium orchid > color sel orchid > color sel blue violet > color sel hot pink > color sel dark violet > color sel deep pink > color sel magenta > color sel plum > color sel hot pink > color sel plum > select clear > distance style color #919191 > distance style color #797979 > distance style color #5e5e5e > select clear > lighting simple > undo > lighting soft > lighting full > lighting soft > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Tm2_distance2.png"" width 2000 height 1372 supersample 3 > define axis #19/A:15-162 name helix1 Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/helix1' centered at [134.57020804 153.82308149 159.60914644] with direction [ 0.2838401 0.08694491 -0.95492166], radius 7.16566, and length 66.8098 > tube helix_axis radius 0.2 Unknown command: tube helix_axis radius 0.2 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class001.mrc Opened run_it025_class001.mrc as #22, grid size 256,256,256, pixel 1.58, shown at level 1.45e-05, step 1, values float32 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class002.mrc Opened run_it025_class002.mrc as #23, grid size 256,256,256, pixel 1.58, shown at level 3.7e-06, step 1, values float32 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class003.mrc Opened run_it025_class003.mrc as #24, grid size 256,256,256, pixel 1.58, shown at level 1.84e-05, step 1, values float32 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class004.mrc Opened run_it025_class004.mrc as #25, grid size 256,256,256, pixel 1.58, shown at level 5.19e-06, step 1, values float32 > hide #!19 models > hide #!20 models > hide #!21 models > tile 4 models tiled > volume #25 level 0.03333 > volume #24 level 0.03377 > volume #23 level 0.03536 > volume #22 level 0.04029 > view matrix models > #24,-0.13795,0.6547,0.74319,-39.079,-0.96379,-0.26161,0.051559,405.56,0.22819,-0.70917,0.66709,65.401 > view matrix models > #24,-0.09808,0.9905,0.096334,11.045,-0.85286,-0.13354,0.50478,259.19,0.51285,-0.03265,0.85786,-189.06 > view matrix models > #23,-0.41384,0.32522,-0.85028,317.07,0.51048,-0.69044,-0.51254,265.69,-0.75375,-0.64616,0.11972,543.58 > view matrix models > #23,0.28316,-0.63997,-0.71433,372.69,0.62838,-0.43888,0.64228,-61.471,-0.72455,-0.63073,0.27786,483.08 > volume #25 level 0.005773 > volume #25 level 0.04583 > volume #24 level 0.03988 > hide #!22 models > hide #!23 models > hide #!24 models > hide #!25 models > show #!22 models > hide #!22 models > show #!19 models > show #!20 models > hide #!19 models > show #!19 models > select #19.2 1 model selected > select #19.2 1 model selected > hide #19.2 models > ui tool show Matchmaker > matchmaker #!20 to #19 Computing secondary structure 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 apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb, chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9 RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs: 1.165) > view orient > matchmaker #!20 to #19 Computing secondary structure 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 apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb, chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9 RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs: 1.165) > ~tile > matchmaker #!20 to #19 Computing secondary structure 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 apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb, chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9 RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs: 1.165) > hide #19.1 models > color #19 #cf88baff > show #!21 models > view orient > lighting soft > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Tm2_distance3_colourfixed.png"" width 2000 height 1372 > supersample 3 > show #21.1 models > color #21 #393939ff models > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Tm2_distance3_colourfixed_withlabels.png"" width 2000 height > 1372 supersample 3 > show #19.2 models > surface style #19 dot > cofr sel > close #19.2 > hide #!19 models > hide #!20 models > show #!4 models > hide #!4 models > show #!5 models > show #!6 models > view orient > color #5 #008f00ff > color #5 #009051ff > color #5 #4f8f00ff > color #5 #008f00ff > color #6 #00fa92ff > color #6 #99ff99ff > color #5 #336633ff > ui tool show Matchmaker > matchmaker #!6 to #5 Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 1610.2 RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs: 10.379) Drag select of 155 atoms, 157 bonds, 1014 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain C (#5) with Kir2.2_Extended , chain C (#6), sequence alignment score = 588.3 RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 125 pairs: 5.614) > select clear > select add #5 10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 10 models selected > hide sel cartoons > hide sel atoms > select #5/A:130-160 243 atoms, 249 bonds, 31 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #5/A:150-180 225 atoms, 227 bonds, 31 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #5/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select #6/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select clear > matchmaker #!6 & sel to #5 & sel No 'to' model specified Drag select of 62 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 148.7 RMSD between 31 pruned atom pairs is 0.597 angstroms; (across all 31 pairs: 0.597) > undo > redo > matchmaker #!6 to #5 Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 1610.2 RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs: 10.379) > select add #5 11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected > show sel cartoons Drag select of 963 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 568.5 RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 117 pairs: 0.945) > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 568.5 RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 117 pairs: 0.945) > select add #5 14503 atoms, 11037 bonds, 8 pseudobonds, 1831 residues, 11 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 14 models selected > hide sel cartoons > select #5/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select #6/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select add #5 11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected > select subtract #5 227 atoms, 229 bonds, 31 residues, 6 models selected > select add #5 11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected > hide sel cartoons > select #6/B:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select #5/B:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select add #6 10423 atoms, 10630 bonds, 10 pseudobonds, 1335 residues, 6 models selected > select add #5 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected > show sel cartoons > select ions 22 atoms, 22 residues, 7 models selected > show #!5-6 atoms > hide #!5-6 atoms > select ::name=""K"" 91 atoms, 91 residues, 8 models selected > show sel & #!5-6 atoms > hide sel & #!5-6 atoms Drag select of 497 residues > ui tool show Matchmaker > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain C (#5) with Kir2.2_Extended , chain C (#6), sequence alignment score = 353 RMSD between 69 pruned atom pairs is 0.301 angstroms; (across all 69 pairs: 0.301) > select add #5 12756 atoms, 11037 bonds, 8 pseudobonds, 1598 residues, 11 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 14 models selected > hide sel cartoons > select #5/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > select up 2659 atoms, 2720 bonds, 332 residues, 2 models selected > select #6/A:156-186 227 atoms, 229 bonds, 31 residues, 1 model selected > show sel cartoons > view orient > select clear > select #5/A:185 @CA, sel #6/A:185 @CA 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #5/A:185@CA #6/A:185@CA Distance between Kir2.2_docked_3SPI #5/A ALA 185 CA and Kir2.2_Extended #6/A ALA 185 CA: 2.8Å > distance style color #666666 > distance style color #333333 > select #5/A:184 @CA, sel #6/A:184 @CA 2 atoms, 2 residues, 2 models selected > distance #5/A:184@CA #6/A:184@CA Distance between Kir2.2_docked_3SPI #5/A MET 184 CA and Kir2.2_Extended #6/A MET 184 CA: 2.7Å > distance style color #666666 > distance style color #333333 > distance style color black > select clear > distance style color white > distance style color #cccccc > distance style color #999999 > distance style color white > distance style color black > distance style color #666666 > hide #21.1 models > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Figures/Kir2_TM2_distances.png"" width 2000 height 1372 > supersample 3 > show #21.1 models > hide #!21 models > hide #21.1 models > select add #5 10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected > select add #6 21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 10 models selected > show sel cartoons > view orient > hide #!5 models > select clear > select #5/A:372 @CA, sel #5/A:118 @CA 2 atoms, 2 residues, 1 model selected > select #6/A:372 @CA, sel #6/A:118 @CA 2 atoms, 2 residues, 1 model selected > distance #6/A:118@CA #6/A:372@CA Distance between Kir2.2_Extended #6/A ASP 118 CA and SER 372 CA: 127.0Å > show #!21 models > select #6/A:372 @CA, sel #6/B:118 @CA 2 atoms, 2 residues, 1 model selected > distance #6/A:372@CA #6/B:118@CA Distance between Kir2.2_Extended #6/A SER 372 CA and /B ASP 118 CA: 122.5Å > hide #!21 models > show #!5 models > hide #!6 models > select #5/A:372 @CA, sel #5/B:118 @CA 2 atoms, 2 residues, 1 model selected > distance #5/A:372@CA #5/B:118@CA Distance between Kir2.2_docked_3SPI #5/A SER 372 CA and /B ASP 118 CA: 116.6Å > show #!21 models > hide #!21 models > show #!6 models Drag select of 1599 residues > matchmaker #!6 & sel to #5 & sel Computing secondary structure 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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A (#6), sequence alignment score = 943.3 RMSD between 177 pruned atom pairs is 0.492 angstroms; (across all 197 pairs: 12.111) > hide #!6 models > hide #!5 models > show #!1 models > show #1.1 models > hide #1.1 models > show #!2 models > show #!4 models > show #!7 models > view orient > hide #!7 models > hide #!4 models > matchmaker #!2 & sel to #1 & sel No 'to' model specified > matchmaker #!2 to #1 Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 1628 RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs: 6.565) Drag select of 90 atoms, 946 residues, 85 bonds > matchmaker #!2 & sel to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain C (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 585.1 RMSD between 80 pruned atom pairs is 1.085 angstroms; (across all 119 pairs: 2.722) Drag select of 3 atoms, 590 residues > matchmaker #!2 & sel to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2), sequence alignment score = 368.3 RMSD between 42 pruned atom pairs is 0.687 angstroms; (across all 74 pairs: 3.087) > color #1 #000099ff > color #1 #0000ccff > color #1 #3333ccff > color #1 #6666ccff > color #1 #3333ccff > color #1 #333399ff > color #1 #6666ccff > color #1 #3333ccff > color #1 #6666ccff > color #2 #3399ccff > color #2 #3366ccff > color #2 #6699ffff > color #2 #3399ffff > color #2 #3399ccff > color #2 #6699ccff > color #2 #99ccffff > color #2 #009999ff > color #2 #66ffffff > color #2 #00ccccff > color #2 #009999ff > color #2 #66ccffff > color #2 #33ccffff > color #2 #00ccffff > color #2 #00d4ffff > color #2 #0099ccff > color #1 #9999ffff > color #1 #3333ccff > color #1 #333399ff > color #1 #3300ffff > color #1 #3300ccff > select clear > select add #1 10403 atoms, 10644 bonds, 16 pseudobonds, 1315 residues, 2 models selected > select add #2 19839 atoms, 20278 bonds, 24 pseudobonds, 2555 residues, 5 models selected > hide sel cartoons > hide sel atoms > select #1/A:156-186 221 atoms, 223 bonds, 31 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #1/A:166-190 168 atoms, 168 bonds, 25 residues, 1 model selected > show sel cartoons > select #1/A:166-195 208 atoms, 209 bonds, 30 residues, 1 model selected > show sel cartoons > select #1/A:166-199 239 atoms, 241 bonds, 34 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #1/A:170-192 162 atoms, 162 bonds, 23 residues, 1 model selected > show sel cartoons > select #1/A:170-193 169 atoms, 169 bonds, 24 residues, 1 model selected > show sel cartoons > select #1/A:170-194 178 atoms, 178 bonds, 25 residues, 1 model selected > show sel cartoons > select #1/A:170-195 186 atoms, 186 bonds, 26 residues, 1 model selected > show sel cartoons > select #1/A:170-196 192 atoms, 192 bonds, 27 residues, 1 model selected > show sel cartoons > select #1/A:170-197 201 atoms, 201 bonds, 28 residues, 1 model selected > show sel cartoons > select #2/A:170-197 182 atoms, 182 bonds, 27 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #2/b:170-197 189 atoms, 189 bonds, 27 residues, 1 model selected > show sel cartoons > select clear > view orient > select #1/A:195 @CA, sel #2/B:195 @CA 2 atoms, 2 residues, 2 models selected > distance #1/A:195@CA #2/B:195@CA Distance between Kir3.2_docked #1/A ILE 195 CA and Kir3.1_extended #2/B ILE 195 CA: 3.4Å > distance #1/A:195@CA #2/B:195@CA Distance already exists; modify distance properties with 'distance style' > show #!21 models > close #22-25 > show #21.1 models > distance style color black > distance style color #333333 > distance style color #666666 > select #1/A:196 @CA, sel #2/B:196 @CA 2 atoms, 2 residues, 2 models selected > distance #1/A:196@CA #2/B:196@CA Distance between Kir3.2_docked #1/A SER 196 CA and Kir3.1_extended #2/B SER 196 CA: 3.5Å > distance style color #333333 > distance style color #999999 > distance style color #666666 > hide #21.1 models > select clear > color #21 white models > color #21 #ccccccff models > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Figures/Kir3_TM2_distances.png"" width 2000 height 1372 > supersample 3 > hide #!1 models > hide #!2 models > show #!4 models > show #!7 models > matchmaker #!7 & sel to #4 & sel No 'to' model specified > matchmaker #!7 to #4 Computing secondary structure 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 Kir3.2_docked_Xtal_3SYA, chain A (#4) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 1649.6 RMSD between 303 pruned atom pairs is 0.557 angstroms; (across all 309 pairs: 0.703) > view orient Drag select of 690 residues > matchmaker #!7 & sel to #4 & sel Computing secondary structure 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 Kir3.2_docked_Xtal_3SYA, chain B (#4) with Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 406.6 RMSD between 79 pruned atom pairs is 0.649 angstroms; (across all 79 pairs: 0.649) > select clear > hide #!4 models > hide #!7 models > show #21.1 models > show #!1 models > show #!2 models > view orient > select add #1 10403 atoms, 10644 bonds, 16 pseudobonds, 1315 residues, 2 models selected > select add #2 19839 atoms, 20278 bonds, 24 pseudobonds, 2555 residues, 5 models selected > show sel cartoons > hide #!21 models > hide #21.1 models > tile 2 models tiled > select #1 @L Nothing selected > select #1 @K 3 atoms, 3 residues, 1 model selected > show sel atoms > color sel purple > select #2 @K Nothing selected > select ligand 599 atoms, 601 bonds, 17 residues, 5 models selected > show sel & #!1 atoms > color (#!1 & sel) gray > color (#!1 & sel) byhetero > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Figures/Kir3Cryo_newcolours.png"" width 2000 height 1372 > supersample 3 > select #1/A:381 @CA, sel #1/B:128 @CA 2 atoms, 2 residues, 1 model selected > distance #1/A:381@CA #1/B:128@CA Distance between Kir3.2_docked #1/A SER 381 CA and /B ASP 128 CA: 117.5Å > show #!21 models > show #21.1 models > select #1/A:381 @CA, sel #1/C:128 @CA 2 atoms, 2 residues, 1 model selected > distance #1/A:381@CA #1/C:128@CA Distance between Kir3.2_docked #1/A SER 381 CA and /C ASP 128 CA: 110.6Å > select #2/A:381 @CA, sel #2/C:128 @CA 2 atoms, 2 residues, 1 model selected > distance #2/A:381@CA #2/C:128@CA Distance between Kir3.1_extended #2/A SER 381 CA and /C ASP 128 CA: 120.5Å > select #2/A:381 @CA, sel #2/B:128 @CA 2 atoms, 2 residues, 1 model selected > distance #2/A:381@CA #2/B:128@CA Distance between Kir3.1_extended #2/A SER 381 CA and /B ASP 128 CA: 117.8Å > hide #!21 models > hide #21.1 models > matchmaker #!2 to #1 Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2), sequence alignment score = 1628 RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs: 6.565) > view orient Drag select of 3 atoms, 728 residues > matchmaker #!2 to #1 & sel Computing secondary structure 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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2), sequence alignment score = 435.8 RMSD between 55 pruned atom pairs is 0.771 angstroms; (across all 87 pairs: 2.917) > select clear > hide #!1 models > hide #!2 models > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job068/run_class001.mrc Opened run_class001.mrc as #22, grid size 256,256,256, pixel 1.58, shown at level 0.0134, step 1, values float32 Cell requested for row 24 is out of bounds for table with 26 rows! Resizing table model. > volume #22 level 0.02948 > volume #22 level 0.02692 > volume #22 level 0.03127 > close #22 > close #18 > close #17 > close #16 > close #15 > close #14 > close #12 > close #9 > show #!8 models > show #!20 models > select add #20 18025 atoms, 18271 bonds, 4 pseudobonds, 1200 residues, 2 models selected > select add #8 26751 atoms, 27227 bonds, 12 pseudobonds, 2358 residues, 5 models selected > show sel cartoons > tile 2 models tiled > select clear Drag select of 331 residues, 1 pseudobonds > view matrix models > #20,-0.16321,-0.21381,-0.96315,470.17,-0.75078,0.66027,-0.019353,155.36,0.64007,0.71995,-0.26828,-23.4 Drag select of 48 residues > view matrix models > #20,0.75528,-0.65366,0.047827,272.81,-0.14093,-0.23324,-0.96215,315.88,0.64007,0.71995,-0.26828,-23.4 > view matrix models > #20,0.29123,-0.95519,0.052933,381.63,0.04883,-0.040417,-0.99799,265.81,0.95541,0.29323,0.034871,-46.716 > view matrix models > #20,0.66256,-0.74856,0.02573,293.46,-0.0818,-0.10646,-0.99095,298.22,0.74452,0.65446,-0.13177,-46.643 > tile 2 models tiled > view matrix models > #20,0.24024,-0.97037,-0.025724,386.52,0.018723,0.031127,-0.99934,265.21,0.97053,0.2396,0.025646,-40.016 > view matrix models > #8,0.38445,0.91981,0.078409,-52.614,0.033901,-0.098947,0.99452,15.975,0.92252,-0.37968,-0.069223,68.157 > view matrix models > #8,-0.15124,0.98446,0.089229,12.157,-0.17678,-0.11575,0.97742,48.541,0.97256,0.13205,0.19154,-47.726 > view matrix models > #20,-0.54084,-0.84105,0.011437,474.92,-0.034471,0.0085763,-0.99937,276.05,0.84042,-0.54089,-0.03363,97.873 > view matrix models > #8,-0.46171,0.88703,-0.00085161,86.316,-0.05421,-0.027258,0.99816,16.795,0.88537,0.4609,0.060671,-64.432 > tile 2 models tiled > select clear > select ions 22 atoms, 22 residues, 7 models selected > show sel & #!8,20 atoms > color (#!8,20 & sel) purple > select ligand 599 atoms, 601 bonds, 17 residues, 5 models selected > show sel & #!20 atoms > color (#!20 & sel) gray > color (#!20 & sel) byhetero > select clear > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Figures/apo_Pip_tiled.png"" width 2000 height 1429 supersample > 3 > hide #20.1 models > hide #8.1 models > save ""/Users/omallen/Library/CloudStorage/OneDrive- > TheFrancisCrickInstitute/PhD/Paper work/Comms > Biol/Revisions/Figures/apo_Pip_tiled.png"" width 2000 height 1429 supersample > 3 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job069/run_class001.mrc Opened run_class001.mrc as #9, grid size 256,256,256, pixel 1.58, shown at level 0.00186, step 1, values float32 > volume #9 level 0.03067 > hide #!20 models > hide #!8 models > hide #!9 models > view orient > show #!9 models > show #!11 models > ui tool show ""Fit in Map"" > fitmap #11 inMap #9 Fit molecule 6sj7 (#11) to map run_class001.mrc (#9) using 10007 atoms average map value = 0.03375, steps = 228 shifted from previous position = 32.3 rotated from previous position = 49.9 degrees atoms outside contour = 4316, contour level = 0.030673 Position of 6sj7 (#11) relative to run_class001.mrc (#9) coordinates: Matrix rotation and translation 0.99433780 -0.09061646 -0.05550682 101.79562929 -0.05910615 -0.90570343 0.41977110 293.48040104 -0.08831090 -0.41411347 -0.90593113 376.53075065 Axis -0.99851560 0.03928048 0.03773129 Axis point 0.00000000 190.30497819 157.71139516 Rotation angle (degrees) 155.31923086 Shift along axis -75.90948186 > volume #9 level 0.04591 > fitmap #11 inMap #9 Fit molecule 6sj7 (#11) to map run_class001.mrc (#9) using 10007 atoms average map value = 0.03375, steps = 88 shifted from previous position = 3.96 rotated from previous position = 0.0427 degrees atoms outside contour = 7849, contour level = 0.045909 Position of 6sj7 (#11) relative to run_class001.mrc (#9) coordinates: Matrix rotation and translation 0.99428878 -0.09129715 -0.05526906 101.84986112 -0.05983739 -0.90571356 0.41964560 293.59742102 -0.08837040 -0.41394176 -0.90600380 376.55342324 Axis -0.99850279 0.03965004 0.03768370 Axis point 0.00000000 190.37015563 157.71751793 Rotation angle (degrees) 155.32827716 Shift along axis -75.86629249 > volume #9 level 0.01687 > open /Volumes/lab- > enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job069/run_class001.mrc Opened run_class001.mrc as #12, grid size 256,256,256, pixel 1.58, shown at level 0.00186, step 1, values float32 > volume #12 level 0.03947 > volume #9 level 0.0521 > close #9 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03418, steps = 224 shifted from previous position = 26.4 rotated from previous position = 54.5 degrees atoms outside contour = 6577, contour level = 0.039471 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation -0.46865470 0.85076609 -0.23782300 185.81509494 0.39283855 0.44184949 0.80650285 27.83733276 0.79122727 0.28454532 -0.54128856 143.19978766 Axis -0.42045772 -0.82894125 -0.36887899 Axis point 67.71969256 0.00000000 90.80998324 Rotation angle (degrees) 141.63261395 Shift along axis -154.02629851 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03418, steps = 28 shifted from previous position = 0.0502 rotated from previous position = 0.0956 degrees atoms outside contour = 6574, contour level = 0.039471 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation -0.46791709 0.85105784 -0.23823117 185.75763912 0.39399654 0.44217314 0.80576026 27.78169444 0.79108803 0.28316674 -0.54221422 143.54115861 Axis -0.42091195 -0.82904350 -0.36813042 Axis point 67.60427484 0.00000000 90.97782049 Rotation angle (degrees) 141.62635577 Shift along axis -154.06171078 > volume #12 level 0.02424 > volume #12 color #ffb2ff5f > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03418, steps = 56 shifted from previous position = 4.76 rotated from previous position = 0.0899 degrees atoms outside contour = 2747, contour level = 0.024235 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation -0.46862597 0.85077202 -0.23785840 185.81524204 0.39290483 0.44188825 0.80644932 27.83241111 0.79121137 0.28446738 -0.54135275 143.22098099 Axis -0.42047597 -0.82895418 -0.36882913 Axis point 67.71499591 0.00000000 90.82172599 Rotation angle (degrees) 141.63246184 Shift along axis -154.02670766 > volume #12 level 0.03328 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03418, steps = 56 shifted from previous position = 3.87 rotated from previous position = 0.0178 degrees atoms outside contour = 5053, contour level = 0.033282 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation -0.46836291 0.85092116 -0.23784302 185.76367610 0.39304706 0.44175420 0.80645346 27.83085898 0.79129649 0.28422940 -0.54135335 143.24058560 Axis -0.42061606 -0.82890206 -0.36878653 Axis point 67.67736784 0.00000000 90.82243602 Rotation angle (degrees) 141.62653563 Shift along axis -154.02943948 > select ~sel & ##selected Nothing selected > ~tile > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.0003262, steps = 236 shifted from previous position = 47.3 rotated from previous position = 45.7 degrees atoms outside contour = 10007, contour level = 0.033282 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation 0.70061388 -0.31864902 -0.63843793 186.55126673 0.36706448 0.92822770 -0.06047317 -54.96602944 0.61188550 -0.19197956 0.76729393 1.56492783 Axis -0.09183000 -0.87309222 0.47882901 Axis point 114.59604058 0.00000000 243.00785344 Rotation angle (degrees) 45.72781528 Shift along axis 31.60874306 > view matrix models > #11,-0.8111,0.11823,0.57284,152.5,0.48208,-0.41949,0.76917,159.64,0.33125,0.90003,0.28325,112.95 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03467, steps = 364 shifted from previous position = 49.5 rotated from previous position = 95.1 degrees atoms outside contour = 5115, contour level = 0.033282 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation 0.50735679 0.69735299 -0.50624884 118.49709550 0.67430608 0.04452072 0.73710866 35.51158285 0.53656351 -0.71534379 -0.44764150 289.74214007 Axis -0.81224938 -0.58316793 -0.01288843 Axis point 0.00000000 84.76514035 157.18697421 Rotation angle (degrees) 116.60787607 Shift along axis -120.69273040 > view matrix models > #11,-0.027121,-0.99858,-0.045791,220.74,0.87327,-0.0013743,-0.48724,230.03,0.48648,-0.053202,0.87207,142.37 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03418, steps = 136 shifted from previous position = 4.26 rotated from previous position = 27.1 degrees atoms outside contour = 5053, contour level = 0.033282 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation -0.46847093 0.85085988 -0.23784964 185.78392314 0.39295787 0.44179848 0.80647268 27.83216714 0.79127688 0.28434413 -0.54132185 143.22248403 Axis -0.42055290 -0.82891874 -0.36882108 Axis point 67.69413823 0.00000000 90.81765829 Rotation angle (degrees) 141.62802180 Shift along axis -154.02604282 > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view matrix models > #11,-0.78356,0.60669,-0.13401,133.8,-0.25607,-0.51186,-0.82002,473.41,-0.5661,-0.60821,0.55643,375.67 > fitmap #11 inMap #12 Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms average map value = 0.03449, steps = 180 shifted from previous position = 8.6 rotated from previous position = 27.8 degrees atoms outside contour = 4970, contour level = 0.033282 Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates: Matrix rotation and translation 0.69569132 -0.62402153 -0.35582401 241.26668748 -0.28241673 -0.69305292 0.66326346 266.39772163 -0.66049556 -0.36093600 -0.65838503 403.86318687 Axis -0.91297186 0.27158435 0.30450667 Axis point 0.00000000 238.23352020 196.25774460 Rotation angle (degrees) 145.88089166 Shift along axis -24.94120924 > volume #12 level 0.03185 > hide #!11 models > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_000.mrc Opened J764_component_000_frame_000.mrc as #9, grid size 256,256,256, pixel 1.58, shown at level 0.186, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_001.mrc Opened J764_component_000_frame_001.mrc as #14, grid size 256,256,256, pixel 1.58, shown at level 0.175, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_002.mrc Opened J764_component_000_frame_002.mrc as #15, grid size 256,256,256, pixel 1.58, shown at level 0.167, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_003.mrc Opened J764_component_000_frame_003.mrc as #16, grid size 256,256,256, pixel 1.58, shown at level 0.158, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_004.mrc Opened J764_component_000_frame_004.mrc as #17, grid size 256,256,256, pixel 1.58, shown at level 0.151, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_005.mrc Opened J764_component_000_frame_005.mrc as #18, grid size 256,256,256, pixel 1.58, shown at level 0.149, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_006.mrc Opened J764_component_000_frame_006.mrc as #22, grid size 256,256,256, pixel 1.58, shown at level 0.148, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_007.mrc Opened J764_component_000_frame_007.mrc as #23, grid size 256,256,256, pixel 1.58, shown at level 0.152, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_008.mrc Opened J764_component_000_frame_008.mrc as #24, grid size 256,256,256, pixel 1.58, shown at level 0.163, step 1, values float32 > open > /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_009.mrc Opened J764_component_000_frame_009.mrc as #25, grid size 256,256,256, pixel 1.58, shown at level 0.173, step 1, values float32 > view orient > volume #12 level 0.03709 > volume #9 level 0.2566 > morph map #9 #14 #15 #16 #17 #18 #22 #23 #24 #25 Missing or invalid ""structures"" argument: invalid structures specifier > volume morph #9 #14 #15 #16 #17 #18 #22 #23 #24 #25 Opened morph as #26, grid size 256,256,256, pixel 1.58, shown at step 1, values float32 > volume #26 level 0.4972 > open /Volumes/lab-enchevr/home/users/omallen/EMReady/J743_Emready.mrc Opened J743_Emready.mrc as #27, grid size 403,403,403, pixel 1, shown at level 0.000534, step 2, values float32 > volume #27 step 1 > volume #27 level 0.6289 > volume #27 level 2.896 > view orient > show #!11 models > ui tool show ""Fit in Map"" > fitmap #11 inMap #27 Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms average map value = -0.01947, steps = 992 shifted from previous position = 5.5 rotated from previous position = 5.01 degrees atoms outside contour = 10007, contour level = 2.8959 Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates: Matrix rotation and translation -0.53074699 0.82519195 0.19330222 28.09888167 -0.59495104 -0.20031971 -0.77839907 460.23133519 -0.60360646 -0.52813836 0.59726791 368.46025924 Axis 0.15189650 0.48368613 -0.86196008 Axis point 200.25391132 320.72389772 0.00000000 Rotation angle (degrees) 124.53429428 Shift along axis -90.72239814 > view matrix models > #11,-0.38608,0.90188,0.1938,-7.2077,-0.9199,-0.39206,-0.0081081,325.1,0.068669,-0.18141,0.98101,98.361 > view matrix models > #11,-0.38608,0.90188,0.1938,114.6,-0.9199,-0.39206,-0.0081081,354.57,0.068669,-0.18141,0.98101,106.94 > fitmap #11 inMap #27 Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms average map value = 2.143, steps = 124 shifted from previous position = 4.77 rotated from previous position = 18 degrees atoms outside contour = 6154, contour level = 2.8959 Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates: Matrix rotation and translation -0.33703701 0.92749782 0.16172107 108.92911063 -0.87849186 -0.37158842 0.30028977 310.11554454 0.33861181 -0.04086187 0.94003838 67.67645465 Axis -0.18476366 -0.09580191 -0.97810244 Axis point 150.00885463 121.91561484 0.00000000 Rotation angle (degrees) 112.59988967 Shift along axis -116.03030750 > view matrix models > #11,-0.34775,0.91745,0.19326,109.05,-0.90859,-0.38062,0.17203,324.1,0.23138,-0.11577,0.96595,87.111 > view matrix models > #11,-0.78514,-0.60638,0.12596,352.48,0.61209,-0.79074,0.0086353,215.43,0.094364,0.083877,0.992,76.048 > view matrix models > #11,-0.24201,-0.9701,0.018102,343.82,0.96841,-0.24035,0.066429,105.28,-0.060093,0.033607,0.99763,99.641 > fitmap #11 inMap #27 Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms average map value = 3.129, steps = 248 shifted from previous position = 5.98 rotated from previous position = 44.6 degrees atoms outside contour = 4087, contour level = 2.8959 Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates: Matrix rotation and translation -0.84058908 -0.52777873 -0.12189943 384.04332990 0.53377744 -0.84537263 -0.02065475 241.32088288 -0.09214932 -0.08242931 0.99232743 115.20977036 Axis -0.05807146 -0.02796672 0.99792062 Axis point 160.20443367 178.41234895 0.00000000 Rotation angle (degrees) 147.86715639 Shift along axis 85.91929558 > volume #27 level 4.522 > volume #27 level 2.255 > volume #27 color #b2ffb267 > molmap #11 16 onGrid #27 Opened 6sj7 map 16 as #28, grid size 403,403,403, pixel 1, shown at level 0.0526, step 1, values float32 > volume #28 level 3.315e-05 > volume #28 level 0.0142 No map chosen to save > save ""/Users/omallen/OneDrive - The Francis Crick > Institute/PP/CRL4DCAF15/6sj7mask.mrc"" models #28 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/omallen/Downloads/cryosparc_P313_J767_002_volume_map.mrc Opened cryosparc_P313_J767_002_volume_map.mrc as #1, grid size 256,256,256, pixel 1.58, shown at level 0.143, step 1, values float32 > open /Users/omallen/Downloads/cryosparc_P313_J767_002_volume_map.mrc Opened cryosparc_P313_J767_002_volume_map.mrc as #2, grid size 256,256,256, pixel 1.58, shown at level 0.143, step 1, values float32 OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: MPHE3B/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.1.2 OS Loader Version: 13822.1.2 Software: System Software Overview: System Version: macOS 26.0 (25A354) Kernel Version: Darwin 25.0.0 Time since boot: 8 days, 4 hours, 14 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL U2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 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: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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: 1.18.1 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 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: 1.41 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX