id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17176 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000328c8f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000327c83000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000326c77000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000325c6b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000324c5f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000323c53000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000322c47000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321c3b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000315563000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000314557000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031354b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000002084d8840 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, 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chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 67) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-21 18:21:59.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""3BA56CF7-EBB8-4B7A-8077-A15083E24A31""} { ""uptime"" : 200000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,7"", ""coalitionID"" : 4012, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kompa012/Desktop/NiP N protein article/7nt5_J377_intactmodel- > coot-0_real_space_refined_030.pdb"" Chain information for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1 --- Chain | Description D E F G H I J K L M N O P Q | No description available Z | No description available > open ""/Users/kompa012/Desktop/NiP N protein article/pdb_extract_3032647.cif"" Summary of feedback from opening /Users/kompa012/Desktop/NiP N protein article/pdb_extract_3032647.cif --- warning | Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for pdb_extract_3032647.cif #2 --- Chain | Description D E F G H I J K L M N O P Q | No description available Z | No description available > hide #1 models > show #1 models > hide #2 models > show #2 models > open 7nt5 fromDatabase pdb format mmcif Summary of feedback from opening 7nt5 fetched from pdb --- note | Fetching compressed mmCIF 7nt5 from http://files.rcsb.org/download/7nt5.cif 7nt5 title: CryoEM structure of the Nipah virus nucleocapsid single helical turn assembly [more info...] Chain information for 7nt5 #3 --- Chain | Description | UniProt A B C D E F G H I J K L M | Nucleoprotein | NCAP_NIPAV 1-532 N | RNA (78-MER) | > open ""/Users/kompa012/Desktop/NiP N protein article/NiV N > protein/cryosparc_P78_J377_009_volume_map.mrc"" Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540, pixel 0.885, shown at level 0.0369, step 4, values float32 > volume #4 step 1 > hide #!3 models > ui tool show ""Hide Dust"" > surface dust #4 size 5.31 > select add #1 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > style sel stick Changed 44996 atom styles > hide #2 models > select add #4 44996 atoms, 45905 bonds, 5656 residues, 3 models selected > select subtract #1 2 models selected > transparency #4.1 70 > volume #4 level 0.03 > volume #4 level 0.02 > volume #4 level 0.015 > volume #4 level 0.05 > ui mousemode right select > select clear > volume #4 level 0.06 > select add #1 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > show sel surfaces > select subtract #1 15 models selected > select add #1.15 1680 atoms, 84 residues, 1 model selected > hide sel surfaces > show sel cartoons > select clear > select add #1 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > color zone #4 near sel & #1 distance 5.31 > select clear > hide #!1 models > open ""/Users/kompa012/Desktop/NiP N protein article/NiV N > protein/cryosparc_P78_J379_map_sharp.mrc"" Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel 0.885, shown at level 0.000704, step 4, values float32 > volume #5 step 1 > volume #5 level 0.02408 > surface dust #5 size 5.31 > volume #5 level 0.06 > volume #4 level 0.025 > show #!5 models > hide #!4 models > show #!1 models > select add #1 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > hide sel surfaces > show sel atoms > select clear > select add #5 2 models selected > transparency #5.1 80 > select clear > volume #5 level 0.04 > transparency #1,5 60 > hide #!5 models > select add #1 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > select subtract #1.10 41902 atoms, 42758 bonds, 5258 residues, 16 models selected > select subtract #1.11 38808 atoms, 39611 bonds, 4860 residues, 15 models selected > select subtract #1.15 37128 atoms, 37764 bonds, 4776 residues, 14 models selected > hide sel atoms > select subtract #1.9 34034 atoms, 34617 bonds, 4378 residues, 13 models selected > select add #1.9 37128 atoms, 34617 bonds, 4776 residues, 12 models selected > select add #1 44996 atoms, 45905 bonds, 5656 residues, 13 models selected > select subtract #1 15 models selected > select add #1.9 3094 atoms, 398 residues, 1 model selected > show sel atoms > select clear Cell requested for row 3 is out of bounds for table with 20 rows! Resizing table model. > ui tool show Contacts > select add #1.15 1680 atoms, 84 residues, 1 model selected > select add #1.10 4774 atoms, 482 residues, 2 models selected > select add #1.11 7868 atoms, 880 residues, 3 models selected > select add #1.9 10962 atoms, 1278 residues, 4 models selected > contacts sel restrict both ignoreHiddenModels true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 5727 contacts atom1 atom2 overlap distance 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1 0.708 3.052 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1 0.578 3.182 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 269 CB 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O 0.363 2.937 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG 0.325 3.195 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG 0.323 3.437 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 124 CD 0.280 3.240 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB 0.265 3.495 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 124 CD 0.261 3.259 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 133 O 0.255 3.045 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 133 O 0.238 3.062 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 133 O 0.236 3.064 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 124 CD 0.234 3.286 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 284 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 288 NE2 0.232 2.428 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 288 NE2 0.228 2.432 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 349 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 51 N3 0.228 3.052 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH 0.222 2.258 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 CD 0.220 3.120 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 154 NH1 0.217 2.443 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 374 CG2 0.216 3.544 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 169 O 0.216 2.964 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 34 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 98 O 0.214 3.086 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 192 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 54 P 0.213 3.527 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 169 O 0.211 2.969 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 376 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 278 CG 0.210 3.310 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 349 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 63 N3 0.208 3.072 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 103 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 41 CB 0.205 3.555 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 287 O 0.204 3.096 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 89 NH1 0.201 3.319 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG 0.198 3.142 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 89 NH1 0.197 3.323 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 169 O 0.191 2.989 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 154 NH1 0.191 2.469 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 279 CD1 0.191 3.209 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 328 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 331 CB 0.189 3.111 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 160 OG1 0.187 3.153 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 280 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CD1 0.187 3.573 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 268 CE1 0.186 3.214 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 3 N 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 381 CD 0.185 3.335 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 332 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 329 O 0.179 2.301 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 268 CE1 0.178 3.222 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 276 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 292 ND2 0.177 2.483 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 233 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 O 0.176 2.664 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1 0.176 3.344 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 318 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 20 NH2 0.176 3.344 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 12 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 0.174 3.106 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 315 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 250 CD 0.174 3.126 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 89 NH1 0.174 3.346 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 144 CD 0.173 3.347 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 154 NH1 0.173 2.487 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CG 0.172 3.128 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 329 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 332 OG 0.171 2.309 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 344 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 342 CG 0.170 3.170 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 373 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 388 CG 0.170 3.130 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 160 OG1 0.169 3.171 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 15 NE2 0.166 3.234 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CG 0.165 3.135 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 0.165 3.235 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CG 0.162 3.138 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2 0.160 3.240 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 344 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 342 CG 0.160 3.180 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 0.159 3.361 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 31 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 48 NH1 0.159 3.361 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 229 CG 0.159 3.601 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 233 OE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 307 NH2 0.158 2.502 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 OD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH 0.158 2.322 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 144 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH1 0.155 3.365 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 287 O 0.155 3.145 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 376 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 278 CG 0.155 3.365 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 52 CG2 0.153 3.607 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 103 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 41 CB 0.153 3.607 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 229 CG 0.153 3.607 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 364 O 0.152 3.148 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 364 O 0.150 3.150 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 332 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 329 O 0.150 2.330 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD2 0.149 3.371 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 315 OE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 228 NH1 0.149 2.511 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 287 O 0.149 3.151 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 38 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 37 C2' 0.149 3.611 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 52 CG2 0.148 3.612 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 328 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 331 CB 0.147 3.153 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 283 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 O 0.147 3.153 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 94 CG 0.143 3.617 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CG 0.143 3.617 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 364 O 0.143 3.157 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 114 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 CA 0.141 3.619 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 392 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 CD2 0.141 3.619 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 44 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 43 C2' 0.141 3.619 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 128 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CG2 0.140 3.160 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 72 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 71 C2' 0.139 3.621 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 139 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1 0.138 3.382 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 144 CD 0.137 3.383 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 131 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 127 O 0.133 3.167 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 139 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1 0.133 3.387 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 160 OG1 0.133 3.207 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 O 0.132 3.168 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 57 CG 0.131 3.209 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 57 CG 0.129 3.211 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 O 0.129 3.171 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 96 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 246 CA 0.128 3.632 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 302 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 14 CB 0.127 3.393 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 50 C5' 0.127 3.633 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CD1 0.126 3.274 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 168 O 0.125 3.175 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 61 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 62 C5' 0.125 3.635 [deleted to fit within ticket limits] > show #!5 models > open ""/Users/kompa012/Desktop/NiP N protein article/NiV N > protein/cryosparc_P78_J377_009_volume_map.mrc"" Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540, pixel 0.885, shown at level 0.0369, step 4, values float32 > hide #!4 models > show #!4 models > volume #4 step 1 > ui tool show ""Hide Dust"" > surface dust #4 size 5.31 > select add #4 2 models selected > color #4.1 gray > transparency #4.1 80 > volume #4 level 0.0199 > volume #4 level 0.02843 > select clear > select add #5 2 models selected > transparency #5.1 50 > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 4 models selected > select subtract #5 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 17 models selected > show sel atoms > hide sel cartoons > select clear > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > style sel ball Changed 44999 atom styles > select clear > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > volume #4 level 0.02843 > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.02112 > volume #4 level 0.03573 > volume #4 level 0.01869 > volume #4 level 0.02477 > volume #4 level 0.03 > volume #4 level 0.027 > volume #4 level 0.026 > ui tool show ""Color Actions"" > set bgColor white > set bgColor #ffffff00 > select clear > volume #4 level 0.0265 > volume #4 level 0.027 > ui tool show ""Hide Dust"" > surface dust #5 size 6 > surface dust #4 size 5.31 > surface dust #4 size 6 > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/4turns > unsharpned_fit.png"" width 3000 height 2729 supersample 3 > transparentBackground true > hide #!4 models > show #!4 models > hide #!4 models > select add #5 2 models selected > transparency #5.1 70 > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/1turn > sharpned_fit.png"" width 3000 height 2729 supersample 3 transparentBackground > true > hide #!5 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > show sel surfaces > transparency (#!1 & sel) 90 > transparency (#!1 & sel) 70 > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/Protein > _surf_second.png"" width 3000 height 2729 supersample 3 transparentBackground > true > select clear > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > hide sel surfaces > select subtract #1 15 models selected > select add #1.9 3094 atoms, 398 residues, 1 model selected > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected > select subtract #1.9 41905 atoms, 42762 bonds, 5258 residues, 16 models selected > hide sel cartoons > select clear > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > show sel cartoons > select clear > show #!4 models > hide #!4 models > show #!5 models > hide #!1 models > volume #5 level 0.06 > volume #5 level 0.07 > show #!1 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > select add #5 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 19 models selected > color zone #5 near sel & #1 distance 5.31 > select clear > hide #!1 models > select clear > volume #5 style mesh > show #!1 models > hide #!1 models > select add #5 2 models selected > transparency #5.1 0 > select clear > select add #5 2 models selected > select clear > hide #!5 models > show #!4 models > hide #!4 models > show #!1 models > show #!3 models > select add #3 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!3 to #1 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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain L (#1) with 7nt5, chain G (#3), sequence alignment score = 1967.3 RMSD between 359 pruned atom pairs is 0.815 angstroms; (across all 395 pairs: 1.674) > select clear > select add #3 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > ui tool show Matchmaker > matchmaker #3/J to #1/K pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K (#1) with 7nt5, chain J (#3), sequence alignment score = 1930.1 RMSD between 357 pruned atom pairs is 0.744 angstroms; (across all 395 pairs: 1.541) > show #!1 models > matchmaker #3/A to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 7nt5, chain A (#3), sequence alignment score = 1937.3 RMSD between 371 pruned atom pairs is 0.854 angstroms; (across all 394 pairs: 1.236) > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select add #1.14 3094 atoms, 398 residues, 1 model selected > hide sel cartoons > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected > select subtract #1 15 models selected > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > select subtract #1.1 41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected > hide sel cartoons > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected > select add #3 85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 19 models selected > select subtract #1 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 17 models selected > show sel surfaces > hide sel surfaces > select subtract #3.2 37226 atoms, 37991 bonds, 2 pseudobonds, 4802 residues, 16 models selected > hide sel cartoons > select add #3 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 15 models selected > select subtract #3 14 models selected > select add #3.15 1556 atoms, 78 residues, 1 model selected > show sel cartoons Cell requested for row 0 is out of bounds for table with 21 rows! Resizing table model. > select add #3 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 3 models selected > select add #1 85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 18 models selected > show sel cartoons > open 7nt6 fromDatabase pdb format mmcif Summary of feedback from opening 7nt6 fetched from pdb --- note | Fetching compressed mmCIF 7nt6 from http://files.rcsb.org/download/7nt6.cif 7nt6 title: CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly [more info...] Chain information for 7nt6 #7 --- Chain | Description | UniProt A B C D E F G H I J K L M N O | Nucleoprotein | NCAP_NIPAV 1-532 X | RNA (48-MER) | Z | RNA (42-MER) | > select subtract #3 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 31 models selected > select subtract #1 15 models selected > select add #7 24128 atoms, 24281 bonds, 10 pseudobonds, 5672 residues, 2 models selected > show sel surfaces > hide sel surfaces > show sel cartoons > hide sel atoms > select clear > select add #7.2 1320 atoms, 330 residues, 1 model selected > ui tool show Matchmaker > matchmaker #7/A to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 7nt6, chain A (#7), sequence alignment score = 1846.7 RMSD between 301 pruned atom pairs is 1.187 angstroms; (across all 330 pairs: 1.360) > hide #!3 models > select clear > ui tool show Matchmaker > matchmaker #7/O to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 7nt6, chain O (#7), sequence alignment score = 1909.1 RMSD between 308 pruned atom pairs is 1.139 angstroms; (across all 364 pairs: 1.853) > matchmaker #7/H to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 7nt6, chain H (#7), sequence alignment score = 1919.9 RMSD between 343 pruned atom pairs is 1.041 angstroms; (across all 381 pairs: 1.530) Cell requested for row 0 is out of bounds for table with 25 rows! Resizing table model. > open 6M7D fromDatabase pdb format mmcif Summary of feedback from opening 6M7D fetched from pdb --- note | Fetching compressed mmCIF 6m7d from http://files.rcsb.org/download/6m7d.cif 6m7d title: Structure of ncleoprotein of sendai virus [more info...] Chain information for 6m7d #8 --- Chain | Description | UniProt A | Nucleoprotein | NCAP_SENDO 1-524 B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | > hide #!7 models > hide #!1 models > open 6C54 fromDatabase pdb format mmcif Summary of feedback from opening 6C54 fetched from pdb --- note | Fetching compressed mmCIF 6c54 from http://files.rcsb.org/download/6c54.cif 6c54 title: Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit [more info...] Chain information for 6c54 #9 --- Chain | Description | UniProt A B | Nucleoprotein | A0A1L7B8E4_9MONO 25-457 6c54 mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > open 4uft fromDatabase pdb format mmcif Summary of feedback from opening 4uft fetched from pdb --- note | Fetching compressed mmCIF 4uft from http://files.rcsb.org/download/4uft.cif 4uft title: Structure of the helical Measles virus nucleocapsid [more info...] Chain information for 4uft #10 --- Chain | Description | UniProt B | NUCLEOPROTEIN | NCAP_MEASH 1-391 R | 5'-R(*CP*CP*CP*CP*CP*CP)-3' | 4uft mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > ui tool show Matchmaker > matchmaker #10/B to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 4uft, chain B (#10), sequence alignment score = 767.3 RMSD between 260 pruned atom pairs is 1.191 angstroms; (across all 367 pairs: 3.339) > matchmaker #9/A to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 6c54, chain A (#9), sequence alignment score = 285.6 RMSD between 64 pruned atom pairs is 1.098 angstroms; (across all 329 pairs: 7.821) > matchmaker #8/A to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D (#1) with 6m7d, chain A (#8), sequence alignment score = 667.3 RMSD between 235 pruned atom pairs is 1.101 angstroms; (across all 366 pairs: 8.432) > show #!7 models > hide #!7 models > show #!1 models > hide #9 models > hide #!10 models > hide #8 models > show #8 models > hide #8 models > show #8 models > show #9 models > show #!10 models > hide #8 models > hide #9 models > hide #!10 models > show #9 models > hide #9 models > show #!4 models > volume #4 level 0.03199 > volume #4 level 0.03448 > volume #4 level 0.03822 > volume #4 level 0.038 > volume #4 level 0.04 > volume #4 level 0.042 > volume #4 level 0.044 > hide #!4 models > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/protein..png"" > width 3000 height 2733 supersample 3 transparentBackground true > show #!5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/1turn > sharpned_fit.png"" width 3000 height 2733 supersample 3 transparentBackground > true > select add #5 2 models selected > transparency #5.1 60 > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/1turn > sharpned_fit.png"" width 3000 height 2733 supersample 3 transparentBackground > true > hide #!5 models > show #!4 models > hide #!1 models > show #!1 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/4turns > unsharpned_fit.png"" width 3000 height 2733 supersample 3 > transparentBackground true > hide #!4 models > show #!5 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/1turn > sharpned_fit.png"" width 3000 height 2733 supersample 3 transparentBackground > true > hide #!5 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/protein..png"" > width 3000 height 2733 supersample 3 transparentBackground true > select clear > turn x #1 90 Expected a number or a keyword > turn x 90 > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/protein90.png"" > width 3000 height 2733 supersample 3 transparentBackground true > show #!5 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/1turn > sharpned_fit 90.png"" width 3000 height 2733 supersample 3 > transparentBackground true > show #!10 models > show #9 models > show #8 models > show #!7 models > hide #!5 models > ui tool show ""Change Chain IDs"" > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/figure 1 > overall.cxs"" > ui tool show ""Change Chain IDs"" > changechains 1.1 Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (1.1/3/) > changechains 1.1 Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (1.1/3/) > select add #1.1 3094 atoms, 398 residues, 1 model selected > open ""/Users/kompa012/Desktop/NiP N protein article/7nt5_J377_intactmodel- > coot-0_real_space_refined_030.pdb"" Chain information for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #11 --- Chain | Description D E F G H I J K L M N O P Q | No description available Z | No description available Cell requested for row 0 is out of bounds for table with 25 rows! Resizing table model. > hide #9 models > hide #!10 models > hide #8 models > hide #!7 models > hide #!1 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected > select subtract #1 15 models selected > rename #11 ""7nt5_J377_intactmodel-coot-Chain D.pdb"" > select add #11 44996 atoms, 45905 bonds, 5656 residues, 1 model selected > show sel surfaces > hide sel surfaces > select subtract #11.1 41902 atoms, 42758 bonds, 5258 residues, 16 models selected > delete atoms (#!11 & sel) > delete bonds (#!11 & sel) > select add #11.1 3094 atoms, 398 residues, 1 model selected > show sel cartoons > hide sel atoms > select clear > select add #11 3094 atoms, 3147 bonds, 398 residues, 1 model selected > select subtract #11 1 model selected > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/NiV Nprote > monomer.pdb"" models #11 relModel #5 > show #!10 models > show #9 models > hide #9 models > show #8 models > show #!7 models > hide #!7 models > hide #!10 models > hide #!11 models > hide #8 models > show #!11 models > hide #11.1 models > show #!1 models > hide #!1 models > show #!5 models > ui tool show Matchmaker > matchmaker #11/D to #1/K pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K (#1) with 7nt5_J377_intactmodel-coot-Chain D.pdb, chain D (#11), sequence alignment score = 1993.7 RMSD between 398 pruned atom pairs is 0.213 angstroms; (across all 398 pairs: 0.213) > select add #5 2 models selected > select subtract #5 Nothing selected > select add #5 2 models selected > select add #11 3094 atoms, 3147 bonds, 398 residues, 3 models selected > open ""/Users/kompa012/Desktop/NiP N protein article/NiV N > protein/cryosparc_P78_J379_map_sharp.mrc"" Opened cryosparc_P78_J379_map_sharp.mrc as #12, grid size 540,540,540, pixel 0.885, shown at level 0.000704, step 4, values float32 > rename #12 cryosparc_P78_J379_map_sharp_one.mrc > volume #12 step 1 > hide #!5 models > select subtract #5 3094 atoms, 3147 bonds, 398 residues, 2 models selected > volume #12 level 0.01236 > volume #12 level 0.07 > show #!5 models > hide #!12 models > show #!12 models > hide #!5 models > volume zone #12 nearAtoms sel & #11 range 5.31 > ui tool show ""Surface Zone"" > surface zone #12 nearAtoms #11 distance 5.31 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 1 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 3.5 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 3.3 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 3.2 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 3.1 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 4 > surface zone #12 nearAtoms #11 distance 5 > surface zone #12 nearAtoms #11 distance 6 > surface zone #12 nearAtoms #11 distance 7 > select subtract #11.1 1 model selected > select add #11 3094 atoms, 3147 bonds, 398 residues, 1 model selected > select subtract #11 1 model selected > select add #12 2 models selected > volume #12 style mesh > transparency #12.1 70 > select clear > surface zone #12 nearAtoms #11 distance 4 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 4 > surface zone #12 nearAtoms #11 distance 5 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.1 > hide #!12 models > show #!12 models > hide #!11 models > show #!1 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > select subtract #1.9 41905 atoms, 42762 bonds, 5258 residues, 16 models selected > hide sel cartoons > show sel cartoons > select subtract #1.8 38811 atoms, 39615 bonds, 4860 residues, 15 models selected > select add #1.9 41905 atoms, 39615 bonds, 5258 residues, 14 models selected > hide sel cartoons > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected > select subtract #1 15 models selected > select add #1.15 1683 atoms, 84 residues, 1 model selected > show sel cartoons > ui mousemode right select > show sel atoms > hide sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 1683 atom styles > select clear > select #1 /z :3-40 760 atoms, 835 bonds, 38 residues, 1 model selected > hide sel atoms > select #1 /z :51-86 723 atoms, 795 bonds, 36 residues, 1 model selected > hide sel atoms > show #!7 models > show #!10 models > show #8 models > show #9 models > hide #!7 models > hide #!10 models > show #!7 models > hide #8 models > hide #9 models > hide #!12 models > hide #!1 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected > show #!1 models > hide #!7 models > show #!3 models > select subtract #1 15 models selected > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > show sel cartoons > select subtract #1.14 41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected > select add #1.14 44999 atoms, 42762 bonds, 9 pseudobonds, 5656 residues, 16 models selected > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 17 models selected > select subtract #1 15 models selected > select add #1.14 3094 atoms, 398 residues, 1 model selected > hide sel surfaces > hide sel atoms > hide sel cartoons > ui mousemode right distance > select add #1.15 4777 atoms, 482 residues, 2 models selected > show sel atoms > select add #3.15 6333 atoms, 560 residues, 4 models selected > show sel atoms > style sel ball Changed 6333 atom styles > distance #3/N:65@N1 #1/Z:65@C5 Distance between 7nt5 #3/N U 65 N1 and 7nt5_J377_intactmodel- coot-0_real_space_refined_030.pdb #1/Z U 65 C5: 4.363Å > ui mousemode right select > select clear Drag select of 37 residues > show sel atoms > style sel ball Changed 276 atom styles > select clear > select add #3 40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected > select add #1 85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 18 models selected > hide sel cartoons > select clear > ui mousemode right distance > distance #1/P:126@CA #3/M:126@CA Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/P GLU 126 CA and 7nt5 #3/M GLU 126 CA: 5.502Å > show #!6 models Cell requested for row 5 is out of bounds for table with 14 rows! Resizing table model. > hide #!6 models > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > show sel cartoons > select add #3 85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 19 models selected > select add #6 85199 atoms, 86925 bonds, 13 pseudobonds, 10852 residues, 34 models selected > select subtract #6 85199 atoms, 86925 bonds, 2 pseudobonds, 10852 residues, 32 models selected > show #!6 models > hide #!6 models > show sel cartoons > hide #!3 models > select subtract #3 44999 atoms, 45909 bonds, 5656 residues, 30 models selected > ui mousemode right select > select clear > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > select subtract #1.7 41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected > hide sel cartoons > select add #6 41905 atoms, 42762 bonds, 11 pseudobonds, 5258 residues, 17 models selected > select subtract #6 41905 atoms, 42762 bonds, 5258 residues, 15 models selected > show #!12 models > hide #!12 models > show #!12 models > select add #1.7 44999 atoms, 42762 bonds, 5656 residues, 15 models selected > hide sel cartoons > show sel cartoons > select subtract #1.8 41905 atoms, 39615 bonds, 5258 residues, 16 models selected > hide sel cartoons > hide sel atoms > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected > select subtract #1 15 models selected > select add #1 44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected > select subtract #1 15 models selected > select add #1.15 1683 atoms, 84 residues, 1 model selected > show sel atoms > select #1 /z :51-86 723 atoms, 795 bonds, 36 residues, 1 model selected > hide sel atoms > select #1 /z :3-40 760 atoms, 835 bonds, 38 residues, 1 model selected > hide sel atoms > select subtract #1.15 1 model selected > select add #1.7 3094 atoms, 398 residues, 1 model selected > select subtract #1.7 1 model selected > select add #1.8 3094 atoms, 398 residues, 1 model selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 3094 atom styles > select clear > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.5 > surface zone #12 nearAtoms #11 distance 3 > select add #1.7 3094 atoms, 398 residues, 1 model selected > select subtract #1.7 1 model selected > select add #1.8 3094 atoms, 398 residues, 1 model selected > hide sel atoms > select clear > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.5 Cell requested for row 5 is out of bounds for table with 28 rows! Resizing table model. > hide #!12 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!12 models > surface zone #12 nearAtoms #11 distance 2.5 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 1 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 1 > surface zone #12 nearAtoms #11 distance 1.9 > hide #!12 models > show #!12 models > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.5 > surface zone #12 nearAtoms #11 distance 4 > surface zone #12 nearAtoms #11 distance 3 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.5 > surface zone #12 nearAtoms #11 distance 2 > surface zone #12 nearAtoms #11 distance 2.5 > surface zone #12 nearAtoms #11 distance 2 > select #1 /k :178, 192,193,196,199,200,258,263, 265, 344, 349,352 104 atoms, 95 bonds, 12 residues, 1 model selected > show sel atoms > style sel ball Changed 104 atom styles > select clear > hide #!12 models > select #1 /k :178, 192,193,196,199,200,258,263, 265, 344, 349,352 104 atoms, 95 bonds, 12 residues, 1 model selected > color (#!1 & sel) byhetero > select #1 /z :41-50 200 atoms, 219 bonds, 10 residues, 1 model selected > color (#!1 & sel) byhetero > select clear > ui mousemode right distance > distance #1/Z:49@N1 #1/K:200@OE1 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 N1 and /K GLN 200 OE1: 3.740Å > show #!6 models > distance #1/Z:49@O4' #1/K:196@NZ Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 O4' and /K LYS 196 NZ: 2.984Å > distance #1/K:199@NE2 #1/Z:50@O2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K GLN 199 NE2 and /Z U 50 O2: 3.210Å > distance #1/K:199@OE1 #1/Z:49@N3 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K GLN 199 OE1 and /Z U 49 N3: 3.255Å > distance #1/Z:49@OP2 #1/K:258@OH Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 OP2 and /K TYR 258 OH: 2.341Å > distance #1/K:193@NH2 #1/Z:48@OP2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K ARG 193 NH2 and /Z U 48 OP2: 3.185Å > distance #1/K:192@NH1 #1/Z:48@OP1 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K ARG 192 NH1 and /Z U 48 OP1: 3.556Å > distance #1/K:192@NH1 #1/Z:48@OP2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K ARG 192 NH1 and /Z U 48 OP2: 2.734Å > ~distance #1/K:192@NH1 #1/Z:48@OP1 > distance #1/K:178@NZ #1/Z:47@OP2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K LYS 178 NZ and /Z U 47 OP2: 2.955Å > distance #1/K:352@NH1 #1/Z:44@OP2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K ARG 352 NH1 and /Z U 44 OP2: 2.806Å > select #1 /k :265 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > distance #1/Z:45@OP1 #1/K:265@N Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 45 OP1 and /K ALA 265 N: 3.167Å > ui mousemode right select > select clear > ui mousemode right distance > distance #1/Z:45@O4 #1/K:349@ND2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 45 O4 and /K ASN 349 ND2: 3.380Å > select #1 /k :263 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > ui mousemode right select > select clear > ui mousemode right distance > distance #1/K:344@OG #1/Z:46@O2 Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K SER 344 OG and /Z U 46 O2: 3.110Å > hide #6.1 models > ui tool show ""Side View"" > show #!12 models > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/one subunit nad > rna.png"" width 3000 height 3072 supersample 3 transparentBackground true > show #!10 models > hide #!10 models > ui tool show Matchmaker > matchmaker #10/B to #1/K pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K (#1) with 4uft, chain B (#10), sequence alignment score = 768.7 RMSD between 261 pruned atom pairs is 1.177 angstroms; (across all 371 pairs: 3.056) > show #!10 models > show #9 models > show #8 models > show #!7 models > hide #!7 models > matchmaker #9/A to #1/K pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K (#1) with 6c54, chain A (#9), sequence alignment score = 283.7 RMSD between 61 pruned atom pairs is 1.090 angstroms; (across all 329 pairs: 8.097) > matchmaker #8/A to #1/K pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K (#1) with 6m7d, chain A (#8), sequence alignment score = 692.5 RMSD between 242 pruned atom pairs is 1.153 angstroms; (across all 366 pairs: 8.444) > hide #9 models > hide #!10 models > hide #8 models > select #1 /z :41-50 200 atoms, 219 bonds, 10 residues, 1 model selected > show sel cartoons > hide sel cartoons > nucleotides sel tube/slab shape box > undo > ui mousemode right select > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/one subunit nad > rna.png"" width 3000 height 3072 supersample 3 transparentBackground true > hide #!12 models > select add #1.9 3094 atoms, 398 residues, 1 model selected > show sel cartoons > select clear > select #1 /z :43-54 240 atoms, 263 bonds, 12 residues, 1 model selected > show sel atoms > select #1 /z :40-43 80 atoms, 87 bonds, 4 residues, 1 model selected > hide sel atoms > select #1 /z :44-54 220 atoms, 241 bonds, 11 residues, 1 model selected > color (#!1 & sel) byhetero > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close > aup.cxs"" > select add #1.6 3094 atoms, 398 residues, 1 model selected > select subtract #1.6 1 model selected > select add #1.7 3094 atoms, 398 residues, 1 model selected > select subtract #1.7 1 model selected > select add #1.8 3094 atoms, 398 residues, 1 model selected > select add #1 44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 3 models selected > select subtract #1 15 models selected > select add #1 44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected > show sel cartoons > select clear > select add #1 44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected > show sel surfaces > transparency (#!1 & sel) 0 > hide sel cartoons > view sel > hide #!6 models > select add #6 44999 atoms, 45909 bonds, 23 pseudobonds, 5656 residues, 18 models selected > select subtract #6 44999 atoms, 45909 bonds, 5656 residues, 16 models selected > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for > measurement.png"" width 3000 height 3072 supersample 3 transparentBackground > true > select add #1 44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 9 models selected > hide sel atoms > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for > measurement.png"" width 3000 height 3072 supersample 3 transparentBackground > true > turn y 90 > turn y -90 > turn x 90 > turn x -180 > turn x 90 > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for > measurement.png"" width 3000 height 3072 supersample 3 transparentBackground > true > turn x -90 > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/side view for > measurement.png"" width 3000 height 3072 supersample 3 transparentBackground > true > turn x 90 > hide #!1 models > show #!1 models > select add #1 44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected > hide sel surfaces > show sel atoms > select clear > save ""/Users/kompa012/Desktop/NiP N protein article/Figures/measurement > spiral.cxs"" > ui mousemode right distance > distance #1/H:380@OD1 #1/N:380@O Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H ASN 380 OD1 and /N ASN 380 O: 64.756Å > show #!6 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S0005DLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 10 days, 10 hours, 32 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 272P7VU: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX