id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17963 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.5-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 0x0000000324d4b000 (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 0x0000000323d3f000 (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 ""/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 0x0000000322d33000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.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 0x0000000321d27000 (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 0x0000000320d1b000 (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 0x000000031fd0f000 (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 0x000000031ed03000 (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 0x000000031dcf7000 (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 0x000000031cceb000 (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 0x000000031bcdf000 (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 0x000000031acd3000 (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 0x00000001f259df00 (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, 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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 > close session > cd Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Cryo- > EM/250205-Krios Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > windowsize width 1000 height 1000 > set bgColor white > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > open 8p5e 8p5e title: S. cerevisiae nexus-sCMGE after DNA replication initiation [more info...] Chain information for 8p5e #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 A | DNA (19-MER) | B | DNA (7-MER) | C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194 D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294 E | Cell division control protein 45 | CDC45_YEAST 1-650 F | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689 G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222 H | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208 I | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213 Non-standard residues in 8p5e #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons > select #1/A,B 539 atoms, 608 bonds, 14 pseudobonds, 26 residues, 2 models selected > color sel grey > select #1/H,C,D,I 6676 atoms, 6804 bonds, 4 pseudobonds, 814 residues, 2 models selected > color sel light sky blue > clear sel Unknown command: clear sel > select #1/E 4282 atoms, 4364 bonds, 4 pseudobonds, 549 residues, 2 models selected > color sel teal > clear sel Unknown command: clear sel > select #1/2-7 30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected > color sel royal blue > select #1/G 6630 atoms, 6770 bonds, 14 pseudobonds, 827 residues, 3 models selected > color sel green > clear self Unknown command: clear self > select #1/F 4381 atoms, 4476 bonds, 3 pseudobonds, 548 residues, 2 models selected > color sel lawn green > select #2:ATP,ADP Nothing selected > show sel atoms > color sel light grey > style sel stick Changed 0 atom styles > color sel byhetero > select clear > select #2/B Nothing selected > style sel cartoons Expected a keyword > hide sel atoms > select clear > open > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown- > models/Pif1-cdc45-unrelaxed-model4.pdb Chain information for Pif1-cdc45-unrelaxed-model4.pdb #2 --- Chain | Description B | No description available C | No description available > matchmaker #2 to #1/E pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C (#2), sequence alignment score = 3024.3 RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs: 1.259) > undo > close session > close session > cd Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Cryo- > EM/250205-Krios Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > windowsize width 1000 height 1000 > set bgColor white > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > open 8p5e 8p5e title: S. cerevisiae nexus-sCMGE after DNA replication initiation [more info...] Chain information for 8p5e #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 A | DNA (19-MER) | B | DNA (7-MER) | C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194 D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294 E | Cell division control protein 45 | CDC45_YEAST 1-650 F | DNA polymerase epsilon subunit B | DPB2_YEAST 1-689 G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222 H | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208 I | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213 Non-standard residues in 8p5e #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons > select #1/A,B 539 atoms, 608 bonds, 14 pseudobonds, 26 residues, 2 models selected > color sel grey > select #1/H,C,D,I 6676 atoms, 6804 bonds, 4 pseudobonds, 814 residues, 2 models selected > color sel light sky blue > clear sel Unknown command: clear sel > select #1/E 4282 atoms, 4364 bonds, 4 pseudobonds, 549 residues, 2 models selected > color sel teal > clear sel Unknown command: clear sel > select #1/2-7 30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected > color sel royal blue > select #1/G 6630 atoms, 6770 bonds, 14 pseudobonds, 827 residues, 3 models selected > color sel green > clear self Unknown command: clear self > select #1/F 4381 atoms, 4476 bonds, 3 pseudobonds, 548 residues, 2 models selected > color sel lawn green > select #2:ATP,ADP Nothing selected > show sel atoms > color sel light grey > style sel stick Changed 0 atom styles > color sel byhetero > select clear > select #2/B Nothing selected > style sel cartoons Expected a keyword > hide sel atoms > select clear > getcrd the Pif1-Cdc45 model 5 Missing or invalid ""atoms"" argument: invalid atom specifier > open > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown- > models/Pif1-cdc45-unrelaxed-model4.pdb Chain information for Pif1-cdc45-unrelaxed-model4.pdb #2 --- Chain | Description B | No description available C | No description available > matchmaker #1/E to #2/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 Pif1-cdc45-unrelaxed-model4.pdb, chain B (#2) with 8p5e, chain E (#1), sequence alignment score = 79.4 RMSD between 5 pruned atom pairs is 1.252 angstroms; (across all 417 pairs: 50.037) > select #2/B,C 11768 atoms, 11970 bonds, 1470 residues, 1 model selected > hide sel cartoons > clear sel Unknown command: clear sel > select #2/B:155-170 130 atoms, 131 bonds, 16 residues, 1 model selected > show sel cartoons > color sel orange red > select clear > ui tool show Matchmaker > select clear > matchmaker #2 to #1/E pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C (#2), sequence alignment score = 3024.3 RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs: 1.259) > select clear > open > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown- > models/Pif1-Dpb2-unrelaxed-model5.pdb Chain information for Pif1-Dpb2-unrelaxed-model5.pdb #3 --- Chain | Description B | No description available C | No description available > matchmaker #3 to #1/F pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain F (#1) with Pif1-Dpb2-unrelaxed-model5.pdb, chain C (#3), sequence alignment score = 3153.4 RMSD between 401 pruned atom pairs is 0.962 angstroms; (across all 548 pairs: 11.367) > select #3/B,C 12051 atoms, 12284 bonds, 1509 residues, 1 model selected > hide sel cartoons > clear sel Unknown command: clear sel > select #3/B:21-39 155 atoms, 157 bonds, 19 residues, 1 model selected > show sel cartoons > color sel orange red > select clear > open > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Data/Predictions/Pif1-AFpulldown- > models/Rrm3(1-80)CMGE.pdb Chain information for Rrm3(1-80)CMGE.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available > select add #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > select subtract #4 Nothing selected > select #4/B:80-130 395 atoms, 400 bonds, 51 residues, 1 model selected > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/G Alignment identifier is 4/G > view sel > view > select add #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > ui tool show Matchmaker Alignment identifier is 4/B Alignment identifier is 4/C Alignment identifier is 4/D Alignment identifier is 4/E Alignment identifier is 4/F Alignment identifier is 4/G > ui tool show Matchmaker > select clear > matchmaker #4 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 8p5e, chain F (#1) with Rrm3(1-80)CMGE.pdb, chain G (#4), sequence alignment score = 3153.4 RMSD between 409 pruned atom pairs is 0.824 angstroms; (across all 548 pairs: 2.582) > matchmaker #4 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 8p5e, chain F (#1) with Rrm3(1-80)CMGE.pdb, chain G (#4), sequence alignment score = 3153.4 RMSD between 409 pruned atom pairs is 0.824 angstroms; (across all 548 pairs: 2.582) > select #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > hide sel cartoons > select #4/G 5513 atoms, 5634 bonds, 689 residues, 1 model selected > show sel cartoons > color sel orange > select clear > select #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > show sel cartoons > color sel orange > select clear > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > color sel #ff2600ff > color sel #ea3115ff > color sel #ea3114ff > color sel #ea3015ff > color sel #ea2f15ff > color sel #ea2e16ff > color sel #ea2918ff > color sel #ea2518ff > color sel #ea2318ff > color sel #ea2019ff > color sel #ea1c1aff > color sel #ea1a1fff > color sel #ea1a27ff > color sel #ea192dff > color sel #ea1931ff > color sel #ea1833ff > color sel #ea1834ff > color sel #ea1835ff > color sel #ea173aff > color sel #ea163eff > color sel #ea1445ff > color sel #ea154eff > color sel #ea1a5cff > color sel #ea1e60ff > color sel #ea2164ff > color sel #ea2467ff > color sel #ea2669ff > color sel #ea2769ff > color sel #ea286cff > color sel #ea2974ff > color sel #ea297eff > color sel #ea2883ff > color sel #ea2886ff > color sel #ea2889ff > color sel #ea288cff > color sel #ea2989ff > color sel #ea2885ff > color sel #ea2884ff > color sel #ea2681ff > color sel #ea2580ff > color sel #ea247fff > color sel #ea227dff > color sel #ea217cff > color sel #ea1f7bff > color sel #ea1e7aff > color sel #ea1c79ff > color sel #ea1a77ff > color sel #ea166fff > color sel #ea1263ff > color sel #ea0f59ff > color sel #ea0d55ff > color sel #ea0b52ff > color sel #ea0951ff > color sel #ea0950ff > color sel #ea084fff > color sel #ea074eff > color sel #ea064eff > color sel orange > select clear > select #1/I 1591 atoms, 1624 bonds, 1 pseudobond, 190 residues, 2 models selected > color sel light sky blue > ui tool show ""Color Actions"" > color sel cyan > select #1/D 2014 atoms, 2056 bonds, 245 residues, 1 model selected > ui tool show ""Color Actions"" > color sel turquoise > color sel medium turquoise > select #1/C 1408 atoms, 1441 bonds, 2 pseudobonds, 175 residues, 2 models selected > color sel light sky blue > ui tool show ""Color Actions"" > color sel powder blue > select #1/2-7 30906 atoms, 31390 bonds, 46 pseudobonds, 3911 residues, 3 models selected > select clear > select add #1 53414 atoms, 54412 bonds, 85 pseudobonds, 6675 residues, 4 models selected > show sel surfaces > select clear > view matrix view matrix camera -0.39023,-0.80478,-0.44727,-27.073,-0.28839,-0.3545,0.88947,732.38,-0.87439,0.47609,-0.09375,232.53 view matrix models #1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06 > turn x 90 > view > turn x -90 > view matrix view matrix camera -0.3869,-0.80478,-0.45015,-229.46,-0.29498,-0.3545,0.88731,1120.3,-0.87367,0.47609,-0.10023,171.05 view matrix models #1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06 > turn x 90 > view name top > turn 180 Expected an axis vector or a keyword > turn y 180 > view name bottom > turn 90 Expected an axis vector or a keyword > turn x 90 > view side Expected an objects specifier or a view name or a keyword > view side Expected an objects specifier or a view name or a keyword > view matrix camera > -0.3869,-0.80478,-0.45015,-229.46,-0.29498,-0.3545,0.88731,1120.3,-0.87367,0.47609,-0.10023,171.05 > view name side > view top > view side > turn x 90 > turn x -90 > turn y -90 > view side > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > view sel > select clear > view > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > view sel > ui tool show ""Side View"" > lighting soft > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_zoom.png > width 766 height 681 supersample 3 transparentBackground true > view side > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_side.png > width 766 height 681 supersample 3 > bottom Unknown command: bottom > view bottom > view front Expected an objects specifier or a view name or a keyword > view side > turn y -90 > view name front > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_front.png > width 766 height 681 supersample 3 > select add #2 11768 atoms, 11970 bonds, 1470 residues, 1 model selected > view sel > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figues/Pif1+Rrm3-CMGE_front- > ZOOM.png width 766 height 681 supersample 3 transparentBackground true > view > view side > select add #2 11768 atoms, 11970 bonds, 1470 residues, 1 model selected > select subtract #2 Nothing selected > select add #3 12051 atoms, 12284 bonds, 1509 residues, 1 model selected > view sel > select add #4 25344 atoms, 25838 bonds, 3158 residues, 2 models selected > view sel > select clear > view side > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_side.png > width 766 height 681 supersample 3 transparentBackground true > view front > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front.png > width 766 height 681 supersample 3 transparentBackground true > view side > view matrix view matrix camera -0.37766,-0.80634,-0.45517,-62.374,-0.3125,-0.35174,0.8824,782.55,-0.87162,0.47549,-0.11914,198.16 view matrix models #1,-0.62133,-0.2275,0.7498,223.16,0.49404,-0.85648,0.14952,333.07,0.60817,0.46333,0.64455,-118.98,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.16784,0.17751,0.9697,31.655,-0.52249,0.81811,-0.2402,271.45,-0.83596,-0.54698,-0.044565,520.32,#3,-0.13634,0.19348,0.97159,22.213,-0.51505,0.82393,-0.23635,267.28,-0.84625,-0.53264,-0.01268,516.05,#4,0.49391,-0.82693,0.26877,165.61,0.83924,0.37251,-0.39613,303.27,0.22745,0.42121,0.87798,235.06 > view name side > turn x 90 > view name top > turn y 180 > view name bottom > view side > turn y -90 > view name front > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front.png > width 766 height 681 supersample 3 transparentBackground true > view side > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_side.png > width 766 height 681 supersample 3 transparentBackground true > select add #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > view sel > select #1/F:189@OE1 1 atom, 1 residue, 1 model selected > select add #4 13294 atoms, 13554 bonds, 1650 residues, 3 models selected > select add #3 25345 atoms, 25838 bonds, 3159 residues, 4 models selected > select add #2 37113 atoms, 37808 bonds, 4629 residues, 5 models selected > show sel atoms > hide sel atoms > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > show sel cartoons > show sel atoms > style sel stick Changed 395 atom styles > select #3/B:21-39 155 atoms, 157 bonds, 19 residues, 1 model selected > show sel atoms > style sel stick Changed 155 atom styles > select #1/H:143@O 1 atom, 1 residue, 1 model selected > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_zoom.png > width 766 height 681 supersample 3 transparentBackground true > view front > select #3/B:21-39 155 atoms, 157 bonds, 19 residues, 1 model selected > show sel atoms > style sel stick Changed 155 atom styles > select #3/B:21-39 155 atoms, 157 bonds, 19 residues, 1 model selected > show sel atoms > style sel stick Changed 155 atom styles > select #5/B:155-170 Nothing selected > show sel atoms > style sel stick Changed 0 atom styles > select #5/B:155-170 Nothing selected > show sel atoms > style sel stick Changed 0 atom styles > matchmaker #2 to #1/E pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C (#2), sequence alignment score = 3024.3 RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs: 1.259) > select #2/B:155-170 130 atoms, 131 bonds, 16 residues, 1 model selected > show sel atoms > style sel stick Changed 130 atom styles > view sel > select clear > view front > matchmaker #2 to #1/E pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain E (#1) with Pif1-cdc45-unrelaxed-model4.pdb, chain C (#2), sequence alignment score = 3024.3 RMSD between 513 pruned atom pairs is 0.991 angstroms; (across all 549 pairs: 1.259) > select #2/B:155-170 130 atoms, 131 bonds, 16 residues, 1 model selected > show sel atoms > style sel stick Changed 130 atom styles > view sel > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1+Rrm3-CMGE_front- > ZOOM.png width 766 height 681 supersample 3 transparentBackground true > select add #4 13293 atoms, 13554 bonds, 1649 residues, 1 model selected > select subtract #4 Nothing selected > view side > lighting soft > graphics silhouettes false > graphics silhouettes true > view side > hide #3 models > show #3 models > hide #3 models > select #4/B:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > select clear > hide #2,4#!1 atoms > interfaces #2,4#!1 & ~solvent 75 buried areas: #4/G #1/F 15496, #2/C #1/E 13818, #4/C #1/D 8225, #4/D #1/H 6788, #4/E #1/I 6546, #4/F #1/C 5556, #1/5 #1/3 4523, #1/2 #1/6 3968, #1/6 #1/4 3958, #1/7 #1/3 3424, #1/5 #1/2 3153, #4/C #1/H 2814, #1/G #1/F 2804, #1/7 #1/4 2789, #1/G #4/G 2707, #4/C #1/I 2644, #4/C #4/E 2526, #4/G #4/D 2392, #1/D #1/I 2266, #4/C #4/D 2218, #1/D #1/H 2130, #4/E #1/C 1959, #4/G #1/H 1944, #1/H #4/F 1878, #1/D #4/E 1523, #2/B #1/3 1522, #4/E #4/F 1490, #4/D #4/F 1456, #1/F #4/D 1333, #1/I #1/C 1317, #4/G #4/B 1306, #1/F #1/H 1253, #1/H #1/C 1187, #1/5 #4/F 1128, #1/F #4/B 1094, #1/5 #4/E 1034, #1/G #1/5 1034, #1/D #4/D 1024, #1/5 #2/C 1018, #2/C #1/H 950, #1/E #1/H 920, #2/C #4/D 848, #1/E #4/D 797, #1/2 #1/E 789, #1/5 #1/E 688, #1/2 #2/C 646, #2/C #4/C 639, #1/E #4/C 625, #2/B #2/C 618, #1/5 #1/C 617, #1/3 #1/C 615, #2/B #1/E 614, #1/5 #1/I 564, #4/C #4/B 530, #4/E #1/H 524, #1/I #4/F 487, #1/3 #4/F 480, #1/5 #1/F 478, #2/B #1/5 474, #1/D #4/B 464, #1/G #1/2 463, #4/G #1/5 458, #1/5 #1/A 430, #1/G #2/C 409, #2/B #4/E 390, #4/G #2/C 388, #4/E #4/D 371, #1/6 #1/A 363, #4/D #1/C 356, #1/H #1/I 352, #4/G #4/C 350, #1/A #1/B 331, #1/G #1/E 323, #2/B #1/7 304, #4/G #1/D 303 > hide #!1 models > hide #2 models > interfaces #4 & ~solvent 9 buried areas: C E 2526, G D 2392, C D 2218, E F 1490, D F 1456, G B 1306, C B 530, E D 371, G C 350 > show #!1 models > show sel atoms > style sel stick Changed 560 atom styles > hide sel atoms > select #1/F:77@CD1 1 atom, 1 residue, 1 model selected > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > ui tool show ""Color Actions"" > color sel crimson > color sel tomato > color sel orange red > color sel coral > color sel fire brick > color sel orange red > select clear > view side > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > view sel > select clear > select #4/B 395 atoms, 400 bonds, 51 residues, 1 model selected > select #4/B:82 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:82 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:86 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/B:85-86 12 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select #4/B:82 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:82 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #4/B:88 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:88-89 19 atoms, 19 bonds, 2 residues, 1 model selected > show sel atoms > select #4/B:120 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/B:120-121 12 atoms, 11 bonds, 2 residues, 1 model selected > show sel cartoons > select #4/B:118 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/B:112-118 61 atoms, 62 bonds, 7 residues, 1 model selected > show sel atoms > select #4/B:96 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/B:92-96 36 atoms, 36 bonds, 5 residues, 1 model selected > show sel atoms > select #4/B:98 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:98 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #4/B:100 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:100-101 15 atoms, 15 bonds, 2 residues, 1 model selected > select #4/B:101 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:101-102 15 atoms, 15 bonds, 2 residues, 1 model selected > select #4/B:99 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:99 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select #4/B:101 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:101-102 15 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > select #4/B:104 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/B:104-105 20 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > select #4/B:107 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/B:107-109 24 atoms, 23 bonds, 3 residues, 1 model selected > show sel atoms > select #4/B:82, 88-89,92-96,99,101-102,104-105,107-109,112-118, 120-121 206 atoms, 203 bonds, 25 residues, 1 model selected > select #1/H:52@OE2 1 atom, 1 residue, 1 model selected > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Rrm3-CMGE_side.png > width 874 height 681 supersample 3 transparentBackground true > hide #4 models > show #2 models > show #3 models > hide #2 models > hide #!1 models > show #2 models > interfaces #2-3 & ~solvent 3 buried areas: #3/B #3/C 1003, #2/B #2/C 618, #3/B #2/C 555 Alignment identifier is 2/C Alignment identifier is 3/B Alignment identifier is 3/C Alignment identifier is 2/C Alignment identifier is 3/B Alignment identifier is 3/C > select add #3 12146 atoms, 12284 bonds, 1521 residues, 2 models selected > select add #2 23819 atoms, 24254 bonds, 2979 residues, 2 models selected > hide #2 models > select subtract #2 12051 atoms, 12284 bonds, 1509 residues, 1 model selected > hide #3 models > show #3 models > hide #3 models > select subtract #3 Nothing selected > show #2 models > show #!1 models > select add #1 53757 atoms, 54412 bonds, 85 pseudobonds, 6718 residues, 6 models selected > open > /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open > /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open > /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open > /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open > /Users/bvd428/Downloads/fold_scpif1_cdc45_gins_pole_dpb2/fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif Chain information for fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif #9 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > select add #5 86131 atoms, 87414 bonds, 85 pseudobonds, 10739 residues, 22 models selected > select add #6 118505 atoms, 120416 bonds, 85 pseudobonds, 14760 residues, 23 models selected > select add #7 150879 atoms, 153418 bonds, 85 pseudobonds, 18781 residues, 24 models selected > select add #8 183253 atoms, 186420 bonds, 85 pseudobonds, 22802 residues, 25 models selected > select add #9 215627 atoms, 219422 bonds, 85 pseudobonds, 26823 residues, 26 models selected > ui tool show Matchmaker > matchmaker #6-9 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 fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif, chain G (#6), sequence alignment score = 4699.3 RMSD between 870 pruned atom pairs is 0.413 angstroms; (across all 914 pairs: 0.829) Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif, chain G (#7), sequence alignment score = 4707.1 RMSD between 882 pruned atom pairs is 0.800 angstroms; (across all 914 pairs: 0.983) Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif, chain G (#8), sequence alignment score = 4707.7 RMSD between 827 pruned atom pairs is 0.790 angstroms; (across all 914 pairs: 2.042) Matchmaker fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5) with fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif, chain G (#9), sequence alignment score = 4704.1 RMSD between 844 pruned atom pairs is 0.873 angstroms; (across all 914 pairs: 1.312) > show sel & #2,5-9#!1 cartoons > hide sel & #2,5-9#!1 surfaces > hide sel & #2,5-9#!1 atoms > select add #3 227610 atoms, 231706 bonds, 85 pseudobonds, 28323 residues, 26 models selected > select add #2 239103 atoms, 243676 bonds, 85 pseudobonds, 29759 residues, 26 models selected > select add #1 239103 atoms, 243676 bonds, 85 pseudobonds, 29759 residues, 27 models selected > select subtract #1 185689 atoms, 189264 bonds, 23084 residues, 22 models selected > select subtract #2 173921 atoms, 177294 bonds, 21614 residues, 6 models selected > select subtract #3 161870 atoms, 165010 bonds, 20105 residues, 5 models selected > select add #1 215284 atoms, 219422 bonds, 85 pseudobonds, 26780 residues, 10 models selected > select add #2 227052 atoms, 231392 bonds, 85 pseudobonds, 28250 residues, 26 models selected > select subtract #2 215284 atoms, 219422 bonds, 85 pseudobonds, 26780 residues, 25 models selected > show sel surfaces > select subtract #1 161870 atoms, 165010 bonds, 20105 residues, 60 models selected > hide sel surfaces > select clear > matchmaker #5 to #1 bring #6-9 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 8p5e, chain G (#1) with fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain G (#5), sequence alignment score = 4302.7 RMSD between 551 pruned atom pairs is 1.266 angstroms; (across all 825 pairs: 2.292) > view > select add #5 32374 atoms, 33002 bonds, 4021 residues, 1 model selected > select add #6 64748 atoms, 66004 bonds, 8042 residues, 10 models selected > select add #7 97122 atoms, 99006 bonds, 12063 residues, 19 models selected > select add #9 129496 atoms, 132008 bonds, 16084 residues, 28 models selected > select add #8 161870 atoms, 165010 bonds, 20105 residues, 37 models selected > color sel bychain > select subtract #7 129496 atoms, 132008 bonds, 16084 residues, 44 models selected > select subtract #8 97122 atoms, 99006 bonds, 12063 residues, 35 models selected > select subtract #9 64748 atoms, 66004 bonds, 8042 residues, 26 models selected > select subtract #6 32374 atoms, 33002 bonds, 4021 residues, 17 models selected > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > select #5-9/A 34295 atoms, 34910 bonds, 4295 residues, 5 models selected Alignment identifier is 1 > select clear > select #1/F:387@CD2 1 atom, 1 residue, 1 model selected > select #1/F:685@CB 1 atom, 1 residue, 1 model selected > select #5/A:89 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:89 #6/A:89 #7/A:89 #8/A:89 #9/A:89 45 atoms, 40 bonds, 5 residues, 5 models selected > select #5/A:77-89 #6/A:77-89 #7/A:77-89 #8/A:77-89 #9/A:77-89 535 atoms, 535 bonds, 65 residues, 5 models selected . [ID: 1] region 5 chains [77-89] RMSD: 18.532 > select #5/A:9-87 #6/A:9-87 #7/A:9-87 #8/A:9-87 #9/A:9-87 3215 atoms, 3285 bonds, 395 residues, 5 models selected > select #5/A:9-89 #6/A:9-89 #7/A:9-89 #8/A:9-89 #9/A:9-89 3305 atoms, 3375 bonds, 405 residues, 5 models selected . [ID: 1] region 5 chains [9-89] RMSD: 28.045 > select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72 #9/A:71-72 70 atoms, 65 bonds, 10 residues, 5 models selected > select #5/A:71-84 #6/A:71-84 #7/A:71-84 #8/A:71-84 #9/A:71-84 585 atoms, 595 bonds, 70 residues, 5 models selected . [ID: 1] region 5 chains [71-84] RMSD: 11.550 > select add #5 32842 atoms, 33478 bonds, 4077 residues, 10 models selected > select add #6 65099 atoms, 66361 bonds, 8084 residues, 17 models selected > select subtract #5 32725 atoms, 33359 bonds, 4063 residues, 23 models selected > hide #!5 models > select subtract #6 351 atoms, 357 bonds, 42 residues, 14 models selected > show #!6 models > select add #7 32608 atoms, 33240 bonds, 4049 residues, 6 models selected > hide #!6 models > show #!7 models > select subtract #7 234 atoms, 238 bonds, 28 residues, 12 models selected > show #!8 models > hide #!7 models > sequence associate #5-9/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 5 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 5 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 5 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 5 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif chain A from 5 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif chain A to 5 chains with 0 mismatches > sequence header rmsd show Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_gins_pole_dpb2_model_4.cif #9/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 > select #5-9/A 34295 atoms, 34910 bonds, 4295 residues, 5 models selected > color byattribute r:seq_rmsd #!5-9 & sel target c palette > 0,blue:3,white:6,red 4295 residues, atom seq_rmsd range 2.32 to 91 > show #!7 models > show #!6 models > show #!5 models > select #5/A:74 #6/A:74 #7/A:74 #8/A:74 #9/A:74 40 atoms, 35 bonds, 5 residues, 5 models selected > select #5/A:74-79 #6/A:74-79 #7/A:74-79 #8/A:74-79 #9/A:74-79 275 atoms, 285 bonds, 30 residues, 5 models selected . [ID: 1] region 5 chains [74-79] RMSD: 6.476 > select #5/A:73 #6/A:73 #7/A:73 #8/A:73 #9/A:73 40 atoms, 35 bonds, 5 residues, 5 models selected > select #5/A:73-86 #6/A:73-86 #7/A:73-86 #8/A:73-86 #9/A:73-86 595 atoms, 605 bonds, 70 residues, 5 models selected . [ID: 1] region 5 chains [73-86] RMSD: 13.603 > show sel & #!5-8 cartoons > select add #5 32850 atoms, 33486 bonds, 4077 residues, 10 models selected > select add #6 65105 atoms, 66367 bonds, 8084 residues, 17 models selected > select add #7 97360 atoms, 99248 bonds, 12091 residues, 24 models selected > select add #8 129615 atoms, 132129 bonds, 16098 residues, 31 models selected > select add #9 161870 atoms, 165010 bonds, 20105 residues, 38 models selected > hide sel & #!5-8 cartoons > select #5/A:70 #6/A:70 #7/A:70 #8/A:70 #9/A:70 30 atoms, 25 bonds, 5 residues, 5 models selected > select #5/A:70-82 #6/A:70-82 #7/A:70-82 #8/A:70-82 #9/A:70-82 530 atoms, 540 bonds, 65 residues, 5 models selected . [ID: 1] region 5 chains [70-82] RMSD: 10.010 > show sel & #!5-8 cartoons > select clear > show #!9 models > hide #!9 models > open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_0.cif Chain information for fold_scpif1_cdc45_model_0.cif #10 --- Chain | Description A | . B | . > open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_1.cif Chain information for fold_scpif1_cdc45_model_1.cif #11 --- Chain | Description A | . B | . > open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_2.cif Chain information for fold_scpif1_cdc45_model_2.cif #12 --- Chain | Description A | . B | . > open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_3.cif Chain information for fold_scpif1_cdc45_model_3.cif #13 --- Chain | Description A | . B | . > open /Users/bvd428/Downloads/fold_scpif1_cdc45/fold_scpif1_cdc45_model_4.cif Chain information for fold_scpif1_cdc45_model_4.cif #14 --- Chain | Description A | . B | . Computing secondary structure > close #9 Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!8 models > show #!7 models > show #!6 models > show #!5 models > select add #10 12090 atoms, 12303 bonds, 1509 residues, 1 model selected > select add #12 24180 atoms, 24606 bonds, 3018 residues, 2 models selected > select add #11 36270 atoms, 36909 bonds, 4527 residues, 3 models selected > select add #13 48360 atoms, 49212 bonds, 6036 residues, 4 models selected > select add #14 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > ui tool show Matchmaker > matchmaker #10-13 to #14 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 fold_scpif1_cdc45_model_4.cif, chain A (#14) with fold_scpif1_cdc45_model_0.cif, chain A (#10), sequence alignment score = 4242.6 RMSD between 535 pruned atom pairs is 0.596 angstroms; (across all 859 pairs: 45.545) Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with fold_scpif1_cdc45_model_1.cif, chain A (#11), sequence alignment score = 4315.2 RMSD between 526 pruned atom pairs is 0.842 angstroms; (across all 859 pairs: 51.531) Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with fold_scpif1_cdc45_model_2.cif, chain A (#12), sequence alignment score = 4264.8 RMSD between 531 pruned atom pairs is 0.943 angstroms; (across all 859 pairs: 42.410) Matchmaker fold_scpif1_cdc45_model_4.cif, chain A (#14) with fold_scpif1_cdc45_model_3.cif, chain A (#13), sequence alignment score = 4174.8 RMSD between 544 pruned atom pairs is 0.589 angstroms; (across all 859 pairs: 43.841) > matchmaker #10 to #1 bring #11-14 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 8p5e, chain E (#1) with fold_scpif1_cdc45_model_0.cif, chain B (#10), sequence alignment score = 3044.1 RMSD between 518 pruned atom pairs is 1.024 angstroms; (across all 549 pairs: 1.242) > select clear > select add #10 12090 atoms, 12303 bonds, 1509 residues, 1 model selected > select add #11 24180 atoms, 24606 bonds, 3018 residues, 2 models selected > select add #12 36270 atoms, 36909 bonds, 4527 residues, 3 models selected > select add #13 48360 atoms, 49212 bonds, 6036 residues, 4 models selected > select add #14 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > hide sel cartoons > select #10-14/A 34295 atoms, 34910 bonds, 4295 residues, 5 models selected > show sel cartoons > select sequence chain Nothing selected > sequence chain #10-15/A Alignment identifier is 2 > sequence associate #10-15/A Associated fold_scpif1_cdc45_model_0.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A Associated fold_scpif1_cdc45_model_1.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A Associated fold_scpif1_cdc45_model_2.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A Associated fold_scpif1_cdc45_model_3.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A Associated fold_scpif1_cdc45_model_4.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_model_0.cif chain A from 5 chains Associated fold_scpif1_cdc45_model_0.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_model_1.cif chain A from 5 chains Associated fold_scpif1_cdc45_model_1.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_model_2.cif chain A from 5 chains Associated fold_scpif1_cdc45_model_2.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_model_3.cif chain A from 5 chains Associated fold_scpif1_cdc45_model_3.cif chain A to 5 chains with 0 mismatches Disassociated fold_scpif1_cdc45_model_4.cif chain A from 5 chains Associated fold_scpif1_cdc45_model_4.cif chain A to 5 chains with 0 mismatches > sequence header rmsd show Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red No atoms specified > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red No atoms specified > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red No atoms specified > select #10/A:2 #11/A:2 #12/A:2 #13/A:2 #14/A:2 35 atoms, 35 bonds, 5 residues, 5 models selected > select #10/A:2-71 #11/A:2-71 #12/A:2-71 #13/A:2-71 #14/A:2-71 2855 atoms, 2925 bonds, 350 residues, 5 models selected . [ID: 2] region 5 chains [2-71] RMSD: 91.536 > select #10/A:2 #11/A:2 #12/A:2 #13/A:2 #14/A:2 35 atoms, 35 bonds, 5 residues, 5 models selected > select #10/A:2-78 #11/A:2-78 #12/A:2-78 #13/A:2-78 #14/A:2-78 3160 atoms, 3245 bonds, 385 residues, 5 models selected . [ID: 2] region 5 chains [2-78] RMSD: 91.003 > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red 385 residues, atom seq_rmsd range 77.7 to 99.6 > select add #14 14618 atoms, 14899 bonds, 1817 residues, 5 models selected > select add #13 26076 atoms, 26553 bonds, 3249 residues, 5 models selected > select add #12 37534 atoms, 38207 bonds, 4681 residues, 5 models selected > select add #11 48992 atoms, 49861 bonds, 6113 residues, 5 models selected > select subtract #11 36902 atoms, 37558 bonds, 4604 residues, 4 models selected > select add #11 48992 atoms, 49861 bonds, 6113 residues, 5 models selected > select add #10 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > select subtract #11 48360 atoms, 49212 bonds, 6036 residues, 4 models selected > select subtract #12 36270 atoms, 36909 bonds, 4527 residues, 3 models selected > select subtract #10 24180 atoms, 24606 bonds, 3018 residues, 2 models selected > select subtract #13 12090 atoms, 12303 bonds, 1509 residues, 1 model selected > select subtract #14 Nothing selected > select #10/A 6859 atoms, 6982 bonds, 859 residues, 1 model selected > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red 859 residues, atom seq_rmsd range 0.121 to 123 > select #10-14/A 34295 atoms, 34910 bonds, 4295 residues, 5 models selected > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red 4295 residues, atom seq_rmsd range 0.121 to 123 > select clear > select #10/A:235-236 #11/A:235-236 #12/A:235-236 #13/A:235-236 #14/A:235-236 70 atoms, 65 bonds, 10 residues, 5 models selected > select #10/A:234-236 #11/A:234-236 #12/A:234-236 #13/A:234-236 #14/A:234-236 105 atoms, 105 bonds, 15 residues, 5 models selected . [ID: 2] region 5 chains [234-236] RMSD: 0.861 > select #10/A:195-202 #11/A:195-202 #12/A:195-202 #13/A:195-202 #14/A:195-202 335 atoms, 335 bonds, 40 residues, 5 models selected > select #10/A:195-209 #11/A:195-209 #12/A:195-209 #13/A:195-209 #14/A:195-209 605 atoms, 610 bonds, 75 residues, 5 models selected . [ID: 2] region 5 chains [195-209] RMSD: 14.324 > hide #!1 models > hide #2 models > select add #10 12574 atoms, 12791 bonds, 1569 residues, 5 models selected > select add #11 24543 atoms, 24972 bonds, 3063 residues, 5 models selected > select add #13 36512 atoms, 37153 bonds, 4557 residues, 5 models selected > select add #14 48481 atoms, 49334 bonds, 6051 residues, 5 models selected > select add #12 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > show sel cartoons > ui tool show Matchmaker > matchmaker #10-13 to #14/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 fold_scpif1_cdc45_model_4.cif, chain B (#14) with fold_scpif1_cdc45_model_0.cif, chain B (#10), sequence alignment score = 3321.3 RMSD between 576 pruned atom pairs is 0.462 angstroms; (across all 650 pairs: 3.529) Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with fold_scpif1_cdc45_model_1.cif, chain B (#11), sequence alignment score = 3323.1 RMSD between 579 pruned atom pairs is 0.358 angstroms; (across all 650 pairs: 4.221) Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with fold_scpif1_cdc45_model_2.cif, chain B (#12), sequence alignment score = 3296.7 RMSD between 595 pruned atom pairs is 0.450 angstroms; (across all 650 pairs: 2.009) Matchmaker fold_scpif1_cdc45_model_4.cif, chain B (#14) with fold_scpif1_cdc45_model_3.cif, chain B (#13), sequence alignment score = 3331.5 RMSD between 566 pruned atom pairs is 0.469 angstroms; (across all 650 pairs: 3.329) > select #10-14/A 34295 atoms, 34910 bonds, 4295 residues, 5 models selected > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,blue:3,white:6,red 4295 residues, atom seq_rmsd range 0.405 to 120 > select #10-14/B 26155 atoms, 26605 bonds, 3250 residues, 5 models selected > select color teal Expected an objects specifier or a keyword > color sel teal > show #4 models > hide #4 models > select #10/A:195 #11/A:195 #12/A:195 #13/A:195 #14/A:195 45 atoms, 40 bonds, 5 residues, 5 models selected > select #10/A:195-210 #11/A:195-210 #12/A:195-210 #13/A:195-210 #14/A:195-210 635 atoms, 640 bonds, 80 residues, 5 models selected . [ID: 2] region 5 chains [195-210] RMSD: 2.329 > select add #5 33009 atoms, 33642 bonds, 4101 residues, 6 models selected > select add #6 65383 atoms, 66644 bonds, 8122 residues, 15 models selected > select add #14 77346 atoms, 78819 bonds, 9615 residues, 23 models selected > select clear > select add #14 12090 atoms, 12303 bonds, 1509 residues, 1 model selected > select add #13 24180 atoms, 24606 bonds, 3018 residues, 2 models selected > select add #12 36270 atoms, 36909 bonds, 4527 residues, 3 models selected > select add #11 48360 atoms, 49212 bonds, 6036 residues, 4 models selected > select add #10 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > hide sel cartoons > select #10/A:193 #11/A:193 #12/A:193 #13/A:193 #14/A:193 45 atoms, 40 bonds, 5 residues, 5 models selected > select #10/A:193-207 #11/A:193-207 #12/A:193-207 #13/A:193-207 #14/A:193-207 605 atoms, 605 bonds, 75 residues, 5 models selected . [ID: 2] region 5 chains [193-207] RMSD: 3.410 > select #10/A:211 #11/A:211 #12/A:211 #13/A:211 #14/A:211 55 atoms, 55 bonds, 5 residues, 5 models selected > select #10/A:195-211 #11/A:195-211 #12/A:195-211 #13/A:195-211 #14/A:195-211 690 atoms, 700 bonds, 85 residues, 5 models selected . [ID: 2] region 5 chains [195-211] RMSD: 2.678 > show sel cartoons > show #!1 models > matchmaker #10/B to #1 bring #11-14 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 8p5e, chain E (#1) with fold_scpif1_cdc45_model_0.cif, chain B (#10), sequence alignment score = 3044.1 RMSD between 518 pruned atom pairs is 1.024 angstroms; (across all 549 pairs: 1.242) > select clear > select #10/A:193-194 #11/A:193-194 #12/A:193-194 #13/A:193-194 #14/A:193-194 90 atoms, 85 bonds, 10 residues, 5 models selected > select #10/A:193-211 #11/A:193-211 #12/A:193-211 #13/A:193-211 #14/A:193-211 780 atoms, 790 bonds, 95 residues, 5 models selected . [ID: 2] region 5 chains [193-211] RMSD: 3.540 > view sel > select clear > view front > select #5-15/A 61731 atoms, 62838 bonds, 7731 residues, 9 models selected Fetching compressed palette 0,orange from https://www.colourlovers.com/api/palettes?keywords=0%2Corange&format=json&numResults=100 Could not find palette 0,orange at COLOURlovers.com using keyword search > color byattribute r:seq_rmsd #!5-9 & sel target c palette > 0,red:3,orange:6,purple 3436 residues, atom seq_rmsd range 58.2 to 141 > color byattribute r:seq_rmsd #!5-14 & sel target c palette > 0,red:3,orange:6,purple 7731 residues, atom seq_rmsd range 0.405 to 141 > color byattribute r:seq_rmsd #!5-14 & sel target c palette > 0,yellow:3,orange:6,purple 7731 residues, atom seq_rmsd range 0.405 to 141 > select clear > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,yellow:3,orange:6,purple No atoms specified > select clear Fetching compressed palette 0,red from https://www.colourlovers.com/api/palettes?keywords=0%2Cred&format=json&numResults=100 Could not find palette 0,red at COLOURlovers.com using keyword search > color byattribute r:seq_rmsd #!5-8 & sel target c palette > Red:0,white:3,blue:6, Invalid ""palette"" argument: Invalid color name or specifier > color byattribute r:seq_rmsd #!5-8 & sel target c palette > red:0,white:3,blue:6, Invalid ""palette"" argument: Missing color name or specifier > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,red:3,white:6,blue No atoms specified > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,red:3,white:6,blue No atoms specified > select add #5 32374 atoms, 33002 bonds, 4021 residues, 1 model selected > select add #6 64748 atoms, 66004 bonds, 8042 residues, 10 models selected > select add #10 76838 atoms, 78307 bonds, 9551 residues, 19 models selected > select add #11 88928 atoms, 90610 bonds, 11060 residues, 20 models selected > select add #12 101018 atoms, 102913 bonds, 12569 residues, 21 models selected > select add #13 113108 atoms, 115216 bonds, 14078 residues, 22 models selected > select add #14 125198 atoms, 127519 bonds, 15587 residues, 23 models selected > color byattribute r:seq_rmsd #!10-14 & sel target c palette > 0,red:3,white:6,blue 7545 residues, atom seq_rmsd range 0.405 to 120 > select clear > select #10/A:133 #11/A:133 #12/A:133 #13/A:133 #14/A:133 40 atoms, 35 bonds, 5 residues, 5 models selected > select #10/A:133-151 #11/A:133-151 #12/A:133-151 #13/A:133-151 #14/A:133-151 760 atoms, 770 bonds, 95 residues, 5 models selected . [ID: 2] region 5 chains [133-151] RMSD: 116.226 > select > #10/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844 > #11/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844 > #12/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844 > #13/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844 > #14/A:3-11,22-30,171-195,209-223,239-249,264-279,291-297,302-306,315-324,326-334,343-345,348-361,367-370,396-398,400-405,422-432,438-448,465-478,497-506,545-556,562-570,572-582,590-601,616-623,630-650,704-707,727-734,748-750,755-763,767-787,817-844 14035 atoms, 14095 bonds, 1690 residues, 5 models selected > select #10/A:212 #11/A:212 #12/A:212 #13/A:212 #14/A:212 35 atoms, 30 bonds, 5 residues, 5 models selected > select #10/A:196-212 #11/A:196-212 #12/A:196-212 #13/A:196-212 #14/A:196-212 680 atoms, 690 bonds, 85 residues, 5 models selected . [ID: 2] region 5 chains [196-212] RMSD: 3.199 > select #10/A:194 #11/A:194 #12/A:194 #13/A:194 #14/A:194 45 atoms, 40 bonds, 5 residues, 5 models selected > select #10/A:194-213 #11/A:194-213 #12/A:194-213 #13/A:194-213 #14/A:194-213 815 atoms, 825 bonds, 100 residues, 5 models selected . [ID: 2] region 5 chains [194-213] RMSD: 3.639 > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected > sequence chain #5-8/A Alignment identifier is 1 > sequence associate #5-8/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains with 0 mismatches > sequence header rmsd > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected Could not find palette 0,orange at COLOURlovers.com using keyword search Could not find palette 0,orange at COLOURlovers.com using keyword search > select add #8 52951 atoms, 53948 bonds, 6598 residues, 8 models selected > select add #7 78466 atoms, 79968 bonds, 9760 residues, 15 models selected > select add #5 103981 atoms, 105988 bonds, 12922 residues, 22 models selected > select add #6 129496 atoms, 132008 bonds, 16084 residues, 29 models selected > select clear Could not find palette 0,orange at COLOURlovers.com using keyword search > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,red:3,white:6,blue No atoms specified > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,red:3,white:6,blue 3436 residues, atom seq_rmsd range 63.2 to 143 > select add #5 52951 atoms, 53948 bonds, 6598 residues, 8 models selected > select add #6 78466 atoms, 79968 bonds, 9760 residues, 15 models selected > select add #7 103981 atoms, 105988 bonds, 12922 residues, 22 models selected > select subtract #7 71607 atoms, 72986 bonds, 8901 residues, 28 models selected > select add #7 103981 atoms, 105988 bonds, 12922 residues, 21 models selected > select add #8 129496 atoms, 132008 bonds, 16084 residues, 29 models selected > show sel cartoons > ui tool show Matchmaker > matchmaker #!5-8 to #1/F pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 8p5e, chain F (#1) with fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif, chain H (#5), sequence alignment score = 3118 RMSD between 402 pruned atom pairs is 1.014 angstroms; (across all 548 pairs: 3.618) Matchmaker 8p5e, chain F (#1) with fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif, chain H (#6), sequence alignment score = 3112 RMSD between 403 pruned atom pairs is 1.008 angstroms; (across all 548 pairs: 3.962) Matchmaker 8p5e, chain F (#1) with fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif, chain H (#7), sequence alignment score = 3145 RMSD between 403 pruned atom pairs is 1.004 angstroms; (across all 548 pairs: 5.556) Matchmaker 8p5e, chain F (#1) with fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif, chain H (#8), sequence alignment score = 3131.8 RMSD between 395 pruned atom pairs is 1.036 angstroms; (across all 548 pairs: 5.353) > select subtract #8 97122 atoms, 99006 bonds, 12063 residues, 35 models selected > select subtract #7 64748 atoms, 66004 bonds, 8042 residues, 26 models selected > select subtract #5 32374 atoms, 33002 bonds, 4021 residues, 17 models selected > select subtract #6 8 models selected > select add #5 32374 atoms, 33002 bonds, 4021 residues, 1 model selected > select subtract #5 8 models selected > hide #!5 models > show #!5 models > select add #5 32374 atoms, 33002 bonds, 4021 residues, 1 model selected > select add #6 64748 atoms, 66004 bonds, 8042 residues, 10 models selected > select add #7 97122 atoms, 99006 bonds, 12063 residues, 19 models selected > select add #8 129496 atoms, 132008 bonds, 16084 residues, 28 models selected > hide sel cartoons > select subtract #5 97122 atoms, 99006 bonds, 12063 residues, 35 models selected > select add #5 129496 atoms, 132008 bonds, 16084 residues, 28 models selected > show sel cartoons > sequence chain #5-8/A Alignment identifier is 3 > sequence associate #5-8/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 5 chains Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 5 chains Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 5 chains Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 5 chains Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 5 chains with 0 mismatches Chains used in RMSD evaluation for alignment 2: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A, fold_scpif1_cdc45_model_0.cif #10/A, fold_scpif1_cdc45_model_1.cif #11/A, fold_scpif1_cdc45_model_2.cif #12/A, fold_scpif1_cdc45_model_3.cif #13/A, fold_scpif1_cdc45_model_4.cif #14/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains with 0 mismatches > sequence header rmsd > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,red:3,white:6,blue 3436 residues, atom seq_rmsd range 63.7 to 143 > sequence header rmsd > show sel & #!5-8 cartoons > sequence chain #5-8/A Alignment identifier is 1 > sequence associate #5-8/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains with 0 mismatches > sequence header rmsd > sequence header rmsd > select #5/A:1-2 #6/A:1-2 #7/A:1-2 #8/A:1-2 60 atoms, 60 bonds, 8 residues, 4 models selected > select #5/A:1-312 #6/A:1-312 #7/A:1-312 #8/A:1-312 9884 atoms, 10064 bonds, 1248 residues, 4 models selected . [ID: 1] region 4 chains [1-312] RMSD: 47.118 > select #5/A:248-312 #6/A:248-312 #7/A:248-312 #8/A:248-312 1856 atoms, 1876 bonds, 260 residues, 4 models selected > select #5/A:181-312 #6/A:181-312 #7/A:181-312 #8/A:181-312 4020 atoms, 4064 bonds, 528 residues, 4 models selected . [ID: 1] region 4 chains [181-312] RMSD: 39.346 > sequence associate #5-8/A sequence header rmsd Expected alignment-id or [alignment-id:]sequence-name-or-number or a keyword > sequence associate #5-8/A Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif chain A to 4 chains with 0 mismatches Disassociated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A from 4 chains Associated fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif chain A to 4 chains with 0 mismatches > sequence header rmsd > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected > sequence header rmsd > sequence header rmsd show Chains used in RMSD evaluation for alignment 1: fold_scpif1_cdc45_gins_pole_dpb2_model_0.cif #5/A, fold_scpif1_cdc45_gins_pole_dpb2_model_1.cif #6/A, fold_scpif1_cdc45_gins_pole_dpb2_model_2.cif #7/A, fold_scpif1_cdc45_gins_pole_dpb2_model_3.cif #8/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 > select #5/A:70 #6/A:70 #7/A:70 #8/A:70 24 atoms, 20 bonds, 4 residues, 4 models selected > select #5/A:70-86 #6/A:70-86 #7/A:70-86 #8/A:70-86 556 atoms, 564 bonds, 68 residues, 4 models selected . [ID: 1] region 4 chains [70-86] RMSD: 6.706 > select #5/A:87-88 #6/A:87-88 #7/A:87-88 #8/A:87-88 72 atoms, 68 bonds, 8 residues, 4 models selected > select #5/A:70-88 #6/A:70-88 #7/A:70-88 #8/A:70-88 628 atoms, 636 bonds, 76 residues, 4 models selected . [ID: 1] region 4 chains [70-88] RMSD: 6.894 > select #5-8/A 27436 atoms, 27928 bonds, 3436 residues, 4 models selected > color byattribute r:seq_rmsd #!5-8 & sel target c palette > 0,red:3,white:6,blue 3436 residues, atom seq_rmsd range 1.28 to 98.1 > hide #5-8 cartoons > select #5/A:70-71 #6/A:70-71 #7/A:70-71 #8/A:70-71 56 atoms, 52 bonds, 8 residues, 4 models selected > select #5/A:70-88 #6/A:70-88 #7/A:70-88 #8/A:70-88 628 atoms, 636 bonds, 76 residues, 4 models selected . [ID: 1] region 4 chains [70-88] RMSD: 6.894 > show sel cartoons > select #5/A:86 #6/A:86 #7/A:86 #8/A:86 36 atoms, 32 bonds, 4 residues, 4 models selected > select #5/A:86-89 #6/A:86-89 #7/A:86-89 #8/A:86-89 144 atoms, 140 bonds, 16 residues, 4 models selected . [ID: 1] region 4 chains [86-89] RMSD: 9.807 > hide sel cartoons > view side > select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72 56 atoms, 52 bonds, 8 residues, 4 models selected > select #5/A:71-87 #6/A:71-87 #7/A:71-87 #8/A:71-87 568 atoms, 576 bonds, 68 residues, 4 models selected . [ID: 1] region 4 chains [71-87] RMSD: 5.778 > view sel > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1rmds- > CMGE_side-zoom.png width 874 height 681 supersample 3 transparentBackground > true > view front > turn x90 Expected an axis vector or a keyword > turn x 90 > turn y 90 > turn y -180 > select add #10 12090 atoms, 12303 bonds, 1509 residues, 1 model selected > select add #11 24180 atoms, 24606 bonds, 3018 residues, 2 models selected > select add #12 36270 atoms, 36909 bonds, 4527 residues, 3 models selected > select add #13 48360 atoms, 49212 bonds, 6036 residues, 4 models selected > select add #14 60450 atoms, 61515 bonds, 7545 residues, 5 models selected > view sel > view bottom > view sel > select clear > save > /Users/bvd428/Library/CloudStorage/Dropbox/Millerlab/Documents/Pif1-Rrm3-manuscript/Figures/Pif1rmds- > CMGE_cdc45side-zoom.png width 874 height 681 supersample 3 > transparentBackground true > select #5/A:86-87 #6/A:86-87 #7/A:86-87 #8/A:86-87 72 atoms, 68 bonds, 8 residues, 4 models selected > select #5/A:82-87 #6/A:82-87 #7/A:82-87 #8/A:82-87 204 atoms, 200 bonds, 24 residues, 4 models selected . [ID: 1] region 4 chains [82-87] RMSD: 6.717 > select #5/A:71-72 #6/A:71-72 #7/A:71-72 #8/A:71-72 56 atoms, 52 bonds, 8 residues, 4 models selected > select #5/A:71-86 #6/A:71-86 #7/A:71-86 #8/A:71-86 532 atoms, 540 bonds, 64 residues, 4 models selected . [ID: 1] region 4 chains [71-86] RMSD: 5.757 ===== 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 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 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: MacBookPro18,3 Model Number: Z15G0007QDK/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 5 days, 21 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LS24A40xU: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 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-Clipper: 0.24.0 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-ISOLDE: 1.9 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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 more-itertools: 10.3.0 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 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 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 platformdirs: 4.2.2 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 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect new normal Unassigned