id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17230 Graphics crash, macOS 14.4, Intel Iris Plus Graphics cmajumdar@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.4-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff84b303100 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 556 in swap_buffers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 58) 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All rights reserved. > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/39models.cxs Log from Wed Mar 12 11:29:24 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Sun Jan 26 22:23:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytu.cif 8ytu.cif title: Mipa-PETase from Micromonospora pattaloongensis [more info...] Chain information for 8ytu.cif #1 --- Chain | Description | UniProt A B C | cutinase | A0A1H3QT72_9ACTN 39-294 Non-standard residues in 8ytu.cif #1 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) 8ytu.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select :EDO 4 atoms, 3 bonds, 1 residue, 1 model selected > select :GOL 6 atoms, 5 bonds, 1 residue, 1 model selected > select :GOL 6 atoms, 5 bonds, 1 residue, 1 model selected > select :GOL 6 atoms, 5 bonds, 1 residue, 1 model selected > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytu_validation_2fo-fc_map_coef.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytu_validation_2fo-fc_map_coef.cif --- warning | No mmCIF models found. > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytu-sf.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytu-sf.cif --- warning | No mmCIF models found. > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytv.cif 8ytv.cif title: The M19 variant of Mipa-Petase from Micromonospora pattaloongensis [more info...] Chain information for 8ytv.cif #2 --- Chain | Description | UniProt A B | cutinase | A0A1H3QT72_9ACTN 39-294 8ytv.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 51 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close #2 > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 558 Unknown polymer entity '1' on line 724 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 8ytv-aligned.cif #2 --- Chain | Description A | No description available B | No description available 51 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytw-aligned.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytw-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 288 Unknown polymer entity '1' on line 428 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 8ytw-aligned.cif #3 --- Chain | Description A | No description available > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 288 Unknown polymer entity '1' on line 430 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 8yty-aligned.cif #4 --- Chain | Description A | No description available 129 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytz-aligned.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytz-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 288 Unknown polymer entity '1' on line 433 Missing or incomplete sequence information. Inferred polymer connectivity. notes | Fetching CCD 1PE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/1PE/1PE.cif Fetching CCD ACT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif Chain information for 8ytz-aligned.cif #5 --- Chain | Description A | No description available > select #2/B:48-296 1852 atoms, 1903 bonds, 249 residues, 1 model selected > delete atoms sel > delete bonds sel > select /B:45-300 1909 atoms, 1965 bonds, 256 residues, 1 model selected > delete atoms sel > delete bonds sel > select /C:44-300 1914 atoms, 1970 bonds, 257 residues, 1 model selected > delete atoms sel > delete bonds sel > save > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/All-str-aligned.cxs > set bgColor white > ui mousemode right select Drag select of 11 atoms, 5 bonds > delete atoms sel > delete bonds sel > select :EDO 4 atoms, 3 bonds, 1 residue, 1 model selected > select :EDO 4 atoms, 3 bonds, 1 residue, 1 model selected > select :EDO 4 atoms, 3 bonds, 1 residue, 1 model selected > select :EDO 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel > color sel pink > view sel > color sel blue > ui tool show ""Side View"" > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/5xjh-aligned.pdb 5xjh-aligned.pdb title: Crystal structure of petase from ideonella sakaiensis [more info...] Chain information for 5xjh-aligned.pdb #6 --- Chain | Description A | petase > select #6/A:106 #6/A:237 #6/A:206 29 atoms, 28 bonds, 3 residues, 1 model selected > show sel > color sel hotpink > color sel magenta > select #6/A:160 #6/A:237 #6/A:206 24 atoms, 22 bonds, 3 residues, 1 model selected > color sel magenta > show sel atoms > color sel byhetero > select add #6 2073 atoms, 1977 bonds, 405 residues, 1 model selected > select subtract #6 Nothing selected > save > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/All-str-aligned.cxs ——— End of log from Sun Jan 26 22:23:23 2025 ——— opened ChimeraX session > hide #2 models > hide #6 models > hide #1 models > show #4-5#!3 cartoons > show #2 models > show #1 models > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Rhea_134_148_Details/8qrj_LCC_ICCG_x.cif 8qrj_LCC_ICCG_x.cif title: LCC-ICCG PETase mutant H218Y [more info...] Chain information for 8qrj_LCC_ICCG_x.cif #7 --- Chain | Description | UniProt A | Leaf-branch compost cutinase | PETH_UNKP 1-293 Non-standard residues in 8qrj_LCC_ICCG_x.cif #7 --- CA — calcium ion EDO — 1,2-ethanediol (ethylene glycol) P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330) 25 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close #7 > close > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/01Group01_8qrj_3pet_6A_m0_id_698.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/02Group01_8qrj_3pet_6A_m1_id_359.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/03Group01_8qrj_3pet_10A_m4_id_401.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/04Group01_8qrj_3pet_6A_m0_id_211.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/05Group01_8qrj_3pet_6A_m0_id_387.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/06Group01_8qrj_3pet_6A_m2_id_580.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/07Group01_8qrj_3pet_6A_m0_id_547.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/08Group01_8qrj_3pet_6A_m2_id_677.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/09Group01_8qrj_3pet_6A_m1_id_709.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/10Group01_8qrj_3pet_6A_m0_id_117.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/11Group01_8qrj_3pet_6A_m0_id_260.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/12Group01_8qrj_3pet_6A_m0_id_58.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/13Group02_8qrj_3pet_6A_m2_id_70.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/14Group02_8qrj_3pet_6A_m0_id_40.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/15Group02_8qrj_3pet_6A_m2_id_638.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/16Group02_8qrj_3pet_10A_m7_id_551.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/17Group02_8qrj_3pet_6A_m0_id_26.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/18Group03_8qrj_3pet_6A_m2_id_78.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/19Group03_8qrj_3pet_6A_m0_id_162.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/20Group03_8qrj_3pet_6A_m0_id_415.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/21Group03_8qrj_3pet_6A_m0_id_146.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/22Group03_8qrj_3pet_6A_m0_id_138.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/23Group03_8qrj_3pet_10A_m4_id_458.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/24Group03_8qrj_3pet_6A_m1_id_330.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/25Group04_8qrj_3pet_6A_m1_id_323.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/26Group04_8qrj_3pet_6A_m2_id_54.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/27Group05_8qrj_3pet_6A_m2_id_322.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/28Group05_8qrj_3pet_6A_m0_id_540.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/29Group05_8qrj_3pet_6A_m2_id_533.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/30Group05_8qrj_3pet_6A_m0_id_669.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/31Group05_8qrj_3pet_6A_m1_id_218.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/32Group05_8qrj_3pet_6A_m2_id_103.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/33Group05_8qrj_3pet_6A_m0_id_408.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/34Group05_8qrj_3pet_6A_m0_id_383.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/35Group06_8qrj_3pet_6A_m1_id_568.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/36Group06_8qrj_3pet_6A_m2_id_148.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/37Group06_8qrj_3pet_6A_m2_id_477.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/38Group07_8qrj_3pet_6A_m2_id_487.pdb > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/39Group07_8qrj_3pet_6A_m2_id_504.pdb Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/01Group01_8qrj_3pet_6A_m0_id_698.pdb --- warning | Ignored bad PDB record found on line 2034 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/02Group01_8qrj_3pet_6A_m1_id_359.pdb --- warning | Ignored bad PDB record found on line 2040 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/03Group01_8qrj_3pet_10A_m4_id_401.pdb --- warning | Ignored bad PDB record found on line 2038 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/04Group01_8qrj_3pet_6A_m0_id_211.pdb --- warning | Ignored bad PDB record found on line 2046 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/05Group01_8qrj_3pet_6A_m0_id_387.pdb --- warning | Ignored bad PDB record found on line 2031 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/06Group01_8qrj_3pet_6A_m2_id_580.pdb --- warning | Ignored bad PDB record found on line 2050 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/07Group01_8qrj_3pet_6A_m0_id_547.pdb --- warning | Ignored bad PDB record found on line 2034 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/08Group01_8qrj_3pet_6A_m2_id_677.pdb --- warning | Ignored bad PDB record found on line 2032 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/09Group01_8qrj_3pet_6A_m1_id_709.pdb --- warning | Ignored bad PDB record found on line 2041 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/10Group01_8qrj_3pet_6A_m0_id_117.pdb --- warning | Ignored bad PDB record found on line 2041 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/11Group01_8qrj_3pet_6A_m0_id_260.pdb --- warning | Ignored bad PDB record found on line 2036 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/12Group01_8qrj_3pet_6A_m0_id_58.pdb --- warning | Ignored bad PDB record found on line 2029 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/13Group02_8qrj_3pet_6A_m2_id_70.pdb --- warning | Ignored bad PDB record found on line 2042 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/14Group02_8qrj_3pet_6A_m0_id_40.pdb --- warning | Ignored bad PDB record found on line 2044 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/15Group02_8qrj_3pet_6A_m2_id_638.pdb --- warning | Ignored bad PDB record found on line 2033 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/16Group02_8qrj_3pet_10A_m7_id_551.pdb --- warning | Ignored bad PDB record found on line 2034 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/17Group02_8qrj_3pet_6A_m0_id_26.pdb --- warning | Ignored bad PDB record found on line 2049 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/18Group03_8qrj_3pet_6A_m2_id_78.pdb --- warning | Ignored bad PDB record found on line 2033 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/19Group03_8qrj_3pet_6A_m0_id_162.pdb --- warning | Ignored bad PDB record found on line 2040 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/20Group03_8qrj_3pet_6A_m0_id_415.pdb --- warning | Ignored bad PDB record found on line 2055 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/21Group03_8qrj_3pet_6A_m0_id_146.pdb --- warning | Ignored bad PDB record found on line 2034 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/22Group03_8qrj_3pet_6A_m0_id_138.pdb --- warning | Ignored bad PDB record found on line 2040 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/23Group03_8qrj_3pet_10A_m4_id_458.pdb --- warning | Ignored bad PDB record found on line 2037 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/24Group03_8qrj_3pet_6A_m1_id_330.pdb --- warning | Ignored bad PDB record found on line 2035 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/25Group04_8qrj_3pet_6A_m1_id_323.pdb --- warning | Ignored bad PDB record found on line 2040 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/26Group04_8qrj_3pet_6A_m2_id_54.pdb --- warning | Ignored bad PDB record found on line 2031 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/27Group05_8qrj_3pet_6A_m2_id_322.pdb --- warning | Ignored bad PDB record found on line 2039 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/28Group05_8qrj_3pet_6A_m0_id_540.pdb --- warning | Ignored bad PDB record found on line 2032 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/29Group05_8qrj_3pet_6A_m2_id_533.pdb --- warning | Ignored bad PDB record found on line 2046 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/30Group05_8qrj_3pet_6A_m0_id_669.pdb --- warning | Ignored bad PDB record found on line 2033 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/31Group05_8qrj_3pet_6A_m1_id_218.pdb --- warning | Ignored bad PDB record found on line 2037 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/32Group05_8qrj_3pet_6A_m2_id_103.pdb --- warning | Ignored bad PDB record found on line 2049 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/33Group05_8qrj_3pet_6A_m0_id_408.pdb --- warning | Ignored bad PDB record found on line 2045 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/34Group05_8qrj_3pet_6A_m0_id_383.pdb --- warning | Ignored bad PDB record found on line 2031 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/35Group06_8qrj_3pet_6A_m1_id_568.pdb --- warning | Ignored bad PDB record found on line 2052 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/36Group06_8qrj_3pet_6A_m2_id_148.pdb --- warning | Ignored bad PDB record found on line 2045 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/37Group06_8qrj_3pet_6A_m2_id_477.pdb --- warning | Ignored bad PDB record found on line 2049 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/38Group07_8qrj_3pet_6A_m2_id_487.pdb --- warning | Ignored bad PDB record found on line 2052 Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/Hit- structures/Final_39_PDBs_One_Fasta_File/39Group07_8qrj_3pet_6A_m2_id_504.pdb --- warning | Ignored bad PDB record found on line 2023 Chain information for 01Group01_8qrj_3pet_6A_m0_id_698.pdb #1 --- Chain | Description A | No description available Chain information for 02Group01_8qrj_3pet_6A_m1_id_359.pdb #2 --- Chain | Description A | No description available Chain information for 03Group01_8qrj_3pet_10A_m4_id_401.pdb #3 --- Chain | Description A | No description available Chain information for 04Group01_8qrj_3pet_6A_m0_id_211.pdb #4 --- Chain | Description A | No description available Chain information for 05Group01_8qrj_3pet_6A_m0_id_387.pdb #5 --- Chain | Description A | No description available Chain information for 06Group01_8qrj_3pet_6A_m2_id_580.pdb #6 --- Chain | Description A | No description available Chain information for 07Group01_8qrj_3pet_6A_m0_id_547.pdb #7 --- Chain | Description A | No description available Chain information for 08Group01_8qrj_3pet_6A_m2_id_677.pdb #8 --- Chain | Description A | No description available Chain information for 09Group01_8qrj_3pet_6A_m1_id_709.pdb #9 --- Chain | Description A | No description available Chain information for 10Group01_8qrj_3pet_6A_m0_id_117.pdb #10 --- Chain | Description A | No description available Chain information for 11Group01_8qrj_3pet_6A_m0_id_260.pdb #11 --- Chain | Description A | No description available Chain information for 12Group01_8qrj_3pet_6A_m0_id_58.pdb #12 --- Chain | Description A | No description available Chain information for 13Group02_8qrj_3pet_6A_m2_id_70.pdb #13 --- Chain | Description A | No description available Chain information for 14Group02_8qrj_3pet_6A_m0_id_40.pdb #14 --- Chain | Description A | No description available Chain information for 15Group02_8qrj_3pet_6A_m2_id_638.pdb #15 --- Chain | Description A | No description available Chain information for 16Group02_8qrj_3pet_10A_m7_id_551.pdb #16 --- Chain | Description A | No description available Chain information for 17Group02_8qrj_3pet_6A_m0_id_26.pdb #17 --- Chain | Description A | No description available Chain information for 18Group03_8qrj_3pet_6A_m2_id_78.pdb #18 --- Chain | Description A | No description available Chain information for 19Group03_8qrj_3pet_6A_m0_id_162.pdb #19 --- Chain | Description A | No description available Chain information for 20Group03_8qrj_3pet_6A_m0_id_415.pdb #20 --- Chain | Description A | No description available Chain information for 21Group03_8qrj_3pet_6A_m0_id_146.pdb #21 --- Chain | Description A | No description available Chain information for 22Group03_8qrj_3pet_6A_m0_id_138.pdb #22 --- Chain | Description A | No description available Chain information for 23Group03_8qrj_3pet_10A_m4_id_458.pdb #23 --- Chain | Description A | No description available Chain information for 24Group03_8qrj_3pet_6A_m1_id_330.pdb #24 --- Chain | Description A | No description available Chain information for 25Group04_8qrj_3pet_6A_m1_id_323.pdb #25 --- Chain | Description A | No description available Chain information for 26Group04_8qrj_3pet_6A_m2_id_54.pdb #26 --- Chain | Description A | No description available Chain information for 27Group05_8qrj_3pet_6A_m2_id_322.pdb #27 --- Chain | Description A | No description available Chain information for 28Group05_8qrj_3pet_6A_m0_id_540.pdb #28 --- Chain | Description A | No description available Chain information for 29Group05_8qrj_3pet_6A_m2_id_533.pdb #29 --- Chain | Description A | No description available Chain information for 30Group05_8qrj_3pet_6A_m0_id_669.pdb #30 --- Chain | Description A | No description available Chain information for 31Group05_8qrj_3pet_6A_m1_id_218.pdb #31 --- Chain | Description A | No description available Chain information for 32Group05_8qrj_3pet_6A_m2_id_103.pdb #32 --- Chain | Description A | No description available Chain information for 33Group05_8qrj_3pet_6A_m0_id_408.pdb #33 --- Chain | Description A | No description available Chain information for 34Group05_8qrj_3pet_6A_m0_id_383.pdb #34 --- Chain | Description A | No description available Chain information for 35Group06_8qrj_3pet_6A_m1_id_568.pdb #35 --- Chain | Description A | No description available Chain information for 36Group06_8qrj_3pet_6A_m2_id_148.pdb #36 --- Chain | Description A | No description available Chain information for 37Group06_8qrj_3pet_6A_m2_id_477.pdb #37 --- Chain | Description A | No description available Chain information for 38Group07_8qrj_3pet_6A_m2_id_487.pdb #38 --- Chain | Description A | No description available Chain information for 39Group07_8qrj_3pet_6A_m2_id_504.pdb #39 --- Chain | Description A | No description available > align #2 toAtoms #1 Unequal number of atoms to pair, 1995 and 1989 > align #2 toAtoms #1 Unequal number of atoms to pair, 1995 and 1989 > align #2 toResidues #1 Expected a keyword > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 02Group01_8qrj_3pet_6A_m1_id_359.pdb, chain A (#2), sequence alignment score = 1241.3 RMSD between 258 pruned atom pairs is 0.280 angstroms; (across all 258 pairs: 0.280) > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 03Group01_8qrj_3pet_10A_m4_id_401.pdb, chain A (#3), sequence alignment score = 1258.8 RMSD between 258 pruned atom pairs is 0.238 angstroms; (across all 258 pairs: 0.238) > matchmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 04Group01_8qrj_3pet_6A_m0_id_211.pdb, chain A (#4), sequence alignment score = 1229.6 RMSD between 258 pruned atom pairs is 0.172 angstroms; (across all 258 pairs: 0.172) > select down Nothing selected > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 05Group01_8qrj_3pet_6A_m0_id_387.pdb, chain A (#5), sequence alignment score = 1276.6 RMSD between 258 pruned atom pairs is 0.192 angstroms; (across all 258 pairs: 0.192) > matchmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 06Group01_8qrj_3pet_6A_m2_id_580.pdb, chain A (#6), sequence alignment score = 1215.5 RMSD between 258 pruned atom pairs is 0.220 angstroms; (across all 258 pairs: 0.220) > matchmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 07Group01_8qrj_3pet_6A_m0_id_547.pdb, chain A (#7), sequence alignment score = 1247.7 RMSD between 258 pruned atom pairs is 0.235 angstroms; (across all 258 pairs: 0.235) > matchmaker #8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 08Group01_8qrj_3pet_6A_m2_id_677.pdb, chain A (#8), sequence alignment score = 1223 RMSD between 258 pruned atom pairs is 0.215 angstroms; (across all 258 pairs: 0.215) > matchmaker #9 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 09Group01_8qrj_3pet_6A_m1_id_709.pdb, chain A (#9), sequence alignment score = 1217.5 RMSD between 258 pruned atom pairs is 0.228 angstroms; (across all 258 pairs: 0.228) > matchmaker #10 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 10Group01_8qrj_3pet_6A_m0_id_117.pdb, chain A (#10), sequence alignment score = 1268.9 RMSD between 258 pruned atom pairs is 0.194 angstroms; (across all 258 pairs: 0.194) > matchmaker #11 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 11Group01_8qrj_3pet_6A_m0_id_260.pdb, chain A (#11), sequence alignment score = 1261 RMSD between 258 pruned atom pairs is 0.171 angstroms; (across all 258 pairs: 0.171) > matchmaker #12 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 12Group01_8qrj_3pet_6A_m0_id_58.pdb, chain A (#12), sequence alignment score = 1218.1 RMSD between 258 pruned atom pairs is 0.293 angstroms; (across all 258 pairs: 0.293) > matchmaker #13 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 13Group02_8qrj_3pet_6A_m2_id_70.pdb, chain A (#13), sequence alignment score = 1252.8 RMSD between 258 pruned atom pairs is 0.305 angstroms; (across all 258 pairs: 0.305) > matchmaker #14 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 14Group02_8qrj_3pet_6A_m0_id_40.pdb, chain A (#14), sequence alignment score = 1231.1 RMSD between 258 pruned atom pairs is 0.239 angstroms; (across all 258 pairs: 0.239) > matchmaker #15 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 15Group02_8qrj_3pet_6A_m2_id_638.pdb, chain A (#15), sequence alignment score = 1239.5 RMSD between 258 pruned atom pairs is 0.282 angstroms; (across all 258 pairs: 0.282) > matchmaker #16 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 16Group02_8qrj_3pet_10A_m7_id_551.pdb, chain A (#16), sequence alignment score = 1220.3 RMSD between 258 pruned atom pairs is 0.232 angstroms; (across all 258 pairs: 0.232) > matchmaker #17 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 17Group02_8qrj_3pet_6A_m0_id_26.pdb, chain A (#17), sequence alignment score = 1226.9 RMSD between 258 pruned atom pairs is 0.216 angstroms; (across all 258 pairs: 0.216) > matchmaker #18 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 18Group03_8qrj_3pet_6A_m2_id_78.pdb, chain A (#18), sequence alignment score = 1224.1 RMSD between 258 pruned atom pairs is 0.248 angstroms; (across all 258 pairs: 0.248) > matchmaker #19 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 19Group03_8qrj_3pet_6A_m0_id_162.pdb, chain A (#19), sequence alignment score = 1248.2 RMSD between 258 pruned atom pairs is 0.218 angstroms; (across all 258 pairs: 0.218) > matchmaker #20 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 20Group03_8qrj_3pet_6A_m0_id_415.pdb, chain A (#20), sequence alignment score = 1237.7 RMSD between 258 pruned atom pairs is 0.227 angstroms; (across all 258 pairs: 0.227) > matchmaker #21 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 21Group03_8qrj_3pet_6A_m0_id_146.pdb, chain A (#21), sequence alignment score = 1263.3 RMSD between 258 pruned atom pairs is 0.268 angstroms; (across all 258 pairs: 0.268) > matchmaker #22 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 22Group03_8qrj_3pet_6A_m0_id_138.pdb, chain A (#22), sequence alignment score = 1261.9 RMSD between 258 pruned atom pairs is 0.162 angstroms; (across all 258 pairs: 0.162) > matchmaker #23 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 23Group03_8qrj_3pet_10A_m4_id_458.pdb, chain A (#23), sequence alignment score = 1248.3 RMSD between 258 pruned atom pairs is 0.214 angstroms; (across all 258 pairs: 0.214) > matchmaker #24 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 24Group03_8qrj_3pet_6A_m1_id_330.pdb, chain A (#24), sequence alignment score = 1248.6 RMSD between 253 pruned atom pairs is 0.219 angstroms; (across all 258 pairs: 0.484) > matchmaker #25 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 25Group04_8qrj_3pet_6A_m1_id_323.pdb, chain A (#25), sequence alignment score = 1252.5 RMSD between 258 pruned atom pairs is 0.261 angstroms; (across all 258 pairs: 0.261) > matchmaker #26 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 26Group04_8qrj_3pet_6A_m2_id_54.pdb, chain A (#26), sequence alignment score = 1242.8 RMSD between 258 pruned atom pairs is 0.240 angstroms; (across all 258 pairs: 0.240) > matchmaker #27 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 27Group05_8qrj_3pet_6A_m2_id_322.pdb, chain A (#27), sequence alignment score = 1271 RMSD between 251 pruned atom pairs is 0.280 angstroms; (across all 258 pairs: 0.875) > matchmaker #28 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 28Group05_8qrj_3pet_6A_m0_id_540.pdb, chain A (#28), sequence alignment score = 1279.2 RMSD between 258 pruned atom pairs is 0.234 angstroms; (across all 258 pairs: 0.234) > matchmaker #29 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 29Group05_8qrj_3pet_6A_m2_id_533.pdb, chain A (#29), sequence alignment score = 1231.2 RMSD between 258 pruned atom pairs is 0.219 angstroms; (across all 258 pairs: 0.219) > matchmaker #30 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 30Group05_8qrj_3pet_6A_m0_id_669.pdb, chain A (#30), sequence alignment score = 1243.8 RMSD between 257 pruned atom pairs is 0.199 angstroms; (across all 258 pairs: 0.246) > matchmaker #31 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 31Group05_8qrj_3pet_6A_m1_id_218.pdb, chain A (#31), sequence alignment score = 1249 RMSD between 258 pruned atom pairs is 0.228 angstroms; (across all 258 pairs: 0.228) > matchmaker #32 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 32Group05_8qrj_3pet_6A_m2_id_103.pdb, chain A (#32), sequence alignment score = 1221.1 RMSD between 250 pruned atom pairs is 0.294 angstroms; (across all 258 pairs: 0.776) > matchmaker #33 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 33Group05_8qrj_3pet_6A_m0_id_408.pdb, chain A (#33), sequence alignment score = 1254.5 RMSD between 258 pruned atom pairs is 0.261 angstroms; (across all 258 pairs: 0.261) > matchmaker #34 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 34Group05_8qrj_3pet_6A_m0_id_383.pdb, chain A (#34), sequence alignment score = 1253.5 RMSD between 258 pruned atom pairs is 0.302 angstroms; (across all 258 pairs: 0.302) > matchmaker #35 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 35Group06_8qrj_3pet_6A_m1_id_568.pdb, chain A (#35), sequence alignment score = 1239.9 RMSD between 257 pruned atom pairs is 0.258 angstroms; (across all 258 pairs: 0.304) > matchmaker #36 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 36Group06_8qrj_3pet_6A_m2_id_148.pdb, chain A (#36), sequence alignment score = 1262.4 RMSD between 258 pruned atom pairs is 0.268 angstroms; (across all 258 pairs: 0.268) > matchmaker #37 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 37Group06_8qrj_3pet_6A_m2_id_477.pdb, chain A (#37), sequence alignment score = 1251 RMSD between 258 pruned atom pairs is 0.272 angstroms; (across all 258 pairs: 0.272) > matchmaker #38 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 38Group07_8qrj_3pet_6A_m2_id_487.pdb, chain A (#38), sequence alignment score = 1223.9 RMSD between 250 pruned atom pairs is 0.325 angstroms; (across all 258 pairs: 0.851) > matchmaker #39 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 39Group07_8qrj_3pet_6A_m2_id_504.pdb, chain A (#39), sequence alignment score = 1218.6 RMSD between 258 pruned atom pairs is 0.220 angstroms; (across all 258 pairs: 0.220) > style stick Changed 77777 atom styles > show atoms [Repeated 1 time(s)] > hide atoms > undo [Repeated 2 time(s)] > save > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/Hit- > structures/Final_39_PDBs_One_Fasta_File/39_aligned_structures.cxs > color #17 #ff40ffff > undo > hide #1 models > hide #2 models > hide #3 models > hide #5 models > hide #4 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > hide #13 models > hide #14 models > hide #15 models > hide #16 models > hide #18 models > hide #19 models > hide #20 models > hide #21 models > hide #22 models > hide #23 models > hide #24 models > hide #25 models > hide #26 models > hide #27 models > hide #28 models > hide #29 models > hide #30 models > hide #32 models > hide #33 models > hide #34 models > hide #35 models > hide #36 models > hide #37 models > hide #38 models > hide #39 models > color #17 #942192ff > show #17,31 atoms > show #16 models > hide #16 models > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/readme.txt Unrecognized file suffix '.txt' > open > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8ytv-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 558 Unknown polymer entity '1' on line 724 Missing or incomplete sequence information. Inferred polymer connectivity. Summary of feedback from opening /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- Science-Fellows_Rheas-factory/Structures/8yty-aligned.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 288 Unknown polymer entity '1' on line 430 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 8ytv-aligned.cif #40 --- Chain | Description A | No description available B | No description available 51 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 8yty-aligned.cif #41 --- Chain | Description A | No description available 129 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #40 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8ytv- aligned.cif, chain A (#40), sequence alignment score = 728.4 RMSD between 232 pruned atom pairs is 0.760 angstroms; (across all 249 pairs: 1.216) > matchmaker #41 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8yty- aligned.cif, chain A (#41), sequence alignment score = 678.5 RMSD between 230 pruned atom pairs is 0.851 angstroms; (across all 247 pairs: 1.310) > matchmaker #40 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 01Group01_8qrj_3pet_6A_m0_id_698.pdb, chain A (#1) with 8ytv- aligned.cif, chain A (#40), sequence alignment score = 728.4 RMSD between 232 pruned atom pairs is 0.760 angstroms; (across all 249 pairs: 1.216) > select #40/B:48-296 1852 atoms, 1903 bonds, 249 residues, 1 model selected > delete atoms sel > delete bonds sel > rename #40 _MipaP-M198ytv-aligned.cif > rename #40 MipaP-M198ytv-aligned.cif > rename #41 Kubu-P-M12+P185-8yty-aligned.cif > hide #40 models > hide #41 models > show #40 models > show #41 models > show #17,31,40-41 atoms > select :LIG 1560 atoms, 1638 bonds, 39 residues, 39 models selected > color sel grey > select clear > select :LIG 1560 atoms, 1638 bonds, 39 residues, 39 models selected > style sel & #17,31 sphere Changed 80 atom styles The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > select :LIG 1560 atoms, 1638 bonds, 39 residues, 39 models selected > transparency 75 sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 75 atoms sel Expected ',' or a keyword > transparency sel 75 atoms > select clear > select :HOH 550 atoms, 550 residues, 2 models selected > delete atoms sel > delete bonds sel > hide #40 models > hide #41 models > show #41 models > hide #41 models > show #41 models > color #41 #00fa92ff > color #41 #00fdffff > color #41 #0096ffff > color #40 #ff8ad8ff > select :LIG 1560 atoms, 1638 bonds, 39 residues, 39 models selected > transparency 50 atoms sel Expected ',' or a keyword > transparency sel 50 atoms > select clear > show #40 models > hide #40 models > show #40 models > hide #41 models > hide #40 models > show #41 models > show #40 models > hide #40 models > show #40 models > hide #40 models > show #40 models > hide #40 models > show #40 models > hide #40 models > show #40 models > hide #40 models > hide #41 models > show #41 models > show #40 models > hide #17,31,40-41 atoms > select :LIG 1560 atoms, 1638 bonds, 39 residues, 39 models selected > show sel atoms > select sel @ show sel atoms > select clear > select #17:LIG 40 atoms, 42 bonds, 1 residue, 1 model selected > color sel grey blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel bluegrey Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel blue > select clear > select #17:LIG 40 atoms, 42 bonds, 1 residue, 1 model selected > color sel purple > select cleaer Expected an objects specifier or a keyword > select clear > hide #31 models > hide #17 models > show #31 models > show #17 models > show #39 models > hide #39 models > show #37 models > hide #37 models > show #36 models > hide #36 models > select #17:87 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > undo > select clear > select #17:84 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel > hide sel > select #17:87 7 atoms, 6 bonds, 1 residue, 1 model selected > select #40:167 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > save > /Users/chandrimamajumdar/Desktop/Chandrima/Professional_Development/Berkeley- > Science-Fellows_Rheas-factory/Structures/39models.cxs ——— End of log from Wed Mar 12 11:29:24 2025 ——— opened ChimeraX session > select :4 :5 :16 :18 :26 :45 :49 :50 :54 :56 :64 :65 :68 :71: 73 :98 :101 > :110 :114 :121 :125 :127 :138 :142 :143 :158 :164 :185 :189 :194 :212 :215 > :216 :218 :219 : 222 :225 :229 :231 :233 :236 :237 :241 :243 :246 :249 :254 14758 atoms, 13295 bonds, 1917 residues, 41 models selected > show sel atoms > select clear ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.10 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4 (23E214) Kernel Version: Darwin 23.4.0 Time since boot: 4 days, 1 hour, 20 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL S2421HN: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: FNJ2ZN3 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Graphics nonchimerax all ChimeraX