id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14604 ChimeraX bug report submission tmckeith@… "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000203202240 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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, 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""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000027 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8A5D9EA78)"" ] } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"" SOS1-AF-Q07889.pdb title: Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) [more info...] Chain information for SOS1-AF-Q07889.pdb #1 --- Chain | Description | UniProt A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333 > set bgColor white > graphics silhouettes true > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #1 --- Chain | Description A | No description available C | No description available > open /Users/tmckeithan/Downloads/Chimera/PDB/3BJI.pdb 3BJI.pdb title: Structural basis of promiscuous guanine nucleotide exchange by the T- cell essential VAV1 [more info...] Chain information for 3BJI.pdb #2 --- Chain | Description | UniProt A B | proto-oncogene vav | VAV_HUMAN 189-565 C D | ras-related C3 botulinum toxin substrate 1 precursor | RAC1_HUMAN 1-177 Non-standard residues in 3BJI.pdb #2 --- ZN — zinc ion > select #2/A 2974 atoms, 2991 bonds, 8 pseudobonds, 409 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/D 1211 atoms, 1229 bonds, 172 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show Matchmaker > matchmaker #2/B to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker VAVtoSOS 2e.pdb, chain A (#1) with 3BJI.pdb, chain B (#2), sequence alignment score = 396.2 RMSD between 134 pruned atom pairs is 1.045 angstroms; (across all 314 pairs: 25.295) > ui tool show Matchmaker > matchmaker #2/C to #1/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker VAVtoSOS 2e.pdb, chain C (#1) with 3BJI.pdb, chain C (#2), sequence alignment score = 898.4 RMSD between 158 pruned atom pairs is 0.850 angstroms; (across all 177 pairs: 1.547) > select #1/C 2583 atoms, 2613 bonds, 177 residues, 1 model selected > select add #2/C 3902 atoms, 3947 bonds, 368 residues, 2 models selected > addh Summary of feedback from adding hydrogens to multiple structures --- warnings | Not adding hydrogens to VAVtoSOS 2e.pdb #1/C MET 1 CA because it is missing heavy-atom bond partners Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLN 2 CB because it is missing heavy-atom bond partners Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLU 31 CB because it is missing heavy-atom bond partners Not adding hydrogens to VAVtoSOS 2e.pdb #1/C ILE 33 CB because it is missing heavy-atom bond partners Not adding hydrogens to VAVtoSOS 2e.pdb #1/C LYS 49 CB because it is missing heavy-atom bond partners 14 messages similar to the above omitted Skipped 18 atom(s) with bad connectivities; see log for details Not adding hydrogens to 3BJI.pdb #2/B LYS 208 CD because it is missing heavy- atom bond partners Not adding hydrogens to 3BJI.pdb #2/B LYS 222 CG because it is missing heavy- atom bond partners Not adding hydrogens to 3BJI.pdb #2/B ARG 226 CB because it is missing heavy- atom bond partners Not adding hydrogens to 3BJI.pdb #2/B ARG 245 CB because it is missing heavy- atom bond partners Not adding hydrogens to 3BJI.pdb #2/B LYS 252 CG because it is missing heavy- atom bond partners 54 messages similar to the above omitted The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 3BJI.pdb #2/B GLU 415 OE2; 3BJI.pdb #2/B ARG 489 NE notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #1/A GLN 189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583, VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 OXT Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY 279 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 OXT Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY 279 OXT 13 messages similar to the above omitted 550 hydrogen bonds Termini for 3BJI.pdb (#2) chain B determined from SEQRES records Termini for 3BJI.pdb (#2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: 3BJI.pdb #2/B MET 189, 3BJI.pdb #2/C MET 1 Chain-initial residues that are not actual N termini: 3BJI.pdb #2/B ASN 464, 3BJI.pdb #2/B GLN 480 Chain-final residues that are actual C termini: 3BJI.pdb #2/B GLY 566, 3BJI.pdb #2/C LEU 177 Chain-final residues that are not actual C termini: 3BJI.pdb #2/B ASP 457, 3BJI.pdb #2/B GLU 475 Missing OXT added to C-terminal residue 3BJI.pdb #2/B GLY 566 Missing OXT added to C-terminal residue 3BJI.pdb #2/C LEU 177 513 hydrogen bonds Adding 'H' to 3BJI.pdb #2/B ASN 464 Adding 'H' to 3BJI.pdb #2/B GLN 480 3BJI.pdb #2/B ASP 457 is not terminus, removing H atom from 'C' 3BJI.pdb #2/B GLU 475 is not terminus, removing H atom from 'C' 4072 hydrogens added > ui tool show Matchmaker > select add sel : ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/C Alignment identifier is 1/C > sequence chain #2/B Alignment identifier is 2/B > interfaces #1 1 buried areas: A C 1482 > interfaces #2 1 buried areas: B C 1354 > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" format pdb Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #1 --- Chain | Description A | No description available C | No description available > show surfaces > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A LYS 214 /C MET 1 /C GLN 2 /C GLU 31 /C ILE 33 /C LYS 49 /C LYS 123 /C ASP 124 /C GLU 127 /C LYS 128 /C GLU 131 /C LYS 132 /C LYS 133 /C LYS 153 /C LEU 160 /C THR 161 /C LYS 166 /C ASP 170 /C ARG 174 /C LEU 177 Using Amber 20 recommended default charges and atom types for standard residues /A LYS 214 CLYS Nonstandard name for heavy atom /A LYS 214 OH > hide surfaces > addh Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 --- warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy- atom bond partners Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond partners 14 messages similar to the above omitted Skipped 18 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 13 messages similar to the above omitted 550 hydrogen bonds 0 hydrogens added > swapaa /A:223 asn Using Dunbrack library /A ASN 223: phi -140.8, psi 26.7 trans Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipped 70 atom(s) with bad connectivities; see log for details Applying ASN rotamer (chi angles: -163.3 -54.4) to /A ASN 223 > addh Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 --- warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy- atom bond partners Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond partners 14 messages similar to the above omitted Skipped 17 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O Skipping possible acceptor with bad geometry: /A GLY 279 OXT Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 OXT Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O 12 messages similar to the above omitted 551 hydrogen bonds 4 hydrogens added > swapaa /A:279 gly Using Dunbrack library Swapping /A GLY 279 to GLY > addh Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 --- warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy- atom bond partners Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond partners 14 messages similar to the above omitted Skipped 17 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 12 messages similar to the above omitted 551 hydrogen bonds 3 hydrogens added > show surfaces > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A LYS 214 /C MET 1 /C GLN 2 /C GLU 31 /C ILE 33 /C LYS 49 /C LYS 123 /C ASP 124 /C GLU 127 /C LYS 128 /C GLU 131 /C LYS 132 /C LYS 133 /C LYS 153 /C LEU 160 /C THR 161 /C LYS 166 /C ASP 170 /C ARG 174 /C LEU 177 Using Amber 20 recommended default charges and atom types for standard residues /A LYS 214 CLYS Nonstandard name for heavy atom /A LYS 214 OH > swapaa /A:214 lys Using Dunbrack library /A LYS 214: phi -51.4, psi -27.4 trans Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 214 > swapaa /C:1 met Using Dunbrack library /C MET 1: phi none, psi -163.4 trans Applying MET rotamer (chi angles: 72.6 -72.0 -71.4) to /C MET 1 > swapaa /C:2 gln Using Dunbrack library /C GLN 2: phi 54.0, psi 43.2 trans Applying GLN rotamer (chi angles: -63.1 -69.2 -63.4) to /C GLN 2 > swapaa /C:31 glu Using Dunbrack library /C GLU 31: phi -67.8, psi -17.2 trans Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /C GLU 31 > swapaa /C:33 ile Using Dunbrack library /C ILE 33: phi -128.5, psi 129.8 trans Applying ILE rotamer (chi angles: 66.2 -71.1) to /C ILE 33 > swapaa /C:49 lys Using Dunbrack library /C LYS 49: phi -105.8, psi 132.8 trans Applying LYS rotamer (chi angles: -177.7 178.5 -176.1 -64.2) to /C LYS 49 > swapaa /C:123 lys Using Dunbrack library /C LYS 123: phi -59.5, psi -24.4 trans Applying LYS rotamer (chi angles: -66.0 -66.1 -174.7 -67.0) to /C LYS 123 > swapaa /C:124 asp Using Dunbrack library /C ASP 124: phi -65.8, psi -32.0 trans Applying ASP rotamer (chi angles: -71.2 -15.9) to /C ASP 124 > swapaa /C:127 glu Using Dunbrack library /C GLU 127: phi -60.7, psi -29.0 trans Applying GLU rotamer (chi angles: -69.3 177.9 -8.3) to /C GLU 127 > swapaa /C:128 lys Using Dunbrack library /C LYS 128: phi -79.9, psi -47.4 trans Applying LYS rotamer (chi angles: -66.0 -173.5 -71.5 -66.9) to /C LYS 128 > swapaa /C:131 glu Using Dunbrack library /C GLU 131: phi -67.4, psi -28.1 trans Applying GLU rotamer (chi angles: -68.4 178.8 -8.3) to /C GLU 131 > swapaa /C:132 lys Using Dunbrack library /C LYS 132: phi -92.6, psi 6.9 trans Applying LYS rotamer (chi angles: -64.3 -174.6 -70.2 -66.8) to /C LYS 132 > swapaa /C:133 lys Using Dunbrack library /C LYS 133: phi 60.7, psi 17.9 trans Applying LYS rotamer (chi angles: -83.6 68.4 178.6 177.6) to /C LYS 133 > swapaa /C:153 lys Using Dunbrack library /C LYS 153: phi -147.1, psi 155.7 trans Applying LYS rotamer (chi angles: -61.9 -73.1 -174.8 -67.0) to /C LYS 153 > swapaa /C:160 leu Using Dunbrack library /C LEU 160: phi -72.4, psi -31.1 trans Applying LEU rotamer (chi angles: -67.8 174.1) to /C LEU 160 > swapaa /C:161 thr Using Dunbrack library /C THR 161: phi -153.7, psi 150.8 trans Applying THR rotamer (chi angles: -174.5) to /C THR 161 > swapaa /C:166 lys Using Dunbrack library /C LYS 166: phi -57.5, psi -38.2 trans Applying LYS rotamer (chi angles: -171.7 -89.7 -173.2 -177.4) to /C LYS 166 > swapaa /C:170 asp Using Dunbrack library /C ASP 170: phi -62.4, psi -45.3 trans Applying ASP rotamer (chi angles: -71.6 -15.7) to /C ASP 170 > swapaa /C:174 arg Using Dunbrack library /C ARG 174: phi -63.3, psi -17.3 trans Applying ARG rotamer (chi angles: -172.3 178.2 -63.1 -83.0) to /C ARG 174 > swapaa /C:177 leu Using Dunbrack library /C LEU 177: phi -148.8, psi none trans Applying LEU rotamer (chi angles: -64.7 174.5) to /C LEU 177 > hide surfaces > show surfaces > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A LYS 214 O Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for VAVtoSOS 2e.pdb_A SES surface #1.1: minimum, -22.41, mean -1.75, maximum 15.42 Coulombic values for VAVtoSOS 2e.pdb_C SES surface #1.2: minimum, -14.81, mean -0.22, maximum 9.43 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > select /C 2639 atoms, 2669 bonds, 177 residues, 1 model selected > select /A 6240 atoms, 6299 bonds, 386 residues, 1 model selected > show sel surfaces > hide sel surfaces > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"" SOS1-AF-Q07889.pdb title: Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) [more info...] Chain information for SOS1-AF-Q07889.pdb #2 --- Chain | Description | UniProt A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/C Alignment identifier is 1/C > sequence chain #2/A Alignment identifier is 2/A > select #2/A:1040-1041 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:1040-1333 2241 atoms, 2331 bonds, 294 residues, 1 model selected > cartoon hide sel > select clear > select #2/A:565 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:554-565 100 atoms, 99 bonds, 12 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2/A & sel to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker VAVtoSOS 2e.pdb, chain A (#1) with SOS1-AF-Q07889.pdb, chain A (#2), sequence alignment score = 61.6 RMSD between 12 pruned atom pairs is 0.349 angstroms; (across all 12 pairs: 0.349) > select #2/A:565 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:271-565 2380 atoms, 2424 bonds, 295 residues, 1 model selected > cartoon hide sel > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-315 2556 atoms, 2610 bonds, 315 residues, 1 model selected > cartoon hide sel > select #2/A:563@CA 1 atom, 1 residue, 1 model selected > cofr sel No displayed objects specified. > select #1/A:563@CA 1 atom, 1 residue, 1 model selected > cofr sel > ui mousemode right zoom > select add #1 8879 atoms, 8968 bonds, 563 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.70271,-0.27973,0.65418,-92.749,0.51877,0.8307,-0.20204,54.743,-0.48691,0.48134,0.72886,1.1474 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.70271,-0.27973,0.65418,-120.91,0.51877,0.8307,-0.20204,77.907,-0.48691,0.48134,0.72886,-7.8518 > roll x 2 180 > cofr sel > roll x 1 60 > roll x 1 300 > roll x 1 90 > show sel surfaces > hide #!1 models > addh Summary of feedback from adding hydrogens to multiple structures --- warning | Skipped 17 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #1/A GLN 189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583, VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 OXT Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY 279 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN 223 OXT 12 messages similar to the above omitted 565 hydrogen bonds Termini for SOS1-AF-Q07889.pdb (#2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: SOS1-AF-Q07889.pdb #2/A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: SOS1-AF-Q07889.pdb #2/A SER 1333 Chain-final residues that are not actual C termini: 1018 hydrogen bonds 10869 hydrogens added Drag select of 474 residues > show sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for SOS1-AF-Q07889.pdb_A SES surface #2.1: minimum, -18.25, mean -0.78, maximum 27.88 To also show corresponding color key, enter the above coulombic command and add key true > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > select add #1 16908 atoms, 9129 bonds, 1037 residues, 3 models selected > select subtract #1 7868 atoms, 474 residues, 4 models selected > show #!1 models > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 4n.pdb"" Chain information for SPTBN2 working 4n.pdb #3 --- Chain | Description A B C D F G | No description available H | No description available J | No description available K | No description available Q | No description available b | No description available > select #2/A:1085 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:1085 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:819 14 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:819-864 786 atoms, 791 bonds, 46 residues, 1 model selected > ui tool show Matchmaker > matchmaker #3/H to #2/A & sel pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SOS1-AF-Q07889.pdb, chain A (#2) with SPTBN2 working 4n.pdb, chain H (#3), sequence alignment score = 242.8 RMSD between 46 pruned atom pairs is 0.746 angstroms; (across all 46 pairs: 0.746) > hide sel atoms > select 98252 atoms, 99312 bonds, 10 pseudobonds, 6212 residues, 4 models selected > hide sel atoms > show sel cartoons > select #2/A:1289-1333 705 atoms, 720 bonds, 45 residues, 1 model selected > select #2/A:1040-1333 4434 atoms, 4524 bonds, 294 residues, 1 model selected > cartoon hide (#!2 & sel) > select #2/A:564-565 30 atoms, 29 bonds, 2 residues, 1 model selected > select #2/A:271-565 4737 atoms, 4781 bonds, 295 residues, 1 model selected > cartoon hide (#!2 & sel) > select #2/A:313-314 28 atoms, 27 bonds, 2 residues, 1 model selected > select #2/A:138-314 2837 atoms, 2865 bonds, 177 residues, 1 model selected > select #2/A:93 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:1-93 1476 atoms, 1493 bonds, 93 residues, 1 model selected > select #2/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:1-246 4024 atoms, 4064 bonds, 246 residues, 1 model selected > cartoon hide (#!2 & sel) > select #2/A:566 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:271-566 4754 atoms, 4798 bonds, 296 residues, 1 model selected > select clear > select #2/A:566 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:271-566 4754 atoms, 4798 bonds, 296 residues, 1 model selected > cartoon hide (#!2 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #3/H Alignment identifier is 3/H > select #3/H:520-565 738 atoms, 741 bonds, 46 residues, 1 model selected > select #3/H:201-565 5911 atoms, 5966 bonds, 365 residues, 1 model selected > cartoon hide sel > select clear > select #2/A 21448 atoms, 21723 bonds, 1333 residues, 1 model selected > hide sel surfaces > hide sel cartoons > view matrix models > #2,-0.16721,0.025947,0.98558,-73.706,0.98583,0.018113,0.16677,74.81,-0.013525,0.9995,-0.028608,160.35 > select #1/A 6251 atoms, 6310 bonds, 386 residues, 1 model selected > hide sel surfaces > select #3/Q 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > close #2 > select #3/H:519-565 760 atoms, 763 bonds, 47 residues, 1 model selected > select #3/H:201-565 5911 atoms, 5966 bonds, 365 residues, 1 model selected > delete atoms sel > delete bonds sel > combine #1,3 name SOS-RacGEF Remapping chain ID 'A' in SPTBN2 working 4n.pdb #3 to 'E' Remapping chain ID 'C' in SPTBN2 working 4n.pdb #3 to 'I' > close #1-2 > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 7g.pdb"" Chain information for SPTBN2 working 7g.pdb #1 --- Chain | Description B C D E F | No description available J | No description available K | No description available Q | No description available S | No description available > select ::name=""ADP"" 195 atoms, 205 bonds, 5 residues, 1 model selected > color sel byelement > select clear > select ::name=""ADP"" 195 atoms, 205 bonds, 5 residues, 1 model selected > show sel atoms > select clear > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #2 --- Chain | Description A | No description available C | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #1/S Alignment identifier is 1/S > select #1/S:570 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/S:565-570 108 atoms, 108 bonds, 6 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2/A to #1/S pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A (#2), sequence alignment score = 117 RMSD between 8 pruned atom pairs is 1.292 angstroms; (across all 276 pairs: 36.428) > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:563 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:563-569 117 atoms, 117 bonds, 7 residues, 1 model selected > select #1/S:570 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/S:565-570 108 atoms, 108 bonds, 6 residues, 1 model selected > name frozen temp sel > select #2/A:569 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:564-569 102 atoms, 102 bonds, 6 residues, 1 model selected > select add temp 210 atoms, 210 bonds, 12 residues, 2 models selected > matchmaker #2/A & sel to #1/S & sel pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A (#2), sequence alignment score = 24.2 RMSD between 5 pruned atom pairs is 0.794 angstroms; (across all 5 pairs: 0.794) > select #1/S 8017 atoms, 8116 bonds, 483 residues, 1 model selected > show sel cartoons > hide sel atoms > select clear > select add #2 8835 atoms, 8924 bonds, 563 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.81869,0.30503,0.48652,-105.62,-0.32525,-0.94456,0.044877,60.514,0.47324,-0.1215,0.87251,-275.68 > undo > view matrix models > #2,-0.33213,0.84204,-0.42503,19.323,-0.92921,-0.21469,0.30078,-30.599,0.16202,0.49484,0.85374,-311.62 > view matrix models > #2,-0.17531,0.79237,-0.58431,50.14,-0.96584,-0.023367,0.2581,-34.351,0.19086,0.60959,0.7694,-303.58 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.17531,0.79237,-0.58431,95.476,-0.96584,-0.023367,0.2581,-65.593,0.19086,0.60959,0.7694,-309.48 > open /Users/tmckeithan/Downloads/Chimera/PDB/6ZNL.pdb 6ZNL.pdb title: Cryo-em structure of the dynactin complex [more info...] Chain information for 6ZNL.pdb #3 --- Chain | Description | UniProt A B C D E F G I | ARP1 actin related protein 1 homolog A | F2Z5G5_PIG 1-376 H | β-actin | ACTB_PIG 1-375 J | ARP11 | I3LHK5_PIG 1-417 K | capping protein (actin filament) muscle Z-line, α 1 | A0PFK5_PIG 1-286 L | F-actin capping protein β subunit | A9XFX6_PIG 1-272 M N m n | dynactin subunit 2 | O o | dynactin subunit 3 isoform 1 | F1SEC0_PIG 1-186 U | dynactin 6 | D0G6S1_PIG 1-190 V | dynactin subunit 5 | Y | dynactin subunit 4 | Z z | dynactin subunit 1 | Non-standard residues in 6ZNL.pdb #3 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate ZN — zinc ion > close #3 > open /Users/tmckeithan/Downloads/Chimera/PDB/8DNH.pdb 8DNH.pdb title: Cryo-em structure of nonmuscle β-actin [more info...] Chain information for 8DNH.pdb #3 --- Chain | Description | UniProt A B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 Non-standard residues in 8DNH.pdb #3 --- ACE — acetyl group ADP — adenosine-5'-diphosphate MG — magnesium ion > ui tool show Matchmaker > matchmaker #3/A to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 7g.pdb, chain B (#1) with 8DNH.pdb, chain A (#3), sequence alignment score = 1845.7 RMSD between 263 pruned atom pairs is 1.168 angstroms; (across all 374 pairs: 2.458) > matchmaker #3/A to #1/D pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 7g.pdb, chain D (#1) with 8DNH.pdb, chain A (#3), sequence alignment score = 1823.5 RMSD between 224 pruned atom pairs is 1.340 angstroms; (across all 374 pairs: 2.714) > save ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8.pdb"" > ui mousemode right zoom > show sel atoms > style sel sphere Changed 8835 atom styles > save ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8.cxs"" > select 74563 atoms, 75470 bonds, 13 pseudobonds, 5520 residues, 5 models selected > show sel cartoons > hide sel atoms > select clear > select #1/S:586-588,601-604,947-950,953-956 272 atoms, 269 bonds, 15 residues, 1 model selected > select add #2 9107 atoms, 9193 bonds, 578 residues, 2 models selected > select sel : ui tool show ""Show Sequence Viewer"" > sequence chain #1/S Destroying pre-existing alignment with identifier 1/S Alignment identifier is 1/S > sequence chain #1/J Alignment identifier is 1/J > sequence chain #1/K Alignment identifier is 1/K > sequence chain #1/Q Alignment identifier is 1/Q > select clear > select #2/A 6252 atoms, 6311 bonds, 386 residues, 1 model selected > select sel : select add #1 60614 atoms, 61233 bonds, 9 pseudobonds, 3865 residues, 3 models selected > select subtract #1 6682 atoms, 6739 bonds, 416 residues, 1 model selected > select add #2 8835 atoms, 8924 bonds, 563 residues, 1 model selected > ui mousemode right ""translate selected atoms"" > select sel : undo > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99927,0.033374,0.018352,2.1816,-0.033789,0.99917,0.022784,6.2974,-0.017577,-0.023387,0.99957,1.8691,#2,-0.20392,0.8022,-0.56115,89.719,-0.95476,-0.036233,0.29516,-69.519,0.21644,0.59595,0.7733,-307.62 > undo > select add #1 62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected > select subtract #1 8835 atoms, 8924 bonds, 563 residues, 1 model selected > view matrix models > #2,-0.12312,0.77457,-0.62039,102.93,-0.97518,0.021485,0.22035,-62.423,0.18401,0.63212,0.7527,-308.28 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.12312,0.77457,-0.62039,105.45,-0.97518,0.021485,0.22035,-62.22,0.18401,0.63212,0.7527,-308.29 > view matrix models > #2,-0.12312,0.77457,-0.62039,105.25,-0.97518,0.021485,0.22035,-61.883,0.18401,0.63212,0.7527,-308.73 > select sel : view matrix models > #1,1,0,0,2.5099,0,1,0,-5.5645,0,0,1,5.9637,#2,-0.12312,0.77457,-0.62039,107.76,-0.97518,0.021485,0.22035,-67.448,0.18401,0.63212,0.7527,-302.77 > undo > ui mousemode right zoom > select add #1 62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected > select subtract #1 8835 atoms, 8924 bonds, 563 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.12312,0.77457,-0.62039,104.94,-0.97518,0.021485,0.22035,-59.617,0.18401,0.63212,0.7527,-307.1 > ui mousemode right zoom > select sel : select #3/A 2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected > select clear > select #3/A 2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > select #2/A:582-583 30 atoms, 29 bonds, 2 residues, 1 model selected > select #2/A:567-583 254 atoms, 257 bonds, 17 residues, 1 model selected > select #2/A:564-583 312 atoms, 315 bonds, 20 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 5097 residues > select add ::name=""ACE""::name=""ADP""::name=""GTP""::name=""MG"" 71302 atoms, 369 bonds, 10 pseudobonds, 5123 residues, 5 models selected > cartoon hide (#2#!1,3 & sel) > select ~sel Nothing selected > cartoon > select ~sel 71302 atoms, 72141 bonds, 12 pseudobonds, 5123 residues, 5 models selected > select ~sel Nothing selected > combine #1,2,3 name combo Remapping chain ID 'C' in VAVtoSOS 2e.pdb #2 to 'G' Remapping chain ID 'B' in 8DNH.pdb #3 to 'H' Remapping chain ID 'C' in 8DNH.pdb #3 to 'I' Remapping chain ID 'D' in 8DNH.pdb #3 to 'L' > addh Summary of feedback from adding hydrogens to multiple structures --- warnings | Not adding hydrogens to SPTBN2 working 7g.pdb #1/J LYS 382 CB because it is missing heavy-atom bond partners Not adding hydrogens to SPTBN2 working 7g.pdb #1/J ARG 432 CB because it is missing heavy-atom bond partners Not adding hydrogens to SPTBN2 working 7g.pdb #1/K GLU 2268 CB because it is missing heavy-atom bond partners Not adding hydrogens to SPTBN2 working 7g.pdb #1/K GLU 2269 CB because it is missing heavy-atom bond partners Not adding hydrogens to SPTBN2 working 7g.pdb #1/K THR 2270 CB because it is missing heavy-atom bond partners 93 messages similar to the above omitted Skipped 18 atom(s) with bad connectivities; see log for details Not adding hydrogens to combo #4/J LYS 382 CB because it is missing heavy-atom bond partners Not adding hydrogens to combo #4/J ARG 432 CB because it is missing heavy-atom bond partners Not adding hydrogens to combo #4/K GLU 2268 CB because it is missing heavy- atom bond partners Not adding hydrogens to combo #4/K GLU 2269 CB because it is missing heavy- atom bond partners Not adding hydrogens to combo #4/K THR 2270 CB because it is missing heavy- atom bond partners 93 messages similar to the above omitted Skipped 18 atom(s) with bad connectivities; see log for details notes | Termini for SPTBN2 working 7g.pdb (#1) chain B determined from SEQRES records Termini for SPTBN2 working 7g.pdb (#1) chain C determined from SEQRES records Termini for SPTBN2 working 7g.pdb (#1) chain D determined from SEQRES records Termini for SPTBN2 working 7g.pdb (#1) chain E determined from SEQRES records Termini for SPTBN2 working 7g.pdb (#1) chain F determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: SPTBN2 working 7g.pdb #1/B ACE 0, SPTBN2 working 7g.pdb #1/C ACE 0, SPTBN2 working 7g.pdb #1/D ACE 0, SPTBN2 working 7g.pdb #1/E ACE 0, SPTBN2 working 7g.pdb #1/F ACE 0, SPTBN2 working 7g.pdb #1/J MET 1, SPTBN2 working 7g.pdb #1/K LYS 2038, SPTBN2 working 7g.pdb #1/Q MET 1, SPTBN2 working 7g.pdb #1/S GLU 565 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: SPTBN2 working 7g.pdb #1/B PHE 374, SPTBN2 working 7g.pdb #1/C PHE 374, SPTBN2 working 7g.pdb #1/D PHE 374, SPTBN2 working 7g.pdb #1/E PHE 374, SPTBN2 working 7g.pdb #1/F PHE 374, SPTBN2 working 7g.pdb #1/K GLY 2416, SPTBN2 working 7g.pdb #1/Q HIS 166, SPTBN2 working 7g.pdb #1/S PRO 1047 Chain-final residues that are not actual C termini: SPTBN2 working 7g.pdb #1/J GLN 534 3613 hydrogen bonds No usable SEQRES records for VAVtoSOS 2e.pdb (#2) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #2/A GLN 189, VAVtoSOS 2e.pdb #2/C MET 1, VAVtoSOS 2e.pdb #2/A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #2/C LEU 177, VAVtoSOS 2e.pdb #2/A GLU 563 Chain-final residues that are not actual C termini: VAVtoSOS 2e.pdb #2/A GLU 563 Missing OXT added to C-terminal residue VAVtoSOS 2e.pdb #2/A GLU 563 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN 223 OXT Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN 223 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A GLY 279 O Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN 223 OXT Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN 223 O 13 messages similar to the above omitted 539 hydrogen bonds Termini for 8DNH.pdb (#3) chain B determined from SEQRES records Termini for 8DNH.pdb (#3) chain C determined from SEQRES records Termini for 8DNH.pdb (#3) chain D determined from SEQRES records Chain-initial residues that are actual N termini: 8DNH.pdb #3/B ACE 0, 8DNH.pdb #3/C ACE 0, 8DNH.pdb #3/D ACE 0 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: 8DNH.pdb #3/B PHE 374, 8DNH.pdb #3/C PHE 374, 8DNH.pdb #3/D PHE 374 Chain-final residues that are not actual C termini: 718 hydrogen bonds Termini for combo (#4) chain B determined from SEQRES records Termini for combo (#4) chain C determined from SEQRES records Termini for combo (#4) chain D determined from SEQRES records Termini for combo (#4) chain E determined from SEQRES records Termini for combo (#4) chain F determined from SEQRES records 4 messages similar to the above omitted No usable SEQRES records for combo (#4) chain A; guessing termini instead Termini for combo (#4) chain G determined from SEQRES records Termini for combo (#4) chain H determined from SEQRES records Termini for combo (#4) chain I determined from SEQRES records Termini for combo (#4) chain L determined from SEQRES records Chain-initial residues that are actual N termini: combo #4/B ACE 0, combo #4/C ACE 0, combo #4/D ACE 0, combo #4/E ACE 0, combo #4/F ACE 0, combo #4/J MET 1, combo #4/K LYS 2038, combo #4/Q MET 1, combo #4/S GLU 565, combo #4/A GLN 189, combo #4/G MET 1, combo #4/H ACE 0, combo #4/I ACE 0, combo #4/L ACE 0, combo #4/A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: combo #4/B PHE 374, combo #4/C PHE 374, combo #4/D PHE 374, combo #4/E PHE 374, combo #4/F PHE 374, combo #4/K GLY 2416, combo #4/Q HIS 166, combo #4/S PRO 1047, combo #4/G LEU 177, combo #4/H PHE 374, combo #4/I PHE 374, combo #4/L PHE 374, combo #4/A GLU 563 Chain-final residues that are not actual C termini: combo #4/J GLN 534, combo #4/A GLU 563 Missing OXT added to C-terminal residue combo #4/A GLU 563 Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT Skipping possible acceptor with bad geometry: combo #4/A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 O Skipping possible acceptor with bad geometry: combo #4/A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor combo #4/A GLY 279 O Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT 13 messages similar to the above omitted 4874 hydrogen bonds 17383 hydrogens added > hide #2 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!4 models > isolde sim start #4/G > set selectionWidth 4 Done loading forcefield ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 75 residues in model #4 to IUPAC-IUB standards. > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: started sim > isolde sim pause > show sel cartoons > hide sel atoms > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #4/G,A ISOLDE: started sim > show sel cartoons > hide sel atoms > show sel atoms > ui tool show ""Ramachandran Plot"" > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #4 Loading residue template for ADP from internal database ISOLDE: started sim > isolde sim start #4 Simulation already running! > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 329 residues in model #4.2 to IUPAC-IUB standards. ISOLDE: stopped sim > interfaces #4 26 buried areas: J K 3655, J S 2384, J F 1932, S A 1560, F D 1380, C E 1335, C H 1304, H L 1239, F B 1228, S Q 1202, A G 1159, C D 976, I L 930, S D 730, J D 725, H I 701, F C 674, S F 649, A D 600, D H 599, F E 559, B E 537, A H 526, J B 490, J C 329, C K 303 > ui tool show ""Show Sequence Viewer"" > sequence chain #4.2/G Alignment identifier is 4.2/G > show sel atoms > ui tool show ""Selection Inspector"" > delete atoms (#!4.2 & sel) /Users/tmckeithan/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py:367: RuntimeWarning: invalid value encountered in log logscores = numpy.log(scores) > delete bonds (#!4.2 & sel) > delete atoms (#!4.2 & sel) > delete bonds (#!4.2 & sel) > delete atoms (#!4.2 & sel) > delete bonds (#!4.2 & sel) > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8.cxs"" format session opened ChimeraX session > select 74563 atoms, 75470 bonds, 13 pseudobonds, 5520 residues, 5 models selected > show sel cartoons > hide sel atoms > select #3/A 2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #2/A:583 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:564-583 312 atoms, 315 bonds, 20 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > select clear > select #1/S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A 5940 atoms, 5995 bonds, 366 residues, 1 model selected > select sel : combine #1-3 close true name combo Remapping chain ID 'C' in VAVtoSOS 2e.pdb #2 to 'G' Remapping chain ID 'B' in 8DNH.pdb #3 to 'H' Remapping chain ID 'C' in 8DNH.pdb #3 to 'I' Remapping chain ID 'D' in 8DNH.pdb #3 to 'L' > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > ui tool show ""Show Sequence Viewer"" > sequence chain /J Alignment identifier is 1/J > sequence chain /K Alignment identifier is 1/K > sequence chain /Q Alignment identifier is 1/Q > sequence chain /S Alignment identifier is 1/S > select /S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > select /S:565 17 atoms, 16 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:562 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:562-563 30 atoms, 29 bonds, 2 residues, 1 model selected > select /S:567 17 atoms, 16 bonds, 1 residue, 1 model selected > select /S:566-567 34 atoms, 33 bonds, 2 residues, 1 model selected > name frozen temp sel > select /A:562 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:562-563 30 atoms, 29 bonds, 2 residues, 1 model selected > select add temp 64 atoms, 62 bonds, 4 residues, 1 model selected > select ~sel 71221 atoms, 72060 bonds, 12 pseudobonds, 5118 residues, 2 models selected > cartoon hide (#!1 & sel) > show sel atoms > hide sel cartoons > color sel byelement > cofr sel > interfaces #1 23 buried areas: J K 3441, J S 2289, J F 1813, A G 1482, E C 1287, F D 1245, S A 1245, F B 1179, C H 1143, H L 1124, S Q 1014, D I 860, C D 614, F C 578, F E 505, B E 493, J B 448, S F 405, S D 398, H I 393, J D 370, I L 319, D H 304 > addh Summary of feedback from adding hydrogens to combo #1 --- warnings | Not adding hydrogens to /J LYS 382 CB because it is missing heavy- atom bond partners Not adding hydrogens to /J ARG 432 CB because it is missing heavy-atom bond partners Not adding hydrogens to /K GLU 2268 CB because it is missing heavy-atom bond partners Not adding hydrogens to /K GLU 2269 CB because it is missing heavy-atom bond partners Not adding hydrogens to /K THR 2270 CB because it is missing heavy-atom bond partners 93 messages similar to the above omitted Skipped 18 atom(s) with bad connectivities; see log for details notes | Termini for combo (#1) chain B determined from SEQRES records Termini for combo (#1) chain C determined from SEQRES records Termini for combo (#1) chain D determined from SEQRES records Termini for combo (#1) chain E determined from SEQRES records Termini for combo (#1) chain F determined from SEQRES records 4 messages similar to the above omitted No usable SEQRES records for combo (#1) chain A; guessing termini instead Termini for combo (#1) chain G determined from SEQRES records Termini for combo (#1) chain H determined from SEQRES records Termini for combo (#1) chain I determined from SEQRES records Termini for combo (#1) chain L determined from SEQRES records Chain-initial residues that are actual N termini: /B ACE 0, /C ACE 0, /D ACE 0, /E ACE 0, /F ACE 0, /J MET 1, /K LYS 2038, /Q MET 1, /A GLN 189, /G MET 1, /H ACE 0, /I ACE 0, /L ACE 0, /A GLN 189 Chain-initial residues that are not actual N termini: /S GLN 566 Chain-final residues that are actual C termini: /B PHE 374, /C PHE 374, /D PHE 374, /E PHE 374, /F PHE 374, /K GLY 2416, /Q HIS 166, /S PRO 1047, /G LEU 177, /H PHE 374, /I PHE 374, /L PHE 374, /A GLU 563 Chain-final residues that are not actual C termini: /J GLN 534, /A GLU 563 Missing OXT added to C-terminal residue /A GLU 563 Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 13 messages similar to the above omitted 4873 hydrogen bonds 8692 hydrogens added > isolde sim start /A,S,Q,G ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 75 residues in model #1 to IUPAC-IUB standards. ISOLDE: started sim > show sel cartoons > hide sel atoms > ui tool show ""Ramachandran Plot"" > show sel cartoons > show sel atoms > ui tool show ""Ramachandran Plot"" > select clear > show sel atoms > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 69 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > interfaces #1 areaCutoff 50 26 buried areas: J K 3624, J S 2327, J F 1914, A G 1376, C E 1327, F D 1299, F B 1228, C H 1191, H L 1190, S A 1123, S Q 1075, D I 922, C D 665, F C 645, F E 551, B E 525, S F 508, J B 479, S D 452, H I 450, J D 374, I L 364, D H 348, C K 280, J C 248, J Q 63 > save ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8a.pdb"" > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8a.pdb"" format pdb SPTBN2 working 8a.pdb title: Cryo-em structure of nonmuscle β-actin [more info...] Chain information for SPTBN2 working 8a.pdb #1 --- Chain | Description | UniProt A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 E F H I L | No description available | G | No description available | J | No description available | K | No description available | Q | No description available | S | No description available | Non-standard residues in SPTBN2 working 8a.pdb #1 --- ACE — acetyl group ADP — adenosine-5'-diphosphate GTP — (GTP) MG — magnesium ion > isolde sim start /A,S,Q,G,J,K,D,F ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... SPTBN2 working 8a.pdb title: Cryo-em structure of nonmuscle β-actin [more info...] Chain information for SPTBN2 working 8a.pdb --- Chain | Description | UniProt 1.2/A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 1.2/B 1.2/C 1.2/D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 1.2/E 1.2/F 1.2/H 1.2/I 1.2/L | No description available | 1.2/G | No description available | 1.2/J | No description available | 1.2/K | No description available | 1.2/Q | No description available | 1.2/S | No description available | Non-standard residues in SPTBN2 working 8a.pdb #1.2 --- ACE — acetyl group ADP — adenosine-5'-diphosphate GTP — (GTP) MG — magnesium ion ISOLDE: started sim > isolde sim pause > hide sel atoms > show sel cartoons > isolde sim resume > select clear > select add /A 5941 atoms, 5996 bonds, 366 residues, 1 model selected > select add /G 8524 atoms, 8609 bonds, 543 residues, 1 model selected > ui mousemode right ""isolde tug selection"" > isolde sim pause > ui mousemode right ""translate selected atoms"" > isolde sim resume > ui mousemode right ""isolde tug selection"" > show sel atoms > ui mousemode right ""isolde tug atom"" > select 79978 atoms, 80817 bonds, 12 pseudobonds, 5122 residues, 18 models selected > show sel atoms > hide sel cartoons > isolde sim pause > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 206 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8b.pdb"" > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8b.pdb"" format pdb SPTBN2 working 8b.pdb title: Cryo-em structure of nonmuscle β-actin [more info...] Chain information for SPTBN2 working 8b.pdb #1 --- Chain | Description | UniProt A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 E F H I L | No description available | G | No description available | J | No description available | K | No description available | Q | No description available | S | No description available | Non-standard residues in SPTBN2 working 8b.pdb #1 --- ACE — acetyl group ADP — adenosine-5'-diphosphate GTP — (GTP) MG — magnesium ion > hide atoms > show cartoons > interfaces #1 areaCutoff 50 29 buried areas: J K 3357, J S 2483, J F 1682, A G 1361, C E 1274, F D 1261, S A 1209, C H 1184, F B 1150, H L 1147, D I 1053, S Q 1028, A D 705, F C 683, S F 583, F E 546, C D 542, B E 493, S D 458, J B 451, D H 439, H I 405, I L 331, J C 237, C K 195, J Q 183, A H 146, J D 142, J A 52 > select /J 8715 atoms, 8791 bonds, 534 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > ui tool show ""Show Sequence Viewer"" > sequence chain /S Alignment identifier is 1/S > sequence chain /J Alignment identifier is 1/J > sequence chain /K Alignment identifier is 1/K > sequence chain /Q Alignment identifier is 1/Q > ui tool show ""Show Sequence Viewer"" > show sel atoms > color N cornflowerblue atoms > color O hotpink atoms > color :arg,hic,his,lys & sidechain & N blue atoms > color :asp,glu & sidechain & O red atoms > ui tool show ""Side View"" > interfaces #1 areaCutoff 50 29 buried areas: J K 3357, J S 2483, J F 1682, A G 1361, C E 1274, F D 1261, S A 1209, C H 1184, F B 1150, H L 1147, D I 1053, S Q 1028, A D 705, F C 683, S F 583, F E 546, C D 542, B E 493, S D 458, J B 451, D H 439, H I 405, I L 331, J C 237, C K 195, J Q 183, A H 146, J D 142, J A 52 > dssp > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #2 --- Chain | Description A | No description available C | No description available > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 8b.pdb, chain A (#1) with VAVtoSOS 2e.pdb, chain A (#2), sequence alignment score = 1799.5 RMSD between 111 pruned atom pairs is 1.010 angstroms; (across all 366 pairs: 4.868) > select #1/A 5941 atoms, 5996 bonds, 366 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/G 2583 atoms, 2613 bonds, 177 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:564-565 34 atoms, 33 bonds, 2 residues, 1 model selected > select #2/A:564-583 312 atoms, 315 bonds, 20 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIC""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 79564 atoms, 80394 bonds, 5096 residues, 2 models selected > hide sel target a > select clear > select add #2 8523 atoms, 8608 bonds, 543 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.066053,0.85096,-0.52106,95.403,-0.97509,0.055775,0.2147,-59.842,0.21176,0.52226,0.82608,-314.22 > view matrix models > #2,-0.10676,0.82746,-0.55128,99.813,-0.97792,0.012787,0.20858,-57.088,0.17964,0.56138,0.80783,-314.15 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.10676,0.82746,-0.55128,97.279,-0.97792,0.012787,0.20858,-56.302,0.17964,0.56138,0.80783,-314.65 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.14656,0.80003,-0.58178,101.93,-0.97794,-0.028708,0.20688,-54.17,0.14881,0.59927,0.7866,-314.09 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.14656,0.80003,-0.58178,101.93,-0.97794,-0.028708,0.20688,-53.507,0.14881,0.59927,0.7866,-315.03 > ui mousemode right ""rotate selected models"" > select clear > select add #2 8523 atoms, 8608 bonds, 543 residues, 1 model selected > view matrix models > #2,-0.21765,0.81132,-0.54258,94.489,-0.96702,-0.1039,0.23256,-53.398,0.1323,0.5753,0.80717,-317.14 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.21765,0.81132,-0.54258,91.305,-0.96702,-0.1039,0.23256,-50.922,0.1323,0.5753,0.80717,-317.16 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.29199,0.75038,-0.59302,99.523,-0.95413,-0.18566,0.23487,-47.234,0.066143,0.6344,0.77017,-316.12 > view matrix models > #2,-0.40874,0.63199,-0.65842,111.55,-0.91041,-0.33287,0.24567,-41.084,-0.063904,0.69985,0.71143,-313.7 > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/SPTBN2 working 8b.pdb"" format pdb SPTBN2 working 8b.pdb title: Cryo-em structure of nonmuscle β-actin [more info...] Chain information for SPTBN2 working 8b.pdb #1 --- Chain | Description | UniProt A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 E F H I L | No description available | G | No description available | J | No description available | K | No description available | Q | No description available | S | No description available | Non-standard residues in SPTBN2 working 8b.pdb #1 --- ACE — acetyl group ADP — adenosine-5'-diphosphate GTP — (GTP) MG — magnesium ion > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #2 --- Chain | Description A | No description available C | No description available > ui tool show Matchmaker > matchmaker #2/C to #1/E pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 8b.pdb, chain E (#1) with VAVtoSOS 2e.pdb, chain C (#2), sequence alignment score = 59.9 RMSD between 5 pruned atom pairs is 1.378 angstroms; (across all 131 pairs: 20.379) > ui tool show Matchmaker > matchmaker #2/C to #1/G pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SPTBN2 working 8b.pdb, chain G (#1) with VAVtoSOS 2e.pdb, chain C (#2), sequence alignment score = 912.2 RMSD between 121 pruned atom pairs is 1.061 angstroms; (across all 177 pairs: 2.356) > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIC""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 88400 atoms, 89319 bonds, 5659 residues, 2 models selected > hide sel atoms > show sel cartoons > select #1/G 2583 atoms, 2613 bonds, 177 residues, 1 model selected > hide sel cartoons > select #1/A 5941 atoms, 5996 bonds, 366 residues, 1 model selected > hide sel cartoons > view matrix models > #1,0.99677,-0.01188,-0.079408,-9.0815,0.020269,0.99419,0.10568,9.696,0.077691,-0.10695,0.99122,-14.274 > select #2/A:480 7 atoms, 6 bonds, 1 residue, 1 model selected > cofr sel > select add #2 8835 atoms, 8924 bonds, 563 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.24209,0.76925,-0.59131,104.63,-0.92355,0.0041076,0.38347,-81.117,0.29741,0.63893,0.70945,-305.94 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select clear > select #2/A:582-583 30 atoms, 29 bonds, 2 residues, 1 model selected > select #2/A:564-583 312 atoms, 315 bonds, 20 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #2 8523 atoms, 8608 bonds, 543 residues, 1 model selected > show sel surfaces > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting simple > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: VAVtoSOS 2e.pdb #2/A LYS 214 VAVtoSOS 2e.pdb #2/C MET 1 VAVtoSOS 2e.pdb #2/C GLN 2 VAVtoSOS 2e.pdb #2/C GLU 31 VAVtoSOS 2e.pdb #2/C ILE 33 VAVtoSOS 2e.pdb #2/C LYS 49 VAVtoSOS 2e.pdb #2/C LYS 123 VAVtoSOS 2e.pdb #2/C ASP 124 VAVtoSOS 2e.pdb #2/C GLU 127 VAVtoSOS 2e.pdb #2/C LYS 128 VAVtoSOS 2e.pdb #2/C GLU 131 VAVtoSOS 2e.pdb #2/C LYS 132 VAVtoSOS 2e.pdb #2/C LYS 133 VAVtoSOS 2e.pdb #2/C LYS 153 VAVtoSOS 2e.pdb #2/C LEU 160 VAVtoSOS 2e.pdb #2/C THR 161 VAVtoSOS 2e.pdb #2/C LYS 166 VAVtoSOS 2e.pdb #2/C ASP 170 VAVtoSOS 2e.pdb #2/C ARG 174 VAVtoSOS 2e.pdb #2/C LEU 177 Using Amber 20 recommended default charges and atom types for standard residues copy of VAVtoSOS 2e.pdb #/A LYS 214 CLYS Nonstandard name for heavy atom copy of VAVtoSOS 2e.pdb #/A LYS 214 OH > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. Chain information for VAVtoSOS 2e.pdb #1 --- Chain | Description A | No description available C | No description available > show surfaces > rainbow > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A LYS 214 /C MET 1 /C GLN 2 /C GLU 31 /C ILE 33 /C LYS 49 /C LYS 123 /C ASP 124 /C GLU 127 /C LYS 128 /C GLU 131 /C LYS 132 /C LYS 133 /C LYS 153 /C LEU 160 /C THR 161 /C LYS 166 /C ASP 170 /C ARG 174 /C LEU 177 Using Amber 20 recommended default charges and atom types for standard residues /A LYS 214 CLYS Nonstandard name for heavy atom /A LYS 214 OH > swapaa /A:214 lys Using Dunbrack library /A LYS 214: phi -51.4, psi -27.4 trans Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 214 > swapaa /C:1 met Using Dunbrack library /C MET 1: phi none, psi -163.4 trans Applying MET rotamer (chi angles: 72.6 -72.0 -71.4) to /C MET 1 > swapaa /C:2 gln Using Dunbrack library /C GLN 2: phi 54.0, psi 43.2 trans Applying GLN rotamer (chi angles: -63.1 -69.2 -63.4) to /C GLN 2 > swapaa /C:31 glu Using Dunbrack library /C GLU 31: phi -67.8, psi -17.2 trans Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /C GLU 31 > swapaa /C:33 ile Using Dunbrack library /C ILE 33: phi -128.5, psi 129.8 trans Applying ILE rotamer (chi angles: 66.2 -71.1) to /C ILE 33 > swapaa /C:49 lys Using Dunbrack library /C LYS 49: phi -105.8, psi 132.8 trans Applying LYS rotamer (chi angles: -177.7 178.5 -176.1 -64.2) to /C LYS 49 > swapaa /C:123 lys Using Dunbrack library /C LYS 123: phi -59.5, psi -24.4 trans Applying LYS rotamer (chi angles: -66.0 -66.1 -174.7 -67.0) to /C LYS 123 > swapaa /C:124 asp Using Dunbrack library /C ASP 124: phi -65.8, psi -32.0 trans Applying ASP rotamer (chi angles: -71.2 -15.9) to /C ASP 124 > swapaa /C:127 glu Using Dunbrack library /C GLU 127: phi -60.7, psi -29.0 trans Applying GLU rotamer (chi angles: -69.3 177.9 -8.3) to /C GLU 127 > swapaa /C:128 lys Using Dunbrack library /C LYS 128: phi -79.9, psi -47.4 trans Applying LYS rotamer (chi angles: -66.0 -173.5 -71.5 -66.9) to /C LYS 128 > swapaa /C:131 glu Using Dunbrack library /C GLU 131: phi -67.4, psi -28.1 trans Applying GLU rotamer (chi angles: -68.4 178.8 -8.3) to /C GLU 131 > swapaa /C:132 lys Using Dunbrack library /C LYS 132: phi -92.6, psi 6.9 trans Applying LYS rotamer (chi angles: -64.3 -174.6 -70.2 -66.8) to /C LYS 132 > swapaa /C:133 lys Using Dunbrack library /C LYS 133: phi 60.7, psi 17.9 trans Applying LYS rotamer (chi angles: -83.6 68.4 178.6 177.6) to /C LYS 133 > swapaa /C:153 lys Using Dunbrack library /C LYS 153: phi -147.1, psi 155.7 trans Applying LYS rotamer (chi angles: -61.9 -73.1 -174.8 -67.0) to /C LYS 153 > swapaa /C:160 leu Using Dunbrack library /C LEU 160: phi -72.4, psi -31.1 trans Applying LEU rotamer (chi angles: -67.8 174.1) to /C LEU 160 > swapaa /C:161 thr Using Dunbrack library /C THR 161: phi -153.7, psi 150.8 trans Applying THR rotamer (chi angles: -174.5) to /C THR 161 > swapaa /C:166 lys Using Dunbrack library /C LYS 166: phi -57.5, psi -38.2 trans Applying LYS rotamer (chi angles: -171.7 -89.7 -173.2 -177.4) to /C LYS 166 > swapaa /C:170 asp Using Dunbrack library /C ASP 170: phi -62.4, psi -45.3 trans Applying ASP rotamer (chi angles: -71.6 -15.7) to /C ASP 170 > swapaa /C:174 arg Using Dunbrack library /C ARG 174: phi -63.3, psi -17.3 trans Applying ARG rotamer (chi angles: -172.3 178.2 -63.1 -83.0) to /C ARG 174 > swapaa /C:177 leu Using Dunbrack library /C LEU 177: phi -148.8, psi none trans Applying LEU rotamer (chi angles: -64.7 174.5) to /C LEU 177 > addh Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 --- warning | Skipped 18 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing termini instead Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN 189 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN 583 Chain-final residues that are not actual C termini: Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A ASN 223 O Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O Skipping possible acceptor with bad geometry: /A GLY 279 O Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O Skipping possible acceptor with bad geometry: /A ASN 223 OXT Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT Skipping possible acceptor with bad geometry: /A GLY 279 OXT Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 OXT 13 messages similar to the above omitted 564 hydrogen bonds 161 hydrogens added > hide surfaces > save ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"" > isolde sim start #1 > set selectionWidth 4 Done loading forcefield ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #1 to IUPAC-IUB standards. Chain information for VAVtoSOS 2e.pdb --- Chain | Description 1.2/A | No description available 1.2/C | No description available > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: started sim > isolde sim pause > isolde sim resume > ui tool show ""Ramachandran Plot"" ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 37 days, 2 hours, 52 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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-ISOLDE: 1.7 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect new normal Unassigned