id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19529 Crash while moving window / changing geometry in QDockWidget::event() howell@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. 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""P"", ""arch"" : ""arm64e"", ""base"" : 6925758464, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 24310400, ""uuid"" : ""4e909aec-68bc-3fc9-a87a-de928e1e36e1"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2685.30.107"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6849859584, ""size"" : 651204, ""uuid"" : ""0975afba-c46b-364c-bd84-a75daa9e455a"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 6848774144, ""size"" : 5653544960, ""uuid"" : ""acb998b6-263c-3634-b0a8-ae8270a116c2"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=2.1G written=1891K(0%) resident=1891K(0%) swapped_out=0K(0%) unallocated=2.1G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 48K 3 ColorSync 80K 5 CoreAnimation 1104K 64 CoreGraphics 64K 4 CoreServices 352K 2 CoreUI image data 2688K 19 Foundation 16K 1 Kernel Alloc Once 96K 2 MALLOC 1.3G 304 MALLOC guard page 4096K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 704K 44 Stack 203.5M 45 Stack Guard 56.0M 1 VM_ALLOCATE 356.8M 224 VM_ALLOCATE (reserved) 320.0M 1 reserved VM address space (unallocated) __AUTH 5935K 652 __AUTH_CONST 89.7M 1042 __CTF 824 1 __DATA 43.5M 1138 __DATA_CONST 59.5M 1185 __DATA_DIRTY 8778K 901 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 622.1M 139 __OBJC_RO 78.4M 1 __OBJC_RW 2570K 1 __TEXT 1.5G 1207 __TPRO_CONST 128K 2 dyld private memory 1456K 14 mapped file 330.2M 58 page table in kernel 1891K 1 shared memory 3664K 25 =========== ======= ======= TOTAL 4.9G 7103 TOTAL, minus reserved VM space 4.6G 7103 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4e65298835e5161026dfc006f6ac66a1faedce1b"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""39a24348-11f1-4b3a-b3e4-d4f5a0872b06"", ""experimentId"" : ""69447451268be96b884ba5bf"", ""deploymentId"" : 400000001 } ] } } Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" Log from Sat Dec 20 13:53:51 2025UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" Log from Fri Dec 19 16:32:43 2025UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" format session Log from Thu Dec 18 15:12:06 2025UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844/fold_alg844_model_0.cif"" Chain information for fold_alg844_model_0.cif #1 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844/fold_alg844_model_1.cif"" Chain information for fold_alg844_model_1.cif #2 --- Chain | Description A | . B | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844/fold_alg844_model_2.cif"" Chain information for fold_alg844_model_2.cif #3 --- Chain | Description A | . B | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844/fold_alg844_model_3.cif"" Chain information for fold_alg844_model_3.cif #4 --- Chain | Description A | . B | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844/fold_alg844_model_4.cif"" Chain information for fold_alg844_model_4.cif #5 --- Chain | Description A | . B | . Computing secondary structure [Repeated 3 time(s)] > ui tool show Matchmaker > matchmaker #2-5 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 fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_1.cif, chain A (#2), sequence alignment score = 2607.3 RMSD between 494 pruned atom pairs is 0.330 angstroms; (across all 494 pairs: 0.330) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_2.cif, chain A (#3), sequence alignment score = 2607.9 RMSD between 480 pruned atom pairs is 0.395 angstroms; (across all 494 pairs: 1.285) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_3.cif, chain A (#4), sequence alignment score = 2610.9 RMSD between 494 pruned atom pairs is 0.414 angstroms; (across all 494 pairs: 0.414) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844_model_4.cif, chain A (#5), sequence alignment score = 2607.9 RMSD between 480 pruned atom pairs is 0.482 angstroms; (across all 494 pairs: 1.301) > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_0.cif"" Chain information for fold_alg844_dimer_g_model_0.cif #6 --- Chain | Description A | . B C | . D | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_1.cif"" Chain information for fold_alg844_dimer_g_model_1.cif #7 --- Chain | Description A | . B C | . D | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_2.cif"" Chain information for fold_alg844_dimer_g_model_2.cif #8 --- Chain | Description A | . B C | . D | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_3.cif"" Chain information for fold_alg844_dimer_g_model_3.cif #9 --- Chain | Description A | . B C | . D | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_4.cif"" Chain information for fold_alg844_dimer_g_model_4.cif #10 --- Chain | Description A | . B C | . D | . Computing secondary structure [Repeated 4 time(s)] > delete #6 > delete #7 > delete #8 > delete #9 > delete #10 > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_0.cif"" Chain information for fold_alg844kxijf_model_0.cif #6 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_1.cif"" Chain information for fold_alg844kxijf_model_1.cif #7 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_2.cif"" Chain information for fold_alg844kxijf_model_2.cif #8 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_3.cif"" Chain information for fold_alg844kxijf_model_3.cif #9 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844kxijf/fold_alg844kxijf_model_4.cif"" Chain information for fold_alg844kxijf_model_4.cif #10 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > hide atoms > show cartoons Computing secondary structure [Repeated 4 time(s)] > ui tool show Matchmaker > matchmaker #6-10 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 fold_alg844_model_0.cif, chain A (#1) with fold_alg844kxijf_model_0.cif, chain A (#6), sequence alignment score = 2602.5 RMSD between 477 pruned atom pairs is 0.798 angstroms; (across all 494 pairs: 1.170) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844kxijf_model_1.cif, chain A (#7), sequence alignment score = 2598.9 RMSD between 464 pruned atom pairs is 0.769 angstroms; (across all 494 pairs: 1.167) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844kxijf_model_2.cif, chain A (#8), sequence alignment score = 2602.5 RMSD between 454 pruned atom pairs is 0.825 angstroms; (across all 494 pairs: 1.324) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844kxijf_model_3.cif, chain A (#9), sequence alignment score = 2598.9 RMSD between 463 pruned atom pairs is 0.889 angstroms; (across all 494 pairs: 1.319) Matchmaker fold_alg844_model_0.cif, chain A (#1) with fold_alg844kxijf_model_4.cif, chain A (#10), sequence alignment score = 2602.5 RMSD between 475 pruned atom pairs is 0.771 angstroms; (across all 494 pairs: 1.188) > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algkxijf/fold_algkxijf_model_0.cif"" Chain information for fold_algkxijf_model_0.cif #11 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algkxijf/fold_algkxijf_model_1.cif"" Chain information for fold_algkxijf_model_1.cif #12 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algkxijf/fold_algkxijf_model_2.cif"" Chain information for fold_algkxijf_model_2.cif #13 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algkxijf/fold_algkxijf_model_3.cif"" Chain information for fold_algkxijf_model_3.cif #14 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algkxijf/fold_algkxijf_model_4.cif"" Chain information for fold_algkxijf_model_4.cif #15 --- Chain | Description A | . B | . C | . D | . E | . > hide atoms > ui tool show Matchmaker > matchmaker #12-15 to #11 Computing secondary structure [Repeated 4 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_algkxijf_model_1.cif, chain C (#12), sequence alignment score = 2723.2 RMSD between 473 pruned atom pairs is 0.361 angstroms; (across all 520 pairs: 3.605) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_algkxijf_model_2.cif, chain C (#13), sequence alignment score = 2740.6 RMSD between 490 pruned atom pairs is 0.411 angstroms; (across all 520 pairs: 3.001) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_algkxijf_model_3.cif, chain C (#14), sequence alignment score = 2737.6 RMSD between 476 pruned atom pairs is 0.416 angstroms; (across all 520 pairs: 3.810) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_algkxijf_model_4.cif, chain C (#15), sequence alignment score = 2719 RMSD between 470 pruned atom pairs is 0.398 angstroms; (across all 520 pairs: 4.424) > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #11-15 cartoons > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_0.cif"" Chain information for fold_alg844ijf_model_0.cif #16 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_1.cif"" Chain information for fold_alg844ijf_model_1.cif #17 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_2.cif"" Chain information for fold_alg844ijf_model_2.cif #18 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_3.cif"" Chain information for fold_alg844ijf_model_3.cif #19 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844ijf/fold_alg844ijf_model_4.cif"" Chain information for fold_alg844ijf_model_4.cif #20 --- Chain | Description A | . B | . C | . D | . E | . > hide #11-20 atoms > show #11-20 cartoons Computing secondary structure [Repeated 4 time(s)] > ui tool show Matchmaker > matchmaker #16-20 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_alg844ijf_model_0.cif, chain D (#16), sequence alignment score = 2672.2 RMSD between 448 pruned atom pairs is 0.473 angstroms; (across all 520 pairs: 4.351) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_alg844ijf_model_1.cif, chain D (#17), sequence alignment score = 2684.2 RMSD between 452 pruned atom pairs is 0.498 angstroms; (across all 520 pairs: 3.450) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_alg844ijf_model_2.cif, chain D (#18), sequence alignment score = 2669.2 RMSD between 450 pruned atom pairs is 0.473 angstroms; (across all 520 pairs: 4.341) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_alg844ijf_model_3.cif, chain D (#19), sequence alignment score = 2669.8 RMSD between 454 pruned atom pairs is 0.534 angstroms; (across all 520 pairs: 5.088) Matchmaker fold_algkxijf_model_0.cif, chain C (#11) with fold_alg844ijf_model_4.cif, chain D (#20), sequence alignment score = 2653.6 RMSD between 454 pruned atom pairs is 0.503 angstroms; (across all 520 pairs: 3.340) > hide #12 models > hide #13 models > hide #14 models > hide #15 models > hide #16 models > hide #17 models > hide #18 models > hide #19 models > hide #20 models > show #12 models > show #13 models > show #14 models > show #15 models > hide #15 models > hide #14 models > hide #13 models > hide #12 models > hide #11 models > show #11 models > show #16 models > show #17 models > show #18 models > show #19 models > delete #16 > delete #17 > delete #18 > delete #19 > delete #20 > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 predictions/Alginate/7ula_XK structure.cif"" Summary of feedback from opening /Users/lynne/SickKids Research Dropbox/Howell Lab's shared workspace/Alphafold 3 predictions/Alginate/7ula_XK structure.cif --- note | Fetching CCD NI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/NI/NI.cif 7ula_XK structure.cif title: Structure of the Pseudomonas putida AlgKX modification and secretion complex [more info...] Chain information for 7ula_XK structure.cif #16 --- Chain | Description | UniProt A | Alginate biosynthesis protein AlgX | ALGX_PSEPK 1-479 B | Alginate biosynthesis protein AlgK | ALGK_PSEPK 33-484 Non-standard residues in 7ula_XK structure.cif #16 --- CL — chloride ion GOL — glycerol (glycerin; propane-1,2,3-triol) NI — nickel (II) ion 16 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5622 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Matchmaker [Repeated 1 time(s)] > matchmaker #!16 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algkxijf_model_0.cif, chain B (#11) with 7ula_XK structure.cif, chain A (#16), sequence alignment score = 1396.4 RMSD between 389 pruned atom pairs is 0.767 angstroms; (across all 420 pairs: 1.711) > hide #11 models > ui tool show ""Show Sequence Viewer"" > sequence chain #16/A Alignment identifier is 16/A > select clear > select #16/A:29 5 atoms, 4 bonds, 1 residue, 1 model selected > select #16/A:29-33 36 atoms, 37 bonds, 5 residues, 1 model selected > show #10 models > show #11 models > hide #10 models > show #6 models > ui tool show Matchmaker > matchmaker #6-15 to #16 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 7ula_XK structure.cif, chain A (#16) with fold_alg844kxijf_model_0.cif, chain D (#6), sequence alignment score = 1405.4 RMSD between 390 pruned atom pairs is 0.803 angstroms; (across all 420 pairs: 1.768) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_alg844kxijf_model_1.cif, chain D (#7), sequence alignment score = 1394 RMSD between 388 pruned atom pairs is 0.827 angstroms; (across all 420 pairs: 1.725) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_alg844kxijf_model_2.cif, chain D (#8), sequence alignment score = 1384.4 RMSD between 391 pruned atom pairs is 0.798 angstroms; (across all 420 pairs: 1.696) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_alg844kxijf_model_3.cif, chain D (#9), sequence alignment score = 1394 RMSD between 383 pruned atom pairs is 0.863 angstroms; (across all 420 pairs: 1.773) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_alg844kxijf_model_4.cif, chain D (#10), sequence alignment score = 1387.4 RMSD between 388 pruned atom pairs is 0.818 angstroms; (across all 420 pairs: 1.732) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algkxijf_model_0.cif, chain B (#11), sequence alignment score = 1396.4 RMSD between 389 pruned atom pairs is 0.767 angstroms; (across all 420 pairs: 1.711) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algkxijf_model_1.cif, chain B (#12), sequence alignment score = 1405.4 RMSD between 387 pruned atom pairs is 0.819 angstroms; (across all 420 pairs: 1.760) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algkxijf_model_2.cif, chain B (#13), sequence alignment score = 1396.4 RMSD between 388 pruned atom pairs is 0.822 angstroms; (across all 420 pairs: 1.753) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algkxijf_model_3.cif, chain B (#14), sequence alignment score = 1419.8 RMSD between 390 pruned atom pairs is 0.832 angstroms; (across all 420 pairs: 1.776) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algkxijf_model_4.cif, chain B (#15), sequence alignment score = 1399.4 RMSD between 392 pruned atom pairs is 0.791 angstroms; (across all 420 pairs: 1.771) > hide #11 models > hide #6 models > show #11 models > show #12 models > show #13 models > show #14 models > show #15 models > hide #11 models > show #11 models > hide #12 models > hide #13 models > hide #14 models > hide #15 models > show #6 models > delete #6 > delete #7 > delete #8 > delete #9 > delete #10 > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_4.cif"" Chain information for fold_algekx_minus_ss_model_4.cif #6 --- Chain | Description A | . B | . C | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_1.cif"" Chain information for fold_algekx_minus_ss_model_1.cif #7 --- Chain | Description A | . B | . C | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_0.cif"" Chain information for fold_algekx_minus_ss_model_0.cif #8 --- Chain | Description A | . B | . C | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_2.cif"" Chain information for fold_algekx_minus_ss_model_2.cif #9 --- Chain | Description A | . B | . C | . > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_3.cif"" Chain information for fold_algekx_minus_ss_model_3.cif #10 --- Chain | Description A | . B | . C | . Computing secondary structure [Repeated 4 time(s)] > ui tool show Matchmaker > matchmaker #6-10 to #16 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 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_4.cif, chain C (#6), sequence alignment score = 1390.2 RMSD between 390 pruned atom pairs is 0.758 angstroms; (across all 420 pairs: 1.653) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_1.cif, chain C (#7), sequence alignment score = 1403.4 RMSD between 387 pruned atom pairs is 0.749 angstroms; (across all 420 pairs: 1.576) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_0.cif, chain C (#8), sequence alignment score = 1384.2 RMSD between 385 pruned atom pairs is 0.763 angstroms; (across all 420 pairs: 1.688) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_2.cif, chain C (#9), sequence alignment score = 1383 RMSD between 386 pruned atom pairs is 0.755 angstroms; (across all 420 pairs: 1.632) Matchmaker 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_3.cif, chain C (#10), sequence alignment score = 1377.6 RMSD between 391 pruned atom pairs is 0.744 angstroms; (across all 420 pairs: 1.608) > hide #11 models > color sel bypolymer > color sel bychain > color sel bypolymer [Repeated 2 time(s)] > hide #7 models > hide #8 models > hide #9 models > hide #10 models > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 predictions/Alginate/AlgE_3RBH.pdb"" AlgE_3RBH.pdb title: Structure of alginate export protein ALGE from pseudomonas aeruginosa [more info...] Chain information for AlgE_3RBH.pdb #17 --- Chain | Description | UniProt A B C D | alginate production protein ALGE | ALGE_PSEAE 33-490 Non-standard residues in AlgE_3RBH.pdb #17 --- C8E — (hydroxyethyloxy)tri(ethyloxy)octane CA — calcium ion EDO — 1,2-ethanediol (ethylene glycol) 65 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 12898 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Matchmaker > matchmaker #!17 to #6 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algekx_minus_ss_model_4.cif, chain A (#6) with AlgE_3RBH.pdb, chain B (#17), sequence alignment score = 2343.2 RMSD between 407 pruned atom pairs is 0.512 angstroms; (across all 429 pairs: 3.730) > save ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" ——— End of log from Thu Dec 18 15:12:06 2025 ——— > view name session-start opened ChimeraX session > hide #!17 models > hide #!16 models > hide #6 models > show #1 models > color #1 bychain > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg844_dimer_g/fold_alg844_dimer_g_model_0.cif"" Chain information for fold_alg844_dimer_g_model_0.cif #18 --- Chain | Description A | . B C | . D | . Computing secondary structure > ui tool show Matchmaker > 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 fold_alg844_model_0.cif, chain A (#1) with fold_alg844_dimer_g_model_0.cif, chain A (#18), sequence alignment score = 2611.5 RMSD between 487 pruned atom pairs is 0.632 angstroms; (across all 494 pairs: 0.691) > color #1,18 bychain > hide #1 models > open ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_alg8_44/fold_alg8_44_model_0.cif"" Chain information for fold_alg8_44_model_0.cif #19 --- Chain | Description A | . B C | . Computing secondary structure > ui tool show Matchmaker > 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 fold_alg844_model_0.cif, chain A (#1) with fold_alg8_44_model_0.cif, chain A (#19), sequence alignment score = 2610.9 RMSD between 494 pruned atom pairs is 0.597 angstroms; (across all 494 pairs: 0.597) > color #18-19 bychain > hide #18 models > show #18 models > color #18 #00fdffff > hide #18 models > show #18 models > hide #18 models > show #1 models > show #18 models > show #6 models > hide #18 models > hide #19 models > hide #1 models > color #6 bychain > coulombic #6 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_algekx_minus_ss_model_4.cif_A SES surface #6.1: minimum, -22.15, mean -5.51, maximum 11.22 Coulombic values for fold_algekx_minus_ss_model_4.cif_B SES surface #6.2: minimum, -19.50, mean -2.49, maximum 10.83 Coulombic values for fold_algekx_minus_ss_model_4.cif_C SES surface #6.3: minimum, -26.63, mean -1.36, maximum 11.86 To also show corresponding color key, enter the above coulombic command and add key true > hide #!6 surfaces > show #!17 models > hide #!6 models > show #!17 surfaces > hide #!17 surfaces > hide #!17 models > show #!16 models > color sel bychain > save ""/Users/lynne/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" ——— End of log from Fri Dec 19 16:32:43 2025 ——— > view name session-start opened ChimeraX session > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x/fold_algg_x_model_0.cif"" Chain information for fold_algg_x_model_0.cif #20 --- Chain | Description A | . B | . Computing secondary structure > ui tool show Matchmaker > matchmaker #20 to #16 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 7ula_XK structure.cif, chain A (#16) with fold_algg_x_model_0.cif, chain B (#20), sequence alignment score = 1387.8 RMSD between 383 pruned atom pairs is 0.757 angstroms; (across all 420 pairs: 3.300) > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algekx_minus_ss/fold_algekx_minus_ss_model_0.cif"" Chain information for fold_algekx_minus_ss_model_0.cif #21 --- Chain | Description A | . B | . C | . Computing secondary structure > ui tool show Matchmaker > matchmaker #21 to #16 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 7ula_XK structure.cif, chain A (#16) with fold_algekx_minus_ss_model_0.cif, chain C (#21), sequence alignment score = 1384.2 RMSD between 385 pruned atom pairs is 0.763 angstroms; (across all 420 pairs: 1.688) > color sel bypolymer [Repeated 1 time(s)] > hide #20 models > hide #!16 models > select add #16 5686 atoms, 5767 bonds, 7 pseudobonds, 784 residues, 4 models selected > select subtract #16 Nothing selected > show #!16 models > color #21#!16 bychain > ui mousemode right translate > select #16/A:104 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 50 atoms, 50 bonds, 6 residues, 1 model selected > select up 1716 atoms, 1761 bonds, 220 residues, 1 model selected > ui tool show ""Color Actions"" > color sel turquoise > color sel dark turquoise > color sel teal > color sel dark cyan > select clear > hide #21 models > show #21 models > hide #!16 models > show #!16 models > select #16/A:242 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 74 atoms, 75 bonds, 9 residues, 1 model selected > select up 1716 atoms, 1761 bonds, 220 residues, 1 model selected > color sel light sea green > align #6/A:59-161@CA toAtoms #14/A:59-161@CA RMSD between 103 atom pairs is 16.130 angstroms > select #16/A:284 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 90 atoms, 92 bonds, 11 residues, 1 model selected > select up 1607 atoms, 1640 bonds, 210 residues, 1 model selected > color sel light sea green > hide #!16 models > select #21/C:197 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 75 atoms, 76 bonds, 10 residues, 1 model selected > select up 3526 atoms, 3613 bonds, 448 residues, 1 model selected > color sel light sea green > select clear > show #!16 models > show #20 models > select clear [Repeated 1 time(s)] > hide #21 models > hide #!16 models > select #20/B:197 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 75 atoms, 76 bonds, 10 residues, 1 model selected > select up 3526 atoms, 3613 bonds, 448 residues, 1 model selected > color sel light sea green > select clear > show #21 models > show #!16 models > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_0.cif"" Chain information for fold_algg_x_44_model_0.cif #22 --- Chain | Description A | . B | . C | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_1.cif"" Chain information for fold_algg_x_44_model_1.cif #23 --- Chain | Description A | . B | . C | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_2.cif"" Chain information for fold_algg_x_44_model_2.cif #24 --- Chain | Description A | . B | . C | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_3.cif"" Chain information for fold_algg_x_44_model_3.cif #25 --- Chain | Description A | . B | . C | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_x_44/fold_algg_x_44_model_4.cif"" Chain information for fold_algg_x_44_model_4.cif #26 --- Chain | Description A | . B | . C | . Computing secondary structure [Repeated 4 time(s)] > ui tool show Matchmaker > matchmaker #22-26 to #20 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algg_x_model_0.cif, chain A (#20) with fold_algg_x_44_model_0.cif, chain A (#22), sequence alignment score = 2572 RMSD between 467 pruned atom pairs is 0.290 angstroms; (across all 508 pairs: 3.356) Matchmaker fold_algg_x_model_0.cif, chain A (#20) with fold_algg_x_44_model_1.cif, chain A (#23), sequence alignment score = 2546.8 RMSD between 447 pruned atom pairs is 0.263 angstroms; (across all 508 pairs: 10.270) Matchmaker fold_algg_x_model_0.cif, chain A (#20) with fold_algg_x_44_model_2.cif, chain A (#24), sequence alignment score = 2564.8 RMSD between 453 pruned atom pairs is 0.225 angstroms; (across all 508 pairs: 3.933) Matchmaker fold_algg_x_model_0.cif, chain A (#20) with fold_algg_x_44_model_3.cif, chain A (#25), sequence alignment score = 2582.8 RMSD between 446 pruned atom pairs is 0.355 angstroms; (across all 508 pairs: 8.046) Matchmaker fold_algg_x_model_0.cif, chain A (#20) with fold_algg_x_44_model_4.cif, chain A (#26), sequence alignment score = 2575.6 RMSD between 454 pruned atom pairs is 0.234 angstroms; (across all 508 pairs: 11.699) > hide #26 models > hide #24 models > show #24 models > hide #24 models > show #24 models > hide #24 models > hide #23 models > show #23 models > hide #21 models > hide #!16 models > hide #20 models > show #20 models > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_44/fold_algg_44_model_0.cif"" Chain information for fold_algg_44_model_0.cif #27 --- Chain | Description A | . B | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_44/fold_algg_44_model_1.cif"" Chain information for fold_algg_44_model_1.cif #28 --- Chain | Description A | . B | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_44/fold_algg_44_model_2.cif"" Chain information for fold_algg_44_model_2.cif #29 --- Chain | Description A | . B | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_44/fold_algg_44_model_3.cif"" Chain information for fold_algg_44_model_3.cif #30 --- Chain | Description A | . B | . > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 > predictions/Alginate/fold_algg_44/fold_algg_44_model_4.cif"" Chain information for fold_algg_44_model_4.cif #31 --- Chain | Description A | . B | . Computing secondary structure [Repeated 4 time(s)] > save ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" > ui tool show Matchmaker > matchmaker #27-31 to #22 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with fold_algg_44_model_0.cif, chain A (#27), sequence alignment score = 2564.8 RMSD between 456 pruned atom pairs is 0.232 angstroms; (across all 508 pairs: 4.454) Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with fold_algg_44_model_1.cif, chain A (#28), sequence alignment score = 2557.6 RMSD between 475 pruned atom pairs is 0.241 angstroms; (across all 508 pairs: 1.783) Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with fold_algg_44_model_2.cif, chain A (#29), sequence alignment score = 2564.8 RMSD between 452 pruned atom pairs is 0.240 angstroms; (across all 508 pairs: 6.558) Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with fold_algg_44_model_3.cif, chain A (#30), sequence alignment score = 2552.8 RMSD between 456 pruned atom pairs is 0.244 angstroms; (across all 508 pairs: 8.914) Matchmaker fold_algg_x_44_model_0.cif, chain A (#22) with fold_algg_44_model_4.cif, chain A (#31), sequence alignment score = 2560 RMSD between 456 pruned atom pairs is 0.187 angstroms; (across all 508 pairs: 3.763) > show #19 models > ui tool show Matchmaker > matchmaker #19 to #22 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algg_x_44_model_0.cif, chain C (#22) with fold_alg8_44_model_0.cif, chain C (#19), sequence alignment score = 1934.8 RMSD between 86 pruned atom pairs is 0.309 angstroms; (across all 389 pairs: 71.368) > hide #19 models > hide #22 models > hide #23 models > hide #25 models > show #25 models > hide #25 models > hide #20 models > color #27-31 bypolymer > hide #31 models > hide #30 models > hide #29 models > hide #28 models > show #22 models > color #22,27 bychain > show #23 models > hide #23 models > show #!16 models > show #19 models > hide #!16 models > hide #22 models > hide #27 models > show #25 models > hide #19 models > color #25 bypolymer > select #25/C:259 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 52 atoms, 51 bonds, 7 residues, 1 model selected > color sel red > hide sel surfaces > show sel surfaces > select clear > select #25/A:252 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 42 atoms, 43 bonds, 5 residues, 1 model selected > select up 3954 atoms, 4037 bonds, 508 residues, 1 model selected > show sel surfaces > hide sel surfaces > select clear > open ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Alphafold 3 predictions/Alginate/4ozy.cif"" 4ozy.cif title: Crystal Structure of the periplasmic alginate epimerase AlgG T265N mutant [more info...] Chain information for 4ozy.cif #32 --- Chain | Description | UniProt A | Poly(beta-D-mannuronate) C5 epimerase | ALGG_PSESM 69-491 4ozy.cif mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly 3261 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Matchmaker > matchmaker #32 to #20 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_algg_x_model_0.cif, chain A (#20) with 4ozy.cif, chain A (#32), sequence alignment score = 1605.6 RMSD between 405 pruned atom pairs is 0.517 angstroms; (across all 423 pairs: 0.920) > save ""/Users/lynnehowell/SickKids Research Dropbox/Howell Lab's shared > workspace/Grants/CIHR 2026 PNAG-alginate/Alginate Section/Alginate > models.cxs"" ——— End of log from Sat Dec 20 13:53:51 2025 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,10 Model Number: MRX83LL/A Chip: Apple M3 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 2 days, 4 hours, 17 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 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sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.13.2 tornado: 6.5.4 tqdm: 4.67.1 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 umap-learn: 0.5.7 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX