id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10217 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00007ff8592aa700 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-11-23 10:30:13.00 +0100"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.6.1 (22G313)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""9B2C6BFD-0565-4C40-93CC-A513BCAC507E""} { ""uptime"" : 330000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Macmini8,1"", ""coalitionID"" : 3797, ""osVersion"" : { ""train"" : ""macOS 13.6.1"", ""build"" : ""22G313"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-11-23 10:29:53.9247 +0100"", ""incident"" : ""9B2C6BFD-0565-4C40-93CC-A513BCAC507E"", ""pid"" : 39678, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-11-21 17:13:24.4665 +0100"", ""procStartAbsTime"" : 250394839595302, ""procExitAbsTime"" : 338236134803316, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""793F310D-059A-5737-977A-EA9554F1DECF"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""7AB8BCDC-6EA7-29DA-5ACB-ECDCDF5A342B"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 54885, ""bridgeVersion"" : {""build"":""21P1069"",""train"":""8.1""}, ""sleepWakeUUID"" : ""B30CC306-E34D-4DC0-9A19-DA6CE277B273"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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Screening"" UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1989.t1.pdb > format pdb Chain information for g1989.t1.pdb #1 --- Chain | Description A | No description available > set bgColor white > open 2aai Summary of feedback from opening 2aai fetched from pdb --- note | Fetching compressed mmCIF 2aai from http://files.rcsb.org/download/2aai.cif 2aai title: Crystallographic refinement of ricin to 2.5 Angstroms [more info...] Chain information for 2aai #2 --- Chain | Description | UniProt A | RICIN (A CHAIN) | RICI_RICCO 1-267 B | RICIN (B CHAIN) | RICI_RICCO 1-262 Non-standard residues in 2aai #2 --- BGC — beta-D-glucopyranose BMA — beta-D-mannopyranose GAL — beta-D-galactopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > mmaker #1 to #2 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 2aai, chain B (#2) with g1989.t1.pdb, chain A (#1), sequence alignment score = 45.4 RMSD between 5 pruned atom pairs is 1.250 angstroms; (across all 89 pairs: 20.196) > view clip false > mmaker #1 to #2/B 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 2aai, chain B (#2) with g1989.t1.pdb, chain A (#1), sequence alignment score = 45.4 RMSD between 5 pruned atom pairs is 1.250 angstroms; (across all 89 pairs: 20.196) > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UDY9.pdb Chain information for A0A0B2UDY9.pdb #1 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UJ21.pdb Chain information for A0A0B2UJ21.pdb #2 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UJ51.pdb Chain information for A0A0B2UJ51.pdb #3 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0B2UKB5.pdb Chain information for A0A0B2UKB5.pdb #4 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WA85.pdb Chain information for A0A0F9WA85.pdb #5 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WE74.pdb Chain information for A0A0F9WE74.pdb #6 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WET1.pdb Chain information for A0A0F9WET1.pdb #7 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WET7.pdb Chain information for A0A0F9WET7.pdb #8 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WGX6.pdb Chain information for A0A0F9WGX6.pdb #9 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WN65.pdb Chain information for A0A0F9WN65.pdb #10 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WPM0.pdb Chain information for A0A0F9WPM0.pdb #11 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WSN9.pdb Chain information for A0A0F9WSN9.pdb #12 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9WSP8.pdb Chain information for A0A0F9WSP8.pdb #13 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YP43.pdb Chain information for A0A0F9YP43.pdb #14 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YP48.pdb Chain information for A0A0F9YP48.pdb #15 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YTP2.pdb Chain information for A0A0F9YTP2.pdb #16 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9YTP9.pdb Chain information for A0A0F9YTP9.pdb #17 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9Z9D8.pdb Chain information for A0A0F9Z9D8.pdb #18 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/A0A0F9ZEM9.pdb Chain information for A0A0F9ZEM9.pdb #19 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g264.t1.pdb Chain information for g264.t1.pdb #20 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g375.t1.pdb Chain information for g375.t1.pdb #21 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g724.t1.pdb Chain information for g724.t1.pdb #22 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g732.t1.pdb Chain information for g732.t1.pdb #23 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g883.t1.pdb Chain information for g883.t1.pdb #24 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g884.t1.pdb Chain information for g884.t1.pdb #25 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g886.t1.pdb Chain information for g886.t1.pdb #26 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g888.t1.pdb Chain information for g888.t1.pdb #27 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g957.t1.pdb Chain information for g957.t1.pdb #28 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g958.t1.pdb Chain information for g958.t1.pdb #29 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g972.t1.pdb Chain information for g972.t1.pdb #30 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g973.t1.pdb Chain information for g973.t1.pdb #31 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g977.t1.pdb Chain information for g977.t1.pdb #32 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g978.t1.pdb Chain information for g978.t1.pdb #33 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1726.t1.pdb Chain information for g1726.t1.pdb #34 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1727.t1.pdb Chain information for g1727.t1.pdb #35 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1987.t1.pdb Chain information for g1987.t1.pdb #36 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1988.t1.pdb Chain information for g1988.t1.pdb #37 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1989.t1.pdb Chain information for g1989.t1.pdb #38 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1991.t1.pdb Chain information for g1991.t1.pdb #39 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g1992.t1.pdb Chain information for g1992.t1.pdb #40 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/g3022.t1.pdb Chain information for g3022.t1.pdb #41 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TKU6.pdb Chain information for I6TKU6.pdb #42 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TV97.pdb Chain information for I6TV97.pdb #43 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6TWE0.pdb Chain information for I6TWE0.pdb #44 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UDH1.pdb Chain information for I6UDH1.pdb #45 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UDI1.pdb Chain information for I6UDI1.pdb #46 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UMG3.pdb Chain information for I6UMG3.pdb #47 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UMG6.pdb Chain information for I6UMG6.pdb #48 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UN97.pdb Chain information for I6UN97.pdb #49 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UQG3.pdb Chain information for I6UQG3.pdb #50 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6UQK2.pdb Chain information for I6UQK2.pdb #51 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZK24.pdb Chain information for I6ZK24.pdb #52 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZUI2.pdb Chain information for I6ZUI2.pdb #53 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZUJ1.pdb Chain information for I6ZUJ1.pdb #54 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I6ZV11.pdb Chain information for I6ZV11.pdb #55 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AF84.pdb Chain information for I7AF84.pdb #56 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AF87.pdb Chain information for I7AF87.pdb #57 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7ANB6.pdb Chain information for I7ANB6.pdb #58 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AP33.pdb Chain information for I7AP33.pdb #59 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/I7AT09.pdb Chain information for I7AT09.pdb #60 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUI3.pdb Chain information for Q8SUI3.pdb #61 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUI4.pdb Chain information for Q8SUI4.pdb #62 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK1.pdb Chain information for Q8SUK1.pdb #63 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK2.pdb Chain information for Q8SUK2.pdb #64 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK3.pdb Chain information for Q8SUK3.pdb #65 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUK4.pdb Chain information for Q8SUK4.pdb #66 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUL9.pdb Chain information for Q8SUL9.pdb #67 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUY7.pdb Chain information for Q8SUY7.pdb #68 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUY8.pdb Chain information for Q8SUY8.pdb #69 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUZ1.pdb Chain information for Q8SUZ1.pdb #70 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SUZ3.pdb Chain information for Q8SUZ3.pdb #71 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/0_RBLs/rbls_viz/pdbs/Q8SV68.pdb Chain information for Q8SV68.pdb #72 --- Chain | Description A | No description available > mmaker #2-72 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 A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 90.8 RMSD between 67 pruned atom pairs is 1.016 angstroms; (across all 207 pairs: 31.340) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UJ51.pdb, chain A (#3), sequence alignment score = 126.7 RMSD between 48 pruned atom pairs is 1.178 angstroms; (across all 203 pairs: 19.794) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0B2UKB5.pdb, chain A (#4), sequence alignment score = 48.9 RMSD between 8 pruned atom pairs is 1.368 angstroms; (across all 201 pairs: 50.983) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 94.1 RMSD between 71 pruned atom pairs is 0.906 angstroms; (across all 210 pairs: 42.489) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WE74.pdb, chain A (#6), sequence alignment score = 149.7 RMSD between 77 pruned atom pairs is 1.121 angstroms; (across all 220 pairs: 12.557) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WET1.pdb, chain A (#7), sequence alignment score = 48.7 RMSD between 46 pruned atom pairs is 0.810 angstroms; (across all 126 pairs: 9.350) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WET7.pdb, chain A (#8), sequence alignment score = 58.6 RMSD between 47 pruned atom pairs is 0.913 angstroms; (across all 140 pairs: 16.056) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WGX6.pdb, chain A (#9), sequence alignment score = 103.7 RMSD between 65 pruned atom pairs is 1.078 angstroms; (across all 198 pairs: 32.837) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WN65.pdb, chain A (#10), sequence alignment score = 137.6 RMSD between 74 pruned atom pairs is 1.023 angstroms; (across all 191 pairs: 22.979) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WPM0.pdb, chain A (#11), sequence alignment score = 83.3 RMSD between 53 pruned atom pairs is 0.882 angstroms; (across all 114 pairs: 12.979) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WSN9.pdb, chain A (#12), sequence alignment score = 68.4 RMSD between 35 pruned atom pairs is 0.802 angstroms; (across all 127 pairs: 13.986) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9WSP8.pdb, chain A (#13), sequence alignment score = 56.4 RMSD between 7 pruned atom pairs is 1.020 angstroms; (across all 159 pairs: 18.708) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YP43.pdb, chain A (#14), sequence alignment score = 103 RMSD between 51 pruned atom pairs is 1.097 angstroms; (across all 173 pairs: 12.062) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YP48.pdb, chain A (#15), sequence alignment score = 91.6 RMSD between 54 pruned atom pairs is 1.089 angstroms; (across all 211 pairs: 19.286) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YTP2.pdb, chain A (#16), sequence alignment score = 100.2 RMSD between 57 pruned atom pairs is 0.810 angstroms; (across all 189 pairs: 28.912) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9YTP9.pdb, chain A (#17), sequence alignment score = 70.1 RMSD between 53 pruned atom pairs is 0.906 angstroms; (across all 130 pairs: 11.673) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9Z9D8.pdb, chain A (#18), sequence alignment score = 101.8 RMSD between 51 pruned atom pairs is 0.916 angstroms; (across all 193 pairs: 21.080) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with A0A0F9ZEM9.pdb, chain A (#19), sequence alignment score = 58.3 RMSD between 42 pruned atom pairs is 0.873 angstroms; (across all 160 pairs: 17.834) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g264.t1.pdb, chain A (#20), sequence alignment score = 100.5 RMSD between 38 pruned atom pairs is 0.861 angstroms; (across all 156 pairs: 16.781) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g375.t1.pdb, chain A (#21), sequence alignment score = 112.4 RMSD between 56 pruned atom pairs is 0.962 angstroms; (across all 153 pairs: 11.797) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g724.t1.pdb, chain A (#22), sequence alignment score = 88.8 RMSD between 47 pruned atom pairs is 0.876 angstroms; (across all 205 pairs: 27.354) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g732.t1.pdb, chain A (#23), sequence alignment score = 67.1 RMSD between 56 pruned atom pairs is 1.042 angstroms; (across all 154 pairs: 17.782) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g883.t1.pdb, chain A (#24), sequence alignment score = 130.9 RMSD between 77 pruned atom pairs is 1.133 angstroms; (across all 183 pairs: 23.062) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g884.t1.pdb, chain A (#25), sequence alignment score = 77 RMSD between 75 pruned atom pairs is 1.058 angstroms; (across all 222 pairs: 21.871) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g886.t1.pdb, chain A (#26), sequence alignment score = 146 RMSD between 44 pruned atom pairs is 1.045 angstroms; (across all 177 pairs: 21.492) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g888.t1.pdb, chain A (#27), sequence alignment score = 102.3 RMSD between 72 pruned atom pairs is 1.072 angstroms; (across all 181 pairs: 12.238) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g957.t1.pdb, chain A (#28), sequence alignment score = 86 RMSD between 57 pruned atom pairs is 1.053 angstroms; (across all 136 pairs: 6.143) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g958.t1.pdb, chain A (#29), sequence alignment score = 94.5 RMSD between 20 pruned atom pairs is 0.884 angstroms; (across all 199 pairs: 24.531) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g972.t1.pdb, chain A (#30), sequence alignment score = 108.2 RMSD between 59 pruned atom pairs is 1.020 angstroms; (across all 133 pairs: 8.026) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g973.t1.pdb, chain A (#31), sequence alignment score = 59.3 RMSD between 35 pruned atom pairs is 0.965 angstroms; (across all 206 pairs: 22.940) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g977.t1.pdb, chain A (#32), sequence alignment score = 76.6 RMSD between 38 pruned atom pairs is 0.790 angstroms; (across all 101 pairs: 11.360) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g978.t1.pdb, chain A (#33), sequence alignment score = 74.3 RMSD between 46 pruned atom pairs is 0.937 angstroms; (across all 148 pairs: 11.865) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1726.t1.pdb, chain A (#34), sequence alignment score = 185.5 RMSD between 84 pruned atom pairs is 0.981 angstroms; (across all 215 pairs: 13.460) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1727.t1.pdb, chain A (#35), sequence alignment score = 133.9 RMSD between 47 pruned atom pairs is 0.917 angstroms; (across all 153 pairs: 14.894) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1987.t1.pdb, chain A (#36), sequence alignment score = 101.7 RMSD between 48 pruned atom pairs is 0.862 angstroms; (across all 155 pairs: 21.929) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1988.t1.pdb, chain A (#37), sequence alignment score = 83.6 RMSD between 46 pruned atom pairs is 1.014 angstroms; (across all 184 pairs: 17.148) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1989.t1.pdb, chain A (#38), sequence alignment score = 87.9 RMSD between 49 pruned atom pairs is 0.880 angstroms; (across all 147 pairs: 15.561) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1991.t1.pdb, chain A (#39), sequence alignment score = 131.8 RMSD between 72 pruned atom pairs is 0.912 angstroms; (across all 168 pairs: 24.547) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g1992.t1.pdb, chain A (#40), sequence alignment score = 112.5 RMSD between 45 pruned atom pairs is 0.929 angstroms; (across all 194 pairs: 26.572) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with g3022.t1.pdb, chain A (#41), sequence alignment score = 75.8 RMSD between 56 pruned atom pairs is 1.098 angstroms; (across all 142 pairs: 13.511) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TKU6.pdb, chain A (#42), sequence alignment score = 100 RMSD between 55 pruned atom pairs is 0.902 angstroms; (across all 208 pairs: 24.414) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TV97.pdb, chain A (#43), sequence alignment score = 43.8 RMSD between 29 pruned atom pairs is 0.853 angstroms; (across all 182 pairs: 48.501) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6TWE0.pdb, chain A (#44), sequence alignment score = 427.6 RMSD between 100 pruned atom pairs is 0.825 angstroms; (across all 254 pairs: 11.405) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UDH1.pdb, chain A (#45), sequence alignment score = 65.5 RMSD between 47 pruned atom pairs is 1.141 angstroms; (across all 166 pairs: 15.530) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UDI1.pdb, chain A (#46), sequence alignment score = 140.6 RMSD between 72 pruned atom pairs is 1.031 angstroms; (across all 181 pairs: 25.019) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UMG3.pdb, chain A (#47), sequence alignment score = 74.4 RMSD between 43 pruned atom pairs is 1.009 angstroms; (across all 193 pairs: 26.517) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UMG6.pdb, chain A (#48), sequence alignment score = 89.3 RMSD between 76 pruned atom pairs is 1.022 angstroms; (across all 207 pairs: 28.399) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UN97.pdb, chain A (#49), sequence alignment score = 68 RMSD between 55 pruned atom pairs is 0.898 angstroms; (across all 187 pairs: 27.666) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UQG3.pdb, chain A (#50), sequence alignment score = 113.6 RMSD between 65 pruned atom pairs is 0.807 angstroms; (across all 206 pairs: 35.493) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6UQK2.pdb, chain A (#51), sequence alignment score = 178.8 RMSD between 100 pruned atom pairs is 0.880 angstroms; (across all 146 pairs: 3.407) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZK24.pdb, chain A (#52), sequence alignment score = 443.9 RMSD between 106 pruned atom pairs is 0.880 angstroms; (across all 257 pairs: 11.250) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZUI2.pdb, chain A (#53), sequence alignment score = 76.5 RMSD between 47 pruned atom pairs is 1.075 angstroms; (across all 172 pairs: 14.626) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZUJ1.pdb, chain A (#54), sequence alignment score = 158.5 RMSD between 61 pruned atom pairs is 0.950 angstroms; (across all 208 pairs: 32.357) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I6ZV11.pdb, chain A (#55), sequence alignment score = 108.2 RMSD between 49 pruned atom pairs is 0.920 angstroms; (across all 210 pairs: 28.657) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AF84.pdb, chain A (#56), sequence alignment score = 82.1 RMSD between 35 pruned atom pairs is 1.013 angstroms; (across all 209 pairs: 30.878) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AF87.pdb, chain A (#57), sequence alignment score = 118.9 RMSD between 73 pruned atom pairs is 1.079 angstroms; (across all 218 pairs: 31.578) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7ANB6.pdb, chain A (#58), sequence alignment score = 37.2 RMSD between 5 pruned atom pairs is 1.196 angstroms; (across all 171 pairs: 35.417) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AP33.pdb, chain A (#59), sequence alignment score = 89.5 RMSD between 60 pruned atom pairs is 0.905 angstroms; (across all 199 pairs: 43.691) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with I7AT09.pdb, chain A (#60), sequence alignment score = 73.6 RMSD between 51 pruned atom pairs is 0.864 angstroms; (across all 182 pairs: 31.243) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUI3.pdb, chain A (#61), sequence alignment score = 131.3 RMSD between 108 pruned atom pairs is 0.872 angstroms; (across all 144 pairs: 3.728) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUI4.pdb, chain A (#62), sequence alignment score = 450.6 RMSD between 121 pruned atom pairs is 0.841 angstroms; (across all 259 pairs: 15.316) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK1.pdb, chain A (#63), sequence alignment score = 98.6 RMSD between 51 pruned atom pairs is 0.862 angstroms; (across all 193 pairs: 22.742) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK2.pdb, chain A (#64), sequence alignment score = 85.1 RMSD between 47 pruned atom pairs is 0.899 angstroms; (across all 196 pairs: 29.044) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK3.pdb, chain A (#65), sequence alignment score = 97.7 RMSD between 46 pruned atom pairs is 0.844 angstroms; (across all 214 pairs: 32.127) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUK4.pdb, chain A (#66), sequence alignment score = 98.9 RMSD between 47 pruned atom pairs is 0.865 angstroms; (across all 212 pairs: 31.768) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUL9.pdb, chain A (#67), sequence alignment score = 116.9 RMSD between 4 pruned atom pairs is 0.926 angstroms; (across all 230 pairs: 30.068) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUY7.pdb, chain A (#68), sequence alignment score = 148.1 RMSD between 63 pruned atom pairs is 0.960 angstroms; (across all 233 pairs: 40.480) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUY8.pdb, chain A (#69), sequence alignment score = 97.7 RMSD between 70 pruned atom pairs is 1.023 angstroms; (across all 215 pairs: 33.292) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUZ1.pdb, chain A (#70), sequence alignment score = 33.7 RMSD between 11 pruned atom pairs is 1.434 angstroms; (across all 206 pairs: 24.633) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SUZ3.pdb, chain A (#71), sequence alignment score = 72.8 RMSD between 50 pruned atom pairs is 1.107 angstroms; (across all 164 pairs: 12.803) Matchmaker A0A0B2UDY9.pdb, chain A (#1) with Q8SV68.pdb, chain A (#72), sequence alignment score = 34 RMSD between 9 pruned atom pairs is 1.166 angstroms; (across all 177 pairs: 43.917) > color lightgrey > color &helix orchid Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1-72 &helix orchid > color #1-72 &strand gold > tile columns 7 spacingFactor 1 72 models tiled > color #1-72:cys orange > color #1-72:glu green > color #1-72:trp blue > color #1-72:phe darkblue > hide #72 models > hide #71 models > hide #70 models > hide #69 models > hide #67 models > hide #68 models > hide #66 models > hide #65 models > hide #63 models > hide #64 models > hide #62 models > hide #61 models > hide #60 models > hide #59 models > hide #58 models > hide #57 models > hide #56 models > hide #55 models > hide #54 models > hide #53 models > hide #52 models > hide #51 models > hide #50 models > hide #48 models > hide #49 models > hide #47 models > hide #46 models > hide #45 models > hide #44 models > hide #43 models > hide #42 models > hide #41 models > hide #40 models > hide #39 models > hide #38 models > hide #37 models > hide #36 models > hide #35 models > hide #34 models > hide #33 models > hide #32 models > hide #31 models > hide #30 models > hide #29 models > hide #28 models > hide #27 models > hide #26 models > hide #25 models > hide #24 models > hide #23 models > hide #22 models > hide #21 models > hide #20 models > hide #19 models > hide #18 models > hide #17 models > hide #16 models > hide #15 models > hide #14 models > hide #13 models > hide #12 models > hide #11 models > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > show #2 models > show #22 models > show #67 models > show #59 models > show #50 models > show #5 models > view #50 clip false > tile #2,5,22,50,59 columns 5 spacingFactor 1 5 models tiled > tile #2,5,22,50,59,67 columns 5 spacingFactor 1 6 models tiled > tile #2,5,22,50,59,67 columns 3 spacingFactor 1 6 models tiled > hide atoms > show cartoons > set bgColor white > graphics silhouettes true > set silhouetteWidth 2 > cartoon style width 2 thickness 1 > cartoon style modeHelix wrap > color #2 #db7a57ff > color #5 #dadb24ff > color #22 #7cdb50ff > color #50 #3ec7dbff > color #59 #db3ecfff > color #59 #db52c6ff > color #67 #c8db9eff > color #67 #d1dbceff > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > hide #59 models > hide #67 models > hide #50 models > hide #22 models > hide #5 models > hide #2:159-404 cartoons > hide #2 models > show #2 models > show #5 models > hide #5:143-483 cartoons > show #22 models > hide #22:143-474 cartoons > show #50 models > hide #50:143-368 cartoons > show #59 models > hide #59:147-379 cartoons > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) > mmaker #2,5,22,50,59 to #67 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 Q8SUL9.pdb, chain A (#67) with A0A0B2UJ21.pdb, chain A (#2), sequence alignment score = 542.7 RMSD between 98 pruned atom pairs is 0.849 angstroms; (across all 338 pairs: 44.250) Matchmaker Q8SUL9.pdb, chain A (#67) with A0A0F9WA85.pdb, chain A (#5), sequence alignment score = 505.1 RMSD between 123 pruned atom pairs is 0.774 angstroms; (across all 365 pairs: 41.997) Matchmaker Q8SUL9.pdb, chain A (#67) with g724.t1.pdb, chain A (#22), sequence alignment score = 467.9 RMSD between 126 pruned atom pairs is 0.827 angstroms; (across all 360 pairs: 40.245) Matchmaker Q8SUL9.pdb, chain A (#67) with I6UQG3.pdb, chain A (#50), sequence alignment score = 1024.4 RMSD between 141 pruned atom pairs is 0.717 angstroms; (across all 355 pairs: 32.941) Matchmaker Q8SUL9.pdb, chain A (#67) with I7AP33.pdb, chain A (#59), sequence alignment score = 1087.1 RMSD between 138 pruned atom pairs is 0.758 angstroms; (across all 365 pairs: 37.256) Drag select of 730 residues > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.33671,0.6339,-0.69627,458.61,0.59846,-0.71495,-0.36151,-161.78,-0.72696,-0.29497,-0.62009,-3.8328,#5,0.3239,0.23139,-0.91736,458.3,0.93637,0.060267,0.34581,-161.63,0.1353,-0.97099,-0.19715,-4.6652,#22,-0.55891,0.19842,0.80514,457.1,0.82359,0.019728,0.56685,-162.48,0.096591,0.97992,-0.17444,-2.4225,#50,0.61026,-0.63985,-0.46709,458.33,-0.2272,0.42348,-0.87695,-160.57,0.75892,0.64129,0.11306,-3.2024,#59,0.83419,-0.54951,-0.04659,457.38,-0.25198,-0.30464,-0.91853,-161.5,0.49055,0.77797,-0.39259,-3.8979 > view matrix models > #2,0.36052,0.060407,-0.93079,462.36,0.81886,-0.49835,0.28482,-163.69,-0.44666,-0.86487,-0.22913,-0.36275,#5,0.77852,-0.071062,-0.62359,461.94,0.53428,0.59638,0.59906,-162.99,0.32932,-0.79955,0.50226,-0.73435,#22,-0.003503,0.46163,0.88707,461.2,0.68518,-0.64501,0.33837,-164.73,0.72836,0.60899,-0.31404,1.167,#50,0.6029,-0.11063,-0.79011,462.94,-0.78869,0.066679,-0.61116,-163.12,0.1203,0.99162,-0.047054,0.76895,#59,0.69139,-0.36768,-0.62193,461.49,-0.69281,-0.58155,-0.42639,-163.14,-0.20491,0.72568,-0.65681,0.37945 > view matrix models > #2,0.40313,0.91365,-0.052317,455.61,0.76734,-0.30632,0.56335,-165.3,0.49868,-0.26725,-0.82456,-4.3451,#5,-0.19641,0.66491,-0.72064,455.76,0.2276,0.7458,0.62609,-164.45,0.95374,-0.041044,-0.29781,-4.5957,#22,-0.79483,-0.37815,0.4746,454,0.4953,-0.85613,0.14736,-166.29,0.3506,0.3522,0.86778,-5.4443,#50,0.14548,-0.98714,-0.066192,454.59,-0.92791,-0.11293,-0.35529,-165.15,0.34325,0.11311,-0.93241,-3.4044,#59,0.46574,-0.70554,0.53414,454.6,-0.79392,-0.59975,-0.099954,-164.71,0.39087,-0.37751,-0.83947,-4.8438 > view matrix models > #2,0.089554,0.96993,-0.22633,455.37,-0.60291,0.23367,0.76282,-171.24,0.79277,0.06814,0.6057,-5.7962,#5,-0.29111,0.35682,-0.88766,455.22,-0.95634,-0.083386,0.28011,-171.09,0.025933,0.93044,0.36552,-4.9226,#22,-0.92853,-0.058384,0.36665,454.25,-0.34435,-0.2337,-0.90929,-169.93,0.13877,-0.97055,0.1969,-7.1433,#50,0.45654,-0.88507,0.090657,454.34,-0.2537,-0.031841,0.96676,-172.11,-0.85276,-0.46437,-0.23908,-6.1269,#59,0.70668,-0.43506,0.55797,454.24,-0.3372,0.4862,0.80617,-170.73,-0.62202,-0.75785,0.19689,-5.5363 > view matrix models > #2,-0.16239,-0.39,0.90638,467.64,-0.89996,0.43519,0.026014,-174.4,-0.40459,-0.81149,-0.42166,-3.1384,#5,-0.48342,0.09472,0.87025,468.18,-0.75016,-0.55721,-0.35606,-174.93,0.45118,-0.82495,0.34042,-3.6185,#22,0.36943,-0.51035,-0.77657,468.69,-0.63303,0.47358,-0.61237,-173.01,0.68029,0.71782,-0.14812,-1.821,#50,-0.78584,0.32419,0.52664,467.51,0.55442,-0.0079688,0.8322,-175.11,0.27398,0.94596,-0.17347,-1.9425,#59,-0.90287,0.30125,0.30673,468.77,0.42877,0.68317,0.59113,-174.62,-0.031466,0.66523,-0.74598,-2.6098 > view matrix models > #2,-0.29885,-0.76485,0.5707,470.27,-0.87257,0.46115,0.16111,-174.41,-0.3864,-0.44983,-0.8052,-7.7682,#5,-0.15491,-0.30407,0.93997,470.53,-0.83513,-0.46799,-0.28902,-174.84,0.52778,-0.82977,-0.18144,-8.5171,#22,0.69105,-0.10464,-0.71519,471.77,-0.64758,0.3499,-0.67691,-173.04,0.32108,0.93093,0.17403,-6.9688,#50,-0.56899,0.75438,0.32735,470.8,0.43978,-0.057221,0.89628,-175.23,0.69487,0.65394,-0.29921,-6.77,#59,-0.81696,0.56003,-0.13764,471.53,0.32996,0.64966,0.68488,-174.55,0.47298,0.5141,-0.71554,-7.899 > view matrix models > #2,-0.32498,-0.93153,-0.16321,471.18,-0.55181,0.046618,0.83267,-169.51,-0.76804,0.36067,-0.52918,-15.238,#5,0.3897,-0.69816,0.60058,470.92,-0.87813,-0.085166,0.47079,-169.27,-0.27754,-0.71086,-0.64626,-16.068,#22,0.82374,0.49407,-0.27812,472.55,-0.14843,-0.2855,-0.94682,-168.11,-0.5472,0.82121,-0.16184,-14.28,#50,-0.013679,0.99242,-0.12217,472.37,-0.39602,0.10681,0.91201,-170.19,0.91814,0.060856,0.39155,-15.479,#59,-0.32242,0.63685,-0.70034,472.01,-0.50976,0.50659,0.69535,-168.78,0.79761,0.5812,0.16131,-15.856 > view matrix models > #2,0.30013,0.93022,0.21123,457.83,0.1036,-0.25192,0.96219,-167.05,0.94826,-0.2669,-0.17198,-10.966,#5,-0.43434,0.6974,-0.57006,458.1,-0.43728,0.39004,0.81034,-166.32,0.78748,0.60125,0.13555,-10.509,#22,-0.82678,-0.51424,0.22803,456.52,0.29939,-0.74543,-0.59556,-166.62,0.47624,-0.42413,0.77026,-12.661,#50,-0.01382,-0.98565,0.16824,456.6,-0.91456,0.080481,0.39637,-167.33,-0.40422,-0.14839,-0.90254,-10.362,#59,0.28918,-0.6127,0.73551,457.04,-0.92951,0.0039759,0.36877,-166.06,-0.22887,-0.79031,-0.56836,-11.033 > view matrix models > #2,-0.010133,0.95541,0.29512,457.02,-0.88037,-0.14848,0.45045,-167.63,0.47418,-0.25525,0.84262,-11.255,#5,-0.67858,0.48802,-0.54897,457.16,-0.71977,-0.59086,0.36444,-167.83,-0.1465,0.64244,0.7522,-10.391,#22,-0.92136,-0.38524,-0.05188,456.33,-0.047966,0.24512,-0.96831,-165.58,0.38575,-0.88967,-0.24432,-11.594,#50,0.075755,-0.88423,0.46086,455.65,0.0098158,0.46283,0.88639,-167.88,-0.99708,-0.062625,0.043741,-11.395,#59,0.30708,-0.33146,0.8921,456.33,-0.24196,0.87939,0.41003,-166.95,-0.92041,-0.34177,0.18985,-10.43 > view matrix models > #2,-0.25218,-0.038667,0.96691,465.34,-0.9406,0.24453,-0.23554,-171.96,-0.22733,-0.96887,-0.098035,-5.6535,#5,-0.751,0.1835,0.63429,465.85,-0.5078,-0.77453,-0.37716,-172.69,0.42206,-0.60534,0.67485,-5.8015,#22,0.0089213,-0.56134,-0.82754,466.29,-0.46556,0.73007,-0.50024,-170.44,0.88497,0.38973,-0.25482,-4.4049,#50,-0.67744,0.040928,0.73443,464.73,0.72471,0.20808,0.65688,-172.28,-0.12593,0.97726,-0.17062,-4.439,#59,-0.73234,0.25915,0.6297,466.2,0.53805,0.78701,0.30185,-172.2,-0.41736,0.55986,-0.7158,-4.7498 > view matrix models > #2,0.51673,0.8313,0.20478,455.88,-0.52399,0.49623,-0.69224,-173.65,-0.67707,0.2504,0.69201,-14.101,#5,-0.25661,0.8337,-0.48897,456.28,-0.10085,-0.52625,-0.84433,-174.45,-0.96124,-0.16735,0.21911,-14.044,#22,-0.68008,-0.62911,0.37644,454.23,-0.62683,0.76526,0.14648,-173.35,-0.38023,-0.13635,-0.91479,-12.695,#50,-0.14521,-0.98893,-0.030422,454.81,0.9772,-0.14817,0.15207,-173.91,-0.15489,-0.0076464,0.9879,-14.968,#59,0.18942,-0.77921,0.59745,455.13,0.94828,0.30303,0.094567,-174.57,-0.25473,0.54863,0.79631,-13.656 > view matrix models > #2,-0.43048,-0.10712,-0.89622,462.48,0.65711,0.64352,-0.39254,-172.99,0.61878,-0.7579,-0.20663,-7.482,#5,0.38884,-0.77041,-0.50524,461.63,0.30523,0.62516,-0.71834,-172.91,0.86927,0.12511,0.47824,-7.2167,#22,-0.025112,0.96661,0.25503,463.03,-0.48355,-0.23503,0.84318,-175.01,0.87496,-0.10215,0.4733,-8.1194,#50,0.90168,0.37479,-0.21562,463.11,0.21184,-0.81764,-0.53534,-173.42,-0.37694,0.43703,-0.81665,-6.31,#59,0.7486,0.43091,-0.5039,461.96,0.5259,-0.84874,0.055491,-174.06,-0.40377,-0.30654,-0.86198,-7.0371 > view matrix models > #2,-0.0076623,-0.94501,0.32694,466.61,-0.62505,0.25973,0.73611,-172.8,-0.78055,-0.19871,-0.59267,-14.116,#5,0.26013,-0.23779,0.93584,466.88,-0.96481,-0.10257,0.24212,-172.68,0.038418,-0.96589,-0.2561,-14.966,#22,0.9267,-0.073688,-0.36852,467.59,-0.37571,-0.20418,-0.90396,-171.48,-0.0086324,0.97616,-0.2169,-12.673,#50,-0.56976,0.81706,-0.088269,467.56,-0.21281,-0.042943,0.97615,-173.7,0.79378,0.57495,0.19835,-13.631,#59,-0.79105,0.35074,-0.50122,467.79,-0.29626,0.4972,0.81549,-172.34,0.53523,0.79359,-0.2894,-14.242 > show #4 models > hide #5 models > hide #2 models > hide #22 models > hide #50 models > hide #59 models > view #50 clip false > select add #4 10196 atoms, 4250 bonds, 1247 residues, 6 models selected > view #50 clip false > select subtract #4 6023 atoms, 730 residues, 5 models selected > color bfactor range 50,90 palette ^rainbow 146029 atoms, 18064 residues, atom bfactor range 18.4 to 98.9 > close #4 > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/7plo_c.pdb Summary of feedback from opening /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/7plo_c.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLU Q 284 SER Q 300 1 17 Start residue of secondary structure not found: HELIX 2 2 THR Q 313 LYS Q 319 1 7 Start residue of secondary structure not found: HELIX 3 3 ARG Q 526 ALA Q 539 1 14 Start residue of secondary structure not found: HELIX 4 4 LYS Q 593 ALA Q 618 1 26 Start residue of secondary structure not found: HELIX 5 5 SER 2 181 SER 2 187 1 7 678 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (2158 ) Cannot find LINK/SSBOND residue CYS (2158 ) Cannot find LINK/SSBOND residue CYS (2161 ) Cannot find LINK/SSBOND residue CYS (2161 ) Cannot find LINK/SSBOND residue CYS (2187 ) 36 messages similar to the above omitted Chain information for 7plo_c.pdb #1 --- Chain | Description C | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/VNE6912_196/VNE69_12196.pdb Chain information for VNE69_12196.pdb #2 --- Chain | Description A | No description available > hide pbonds > set bgColor white > graphics silhouettes true > set silhouetteWidth 5 > cartoon style width 3 thickness 1.5 > cartoon style modeHelix wrap > color #1 lightgrey transparency 0 > color #1 & strand orchid transparency 0 > color #1 & helix medium violet red transparency 0 > color #2 lightgrey transparency 0 > color #2 & strand gold transparency 0 > color #2 & helix goldenrod transparency 0 > tile columns 2 spacingFactor 1 2 models tiled > lighting flat > tile columns 2 spacingFactor 1.5 2 models tiled > tile columns 2 spacingFactor 1 2 models tiled > lighting flat > mmaker #1 to #2 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 VNE69_12196.pdb, chain A (#2) with 7plo_c.pdb, chain C (#1), sequence alignment score = 274.1 RMSD between 100 pruned atom pairs is 1.209 angstroms; (across all 391 pairs: 12.197) > tile columns 2 spacingFactor 1 2 models tiled > lighting flat > view matrix view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64 view matrix models #1,0.60041,-0.69448,-0.39649,413.82,-0.17325,0.37106,-0.9123,378.8,0.7807,0.61645,0.10247,-142.24,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.95287,-0.022244,0.30258,430.73,0.2613,0.44661,0.85572,221.82,-0.15417,0.89445,-0.41975,216.43 > view matrix view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64 view matrix models #1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46 > view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64 > save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo- > c_view01.png width 3000 height 3000 transparentBackground true > view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64 > save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo- > c_view02.png width 3000 height 3000 transparentBackground true > view matrix camera 1,0,0,387.58,0,1,0,216.74,0,0,1,636.64 > view matrix models > #1,0.60041,-0.69448,-0.39649,413.82,-0.17325,0.37106,-0.9123,378.8,0.7807,0.61645,0.10247,-142.24,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.95287,-0.022244,0.30258,430.73,0.2613,0.44661,0.85572,221.82,-0.15417,0.89445,-0.41975,216.43 > save /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/Fig4C/12_196_7plo- > c_view01.png width 3000 height 3000 transparentBackground true > view matrix models > #1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Could not find tool ""Structural Screening"" UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/alexandra/Desktop/Projects/Vn_Genome/ColabFold_&_proteinFASTA/AF_models/v_necatrix_alphafold/VNE6909_017.pdb Chain information for VNE6909_017.pdb #1 --- Chain | Description A | No description available > color bfactor range 50,90 palette ^rainbow 3781 atoms, 460 residues, atom bfactor range 18.8 to 59.8 > set bgColor white > open > /Users/alexandra/Desktop/Projects/Vn_Genome/ColabFold_&_proteinFASTA/AF_models/v_necatrix_alphafold/VNE6903_368.pdb Chain information for VNE6903_368.pdb #2 --- Chain | Description A | No description available > view matrix models > #1,-0.53403,0.74583,0.39819,234.45,-0.13931,0.38691,-0.91153,366.47,-0.83391,-0.54226,-0.10272,566.19,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.93818,0.099668,-0.33149,430.1,0.24688,0.4786,0.84261,221.95,0.24263,-0.87236,0.42441,209.46 Invalid ""models"" argument: No models specified by ""#1.1"" > color bfactor range 50,90 palette ^rainbow 5261 atoms, 641 residues, atom bfactor range 18.8 to 95.5 > hide #1 models > close #1 > close > devel build > /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- > main/ANNOTEX/ running build running build_py creating build creating build/lib creating build/lib/chimerax creating build/lib/chimerax/annotex copying src/proteome.py -> build/lib/chimerax/annotex copying src/__init__.py -> build/lib/chimerax/annotex copying src/tool.py -> build/lib/chimerax/annotex running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib creating build/bdist.macosx-10.9-universal2 creating build/bdist.macosx-10.9-universal2/wheel creating build/bdist.macosx-10.9-universal2/wheel/chimerax creating build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/proteome.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/__init__.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/tool.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex running install_egg_info running egg_info creating ChimeraX_ANNOTEX.egg-info writing ChimeraX_ANNOTEX.egg-info/PKG-INFO writing dependency_links to ChimeraX_ANNOTEX.egg-info/dependency_links.txt writing requirements to ChimeraX_ANNOTEX.egg-info/requires.txt writing top-level names to ChimeraX_ANNOTEX.egg-info/top_level.txt writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt' listing git files failed - pretending there aren't any reading manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt' writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt' Copying ChimeraX_ANNOTEX.egg-info to build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0-py3.9.egg-info running install_scripts creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0.dist- info/WHEEL creating 'dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-universal2/wheel' to it adding 'chimerax/annotex/__init__.py' adding 'chimerax/annotex/proteome.py' adding 'chimerax/annotex/tool.py' adding 'ChimeraX_ANNOTEX-1.0.dist-info/METADATA' adding 'ChimeraX_ANNOTEX-1.0.dist-info/WHEEL' adding 'ChimeraX_ANNOTEX-1.0.dist-info/top_level.txt' adding 'ChimeraX_ANNOTEX-1.0.dist-info/RECORD' removing build/bdist.macosx-10.9-universal2/wheel Distribution is in /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl > devel install > /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- > main/ANNOTEX/ running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib creating build/bdist.macosx-10.9-universal2/wheel creating build/bdist.macosx-10.9-universal2/wheel/chimerax creating build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/proteome.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/__init__.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex copying build/lib/chimerax/annotex/tool.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/annotex running install_egg_info running egg_info writing ChimeraX_ANNOTEX.egg-info/PKG-INFO writing dependency_links to ChimeraX_ANNOTEX.egg-info/dependency_links.txt writing requirements to ChimeraX_ANNOTEX.egg-info/requires.txt writing top-level names to ChimeraX_ANNOTEX.egg-info/top_level.txt listing git files failed - pretending there aren't any reading manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt' writing manifest file 'ChimeraX_ANNOTEX.egg-info/SOURCES.txt' Copying ChimeraX_ANNOTEX.egg-info to build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0-py3.9.egg-info running install_scripts creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_ANNOTEX-1.0.dist- info/WHEEL creating 'dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-universal2/wheel' to it adding 'chimerax/annotex/__init__.py' adding 'chimerax/annotex/proteome.py' adding 'chimerax/annotex/tool.py' adding 'ChimeraX_ANNOTEX-1.0.dist-info/METADATA' adding 'ChimeraX_ANNOTEX-1.0.dist-info/WHEEL' adding 'ChimeraX_ANNOTEX-1.0.dist-info/top_level.txt' adding 'ChimeraX_ANNOTEX-1.0.dist-info/RECORD' removing build/bdist.macosx-10.9-universal2/wheel Distribution is in /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl [toolshed install](help:user/commands/toolshed.html#install) /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl [toolshed install /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl](cxcmd:toolshed install /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl) Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.3.1 [notice] To update, run: /Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- main/ANNOTEX/dist/ChimeraX_ANNOTEX-1.0-py3-none-any.whl Requirement already satisfied: ChimeraX-Core~=1.2 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ANNOTEX==1.0) (1.6.1) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ANNOTEX==1.0) (1.28.4) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.0) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.2) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-ANNOTEX==1.0) (1.1.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX- ANNOTEX==1.0) (1.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX- ANNOTEX==1.0) (1.3) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- ANNOTEX==1.0) (1.0.1) Installing collected packages: ChimeraX-ANNOTEX Successfully installed ChimeraX-ANNOTEX-1.0 \--- Successfully installed ChimeraX-ANNOTEX-1.0 Installed ChimeraX-ANNOTEX (1.0) > devel clean > /Users/alexandra/Desktop/Projects/Vn_Genome/Rebuttal/ANNOTEX2.0/ANNOTEX- > main/ANNOTEX/ > ui tool show ANNOTEX > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g1.t1.pdb Chain information for g1.t1.pdb #1 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_1.pdb Chain information for g1.t1_domain_1.pdb #2 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_2.pdb Chain information for g1.t1_domain_2.pdb #3 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_3.pdb Chain information for g1.t1_domain_3.pdb #4 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_4.pdb Chain information for g1.t1_domain_4.pdb #5 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g1.t1_domain_5.pdb Chain information for g1.t1_domain_5.pdb #6 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 9047 atoms, 1121 residues, atom bfactor range 23 to 97.7 > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-E7F1X4-F1-model_v2.pdb AF-E7F1X4-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for reverse transcriptase (E7F1X4) [more info...] Chain information for AF-E7F1X4-F1-model_v2.pdb #7 --- Chain | Description | UniProt A | reverse transcriptase | E7F1X4_DANRE 1-1344 > mmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker g1.t1.pdb, chain A (#1) with AF-E7F1X4-F1-model_v2.pdb, chain A (#7), sequence alignment score = 1773 RMSD between 13 pruned atom pairs is 1.481 angstroms; (across all 1104 pairs: 43.841) > close #7 > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-A0A2R8QA15-F1-model_v2.pdb Summary of feedback from opening /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-A0A2R8QA15-F1-model_v2.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 1429 UNP A0A2R8QA15 A0A2R8QA15_DANRE 1 1429 AF-A0A2R8QA15-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for reverse transcriptase (A0A2R8QA15) [more info...] Chain information for AF-A0A2R8QA15-F1-model_v2.pdb #7 --- Chain | Description A | reverse transcriptase > mmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker g1.t1.pdb, chain A (#1) with AF-A0A2R8QA15-F1-model_v2.pdb, chain A (#7), sequence alignment score = 1704.4 RMSD between 13 pruned atom pairs is 1.189 angstroms; (across all 1083 pairs: 43.479) > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g30.t1.pdb Chain information for g30.t1.pdb #1 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g30.t1_domain_1.pdb Chain information for g30.t1_domain_1.pdb #2 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 1381 atoms, 165 residues, atom bfactor range 39.5 to 94.8 > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-Q99MU0-F1-model_v2.pdb AF-Q99MU0-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for protein DBF4 homolog A (Q99Μ0) [more info...] Chain information for AF-Q99MU0-F1-model_v2.pdb #3 --- Chain | Description | UniProt A | protein DBF4 homolog A | DBF4A_CRIGR 1-676 > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker g30.t1.pdb, chain A (#1) with AF-Q99MU0-F1-model_v2.pdb, chain A (#3), sequence alignment score = 226.8 RMSD between 25 pruned atom pairs is 0.884 angstroms; (across all 144 pairs: 47.262) > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g51.t1.pdb Chain information for g51.t1.pdb #1 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g51.t1_domain_1.pdb Chain information for g51.t1_domain_1.pdb #2 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g51.t1_domain_2.pdb Chain information for g51.t1_domain_2.pdb #3 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 3005 atoms, 356 residues, atom bfactor range 37.6 to 90.8 > open 7a6h 7a6h title: Cryo-EM structure of human apo RNA Polymerase III [more info...] Chain information for 7a6h #4 --- Chain | Description | UniProt A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390 B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133 C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346 D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148 E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN 1-210 F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN 1-127 G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN 1-150 I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108 J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN 1-67 K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133 L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN 1-58 M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708 N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398 O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534 P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316 Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223 Non-standard residues in 7a6h #4 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > mmaker #4/O 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 g51.t1.pdb, chain A (#1) with 7a6h, chain O (#4), sequence alignment score = 281.1 RMSD between 93 pruned atom pairs is 1.329 angstroms; (across all 339 pairs: 10.872) > hide #4 atoms > show #4 cartoons > color #4/O green > hide #1 models > show #1 models > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g86.t1.pdb Chain information for g86.t1.pdb #1 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 1493 atoms, 177 residues, atom bfactor range 27.8 to 73.6 > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g137.t1.pdb Chain information for g137.t1.pdb #1 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 1686 atoms, 199 residues, atom bfactor range 36.4 to 69.9 > close > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/pdbs/g213.t1.pdb Chain information for g213.t1.pdb #1 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g213.t1_domain_1.pdb Chain information for g213.t1_domain_1.pdb #2 --- Chain | Description A | No description available > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/domains/g213.t1_domain_2.pdb Chain information for g213.t1_domain_2.pdb #3 --- Chain | Description A | No description available > color bfactor #1 range 50,90 palette ^rainbow 3492 atoms, 418 residues, atom bfactor range 39.3 to 98.1 > open > /Users/alexandra/Desktop/Projects/Vn_Genome/Annotation/annotation_data/afdb_needed/AF-Q6C3V4-F1-model_v2.pdb AF-Q6C3V4-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for probable kinetochore protein NUF2 (Q6C3V4) [more info...] Chain information for AF-Q6C3V4-F1-model_v2.pdb #4 --- Chain | Description | UniProt A | probable kinetochore protein NUF2 | NUF2_YARLI 1-452 > mmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker g213.t1.pdb, chain A (#1) with AF-Q6C3V4-F1-model_v2.pdb, chain A (#4), sequence alignment score = 795.1 RMSD between 29 pruned atom pairs is 1.304 angstroms; (across all 418 pairs: 65.526) OpenGL version: 4.1 INTEL-20.6.4 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini8,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 3,2 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.6.1 (22G313) Kernel Version: Darwin 22.6.0 Time since boot: 5 days, 7 hours, 42 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Metal Support: Metal 3 Displays: LG Ultra HD: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort S27H85x: Resolution: 2048 x 1152 UI Looks like: 2048 x 1152 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H1AK500000 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: 2,19 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Platform duplicate Tom Goddard all ChimeraX