id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4684 MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted mm2303@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.14.6-x86_64-i386-64bit ChimeraX Version: 1.3.dev202104240152 (2021-04-24 01:52:36 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears'-discard.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0137, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 1, values float32 Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown at level 0.00634, step 1, values float32 Log from Sun May 23 03:46:49 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears-BT.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0137, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 1, values float32 Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown at level 0.00634, step 1, values float32 Log from Wed May 19 14:45:04 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0137, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 1, values float32 Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown at level 0.00634, step 1, values float32 Log from Tue May 18 20:24:40 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0181, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 1, values float32 Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown at level 0.00634, step 1, values float32 Log from Mon May 17 05:23:44 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs format > session Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0181, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Opened Earsj669post_erased.mrc as #6, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 1, values float32 Log from Mon May 17 03:52:16 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs format > session Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0181, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00589, step 2, values float32 Log from Mon May 17 03:37:02 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs format > session Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00553, step 2, values float32 Log from Sun May 16 01:36:06 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Desktop/paper/Figs2021Apr/20210427_colorB_1.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown at level 0.023, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Opened whole-j532post copy.mrc 1 as #6.2, grid size 210,210,210, pixel 1.66, shown at level 0.014, step 1, values float32 Opened whole-j532post copy.mrc 2 as #6.3, grid size 210,210,210, pixel 1.66, shown at level 0.0153, step 1, values float32 Opened whole-j532post copy.mrc 3 as #6.4, grid size 210,210,210, pixel 1.66, shown at level 0.0153, step 1, values float32 Log from Tue Apr 27 22:25:14 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0204, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown at level 0.0244, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Log from Tue Apr 27 19:58:11 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0204, step 1, values float32 Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0314, step 1, values float32 Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown at level 0.0244, step 1, values float32 Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 Log from Tue Apr 27 19:38:10 2021UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/miao/Downloads/coot/Figs2021Apr/whole-j532post copy.mrc"" Opened whole-j532post copy.mrc as #1, grid size 210,210,210, pixel 1.66, shown at level 0.0217, step 1, values float32 > open ""/Users/miao/Downloads/coot/Figs2021Apr/core-j577post copy.mrc"" Opened core-j577post copy.mrc as #2, grid size 210,210,210, pixel 1.66, shown at level 0.0168, step 1, values float32 > open ""/Users/miao/Downloads/coot/Figs2021Apr/Ears-j544post copy.mrc"" Opened Ears-j544post copy.mrc as #3, grid size 210,210,210, pixel 1.66, shown at level 0.017, step 1, values float32 > open ""/Users/miao/Downloads/coot/Figs2021Apr/C2E-j542post copy.mrc"" Opened C2E-j542post copy.mrc as #4, grid size 210,210,210, pixel 1.66, shown at level 0.0218, step 1, values float32 > select #4 2 models selected > select #2 2 models selected > ~select #2 Nothing selected > select #2 2 models selected > ~select #2 Nothing selected > volume #2 level 0.0255 > hide #!1 models > hide #!3 models > hide #!4 models > volume #1 level 0.02176 > hide #!1 models > volume #2 level 0.02985 > volume #2 level 0.02923 > volume #2 level 0.0314 > surface dust #2 size 16.6 > show #!4 models > select #4 2 models selected > select #2 2 models selected > ~select #2 Nothing selected > select #2 2 models selected > fitmap #2 inMap #4 Fit map core-j577post copy.mrc in map C2E-j542post copy.mrc using 38598 points correlation = 0.9669, correlation about mean = 0.3607, overlap = 45.22 steps = 48, shift = 0.474, angle = 0.526 degrees Position of core-j577post copy.mrc (#2) relative to C2E-j542post copy.mrc (#4) coordinates: Matrix rotation and translation 0.99998434 0.00483252 -0.00282164 -0.40654303 -0.00481186 0.99996191 0.00728217 -0.04881033 0.00285672 -0.00726848 0.99996950 0.90466921 Axis -0.79264881 -0.30932952 -0.52537901 Axis point 0.00000000 114.43819001 13.16112241 Rotation angle (degrees) 0.52589670 Shift along axis -0.13794989 > ~select #2 Nothing selected > select #3 2 models selected > hide #!2 models > show #!3 models > hide #!4 models > volume #3 level 0.02268 > volume #3 level 0.02438 > surface dust #3 size 16.6 > select #4 2 models selected > show #!4 models > ~select #4 Nothing selected > select #4 2 models selected > ~select #3 2 models selected > select #3 2 models selected > fitmap #3 inMap #4 Fit map Ears-j544post copy.mrc in map C2E-j542post copy.mrc using 35585 points correlation = 0.9916, correlation about mean = 0.6487, overlap = 29.37 steps = 44, shift = 0.351, angle = 0.267 degrees Position of Ears-j544post copy.mrc (#3) relative to C2E-j542post copy.mrc (#4) coordinates: Matrix rotation and translation 0.99999306 0.00243421 -0.00281987 -0.02007499 -0.00244208 0.99999313 -0.00278912 0.39707369 0.00281306 0.00279599 0.99999213 -0.85931214 Axis 0.59981627 -0.60495218 -0.52369200 Axis point 268.51643092 0.00000000 -49.84611442 Rotation angle (degrees) 0.26675196 Shift along axis 0.19776299 > ~select #3 Nothing selected > hide #!3 models > show #!1 models > select #1 2 models selected > hide #!4 models > volume #1 level 0.02077 > volume #1 level 0.02037 > show #!4 models > select #4 2 models selected > ~select #4 Nothing selected > select #4 2 models selected > ~select #1 2 models selected > select #1 2 models selected > fitmap #1 inMap #4 Fit map whole-j532post copy.mrc in map C2E-j542post copy.mrc using 128057 points correlation = 0.8969, correlation about mean = 0.05034, overlap = 52.69 steps = 88, shift = 0.852, angle = 5.6 degrees Position of whole-j532post copy.mrc (#1) relative to C2E-j542post copy.mrc (#4) coordinates: Matrix rotation and translation 0.99626467 -0.06341774 0.05860803 2.02692477 0.06067742 0.99703082 0.04741101 -18.37332373 -0.06144072 -0.04367773 0.99715460 18.85954601 Axis -0.46660987 0.61496004 0.63568811 Axis point 300.81511332 12.36084184 0.00000000 Rotation angle (degrees) 5.60138469 Shift along axis -0.25585376 > ~select #1 Nothing selected > select #1 2 models selected > ~select #1 Nothing selected > save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs ——— End of log from Tue Apr 27 19:38:10 2021 ——— opened ChimeraX session > open ""/Users/miao/Downloads/coot/Figs2021Apr/j532_fitall copy.pdb"" Summary of feedback from opening /Users/miao/Downloads/coot/Figs2021Apr/j532_fitall copy.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 24 SER A 39 1 16 Start residue of secondary structure not found: HELIX 2 2 GLY A 44 LYS A 54 1 11 Start residue of secondary structure not found: HELIX 3 3 THR A 58 LEU A 67 1 10 Start residue of secondary structure not found: HELIX 4 4 VAL A 119 SER A 123 1 5 Start residue of secondary structure not found: HELIX 5 5 GLY A 125 GLY A 143 1 19 160 messages similar to the above omitted End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B 354 0 Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B 391 0 Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B 432 0 Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B 451 0 Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B 458 0 Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B 514 0 231 messages similar to the above omitted End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B 354 0 Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B 391 0 Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B 432 0 Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B 451 0 Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B 458 0 Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B 514 0 468 messages similar to the above omitted End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B 354 0 Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B 391 0 Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B 432 0 Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B 451 0 Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B 458 0 Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B 514 0 468 messages similar to the above omitted End residue of secondary structure not found: SHEET 26 26 1 ARG B 347 ASN B 354 0 Start residue of secondary structure not found: SHEET 27 27 1 ILE B 385 VAL B 391 0 Start residue of secondary structure not found: SHEET 28 28 1 LYS B 423 TYR B 432 0 Start residue of secondary structure not found: SHEET 29 29 1 VAL B 448 ALA B 451 0 Start residue of secondary structure not found: SHEET 30 30 1 GLN B 456 ALA B 458 0 Start residue of secondary structure not found: SHEET 31 31 1 ALA B 513 VAL B 514 0 66 messages similar to the above omitted j532_fitall copy.pdb title: Crystal structure of the acyl-coa carboxylase, ACCD5, from mycobacterium tuberculosis [more info...] Chain information for j532_fitall copy.pdb --- Chain | Description 5.4/? 5.6/? | No description available 5.1/A 5.1/B 5.1/C 5.1/D 5.1/E 5.1/F | probable propionyl-coa carboxylase β chain 5 5.2/A 5.3/A 5.5/A 5.7/A 5.2/B 5.3/B 5.5/B 5.7/B | probable propionyl-coa carboxylase β chain 5 > hide #!1 models > hide #!4 models > color bychain > color byhetero > color bychain > style sphere Changed 56388 atom styles > style sphere Changed 56388 atom styles > color bychain > hide #5.1 models > show #5.1 models > color #5.1 #fffb00 > hide #5.1 models > show #5.1 models > hide #!5.2 models > show #!5.2 models > color #5.1 #8efa00 > color #5.1 #fffb00 > hide #!5.2 models > show #!5.2 models > color #5.2 #d4fb79 > color #5.2 #8efa00 > hide #!5.3 models > show #!5.3 models > hide #!5.3 models > show #!5.3 models > color #5.2 #4f8f00 > color #5.2 #8efa00 > color #5.3 #008f00 > color #5.3 #4f8f00 > color #5.3 #008f00 > color #5.3 #009051 > color #5.3 #008f00 > hide #5.4 models > show #5.4 models > hide #!5.5 models > show #!5.5 models > color #5.5 #7a81ff > hide #5.6 models > show #5.6 models > hide #!5.7 models > show #!5.7 models > color #5.7 #0433ff > color #5.7 #9437ff > hide #!5.5 models > show #!5.5 models > color #5.5 #d783ff > color #5.5 #ff85ff > color #5.5 #ff8ad8 > color #5.5 #ff2f92 > color #5.5 #d783ff > hide #5.6 models > show #5.6 models > color #5.6 #ff9300 > color #5.6 #ffd479 > color #5.6 #ff9300 > color #5.6 #ffd479 > color #5.6 #d4fb79 > color #5.6 #ffd479 > color #5.6 #ff7e79 > color #5.6 #ff9300 > set bgColor white > hide #5.4 models > show #5.4 models > color #5.6 #0096ff > color #5.6 #ff9300 > hide #5.4 models > show #5.4 models > color #5.4 #0096ff > color #5.4 #9437ff > color #5.4 #0433ff > color #5.4 #0096ff > hide #!5.5 models > show #!5.5 models > color #5.5 #0433ff > hide #!5.7 models > show #!5.7 models > color #5.7 #0096ff > hide #5.4 models > color #5.4 #9437ff > show #5.4 models > undo [Repeated 8 time(s)] > color #5.4 #7a81ff > save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs > color #5.2 #73fa79 > color #5.2 #00f900 > color #5.2 #00fa92 > color #5.2 #00f900 > color #5.3 #009051 > color #5.3 #008f00 > save /Users/miao/Downloads/coot/Figs2021Apr/20210427.cxs ——— End of log from Tue Apr 27 19:58:11 2021 ——— opened ChimeraX session > hide #!5 models > show #!5 models > color bychain > show #!1 models > volume #1 level 0.01991 > hide #!1 models > show #!3 models > hide #!3 models Drag select of 1894 residues, 8 pseudobonds > select up 14615 atoms, 14927 bonds, 8 pseudobonds, 1919 residues, 5 models selected > show #!3 models Color zone shortcut requires 1 displayed atomic model and 1 map, got 7 atomic models, 1 maps. > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > color zone #3 near sel & #5.3 distance 9.96 > ui tool show ""Color Zone"" > color zone #3 near #5.1 distance 1.66 > color zone #3 near #5.3 distance 14.15 > color zone #3 near #5.4 distance 14.15 > color zone #3 near #5.3 distance 14.15 > color zone #3 near #5.3 distance 13.15 > color zone #3 near #5.3 distance 12.15 > color zone #3 near #5.3 distance 11.15 > color zone #3 near #5.3 distance 12.15 > color zone #3 near #5.3 distance 13.15 > color zone #3 near #5.3 distance 13.1 > color zone #3 near #5.3 distance 13 > color zone #3 near #5.3 distance 13.5 > color zone #3 near #5.3 distance 13 > color zone #3 near #5.3 distance 14 > ~select #5.3 Nothing selected > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > color zone #3 near #5.4 distance 14 > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > color zone #3 near #5.3 distance 14 > ~select #5.3 Nothing selected > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.4 Nothing selected > select #5.5 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > ~select #5.5 Nothing selected > select #5.1 25316 atoms, 24642 bonds, 4310 residues, 1 model selected > ~select #5.1 Nothing selected > select #5.2 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > color zone #3 near #5.2 distance 14 > hide #!3 models > select clear Drag select of 1751 residues, 8 pseudobonds > select up 14398 atoms, 14699 bonds, 8 pseudobonds, 1891 residues, 5 models selected > show #!3 models > color zone #3 near sel distance 14 > select clear > hide #!3 models Drag select of 25157 atoms, 13 residues > select up 25350 atoms, 24591 bonds, 4298 residues, 3 models selected > select up 25519 atoms, 24864 bonds, 4319 residues, 3 models selected > select down 25350 atoms, 24591 bonds, 4298 residues, 3 models selected > select up 25519 atoms, 24864 bonds, 4319 residues, 3 models selected > select down 25350 atoms, 24591 bonds, 4298 residues, 3 models selected > show #!2 models > color zone #2 near sel distance 9.96 > hide #5.1 models > show #5.1 models > hide #!5 models > select #5.1 25316 atoms, 24642 bonds, 4310 residues, 1 model selected > hide #5.1 models > show #5.1 models > hide #5.1 models > show #5.1 models > color sel bychain > style sel sphere Changed 25316 atom styles > color #5.1 #fffb00 > color zone #2 near sel distance 9.96 > color zone #2 near sel distance 9.78 > color zone #2 near sel distance 17.65 > color zone #2 near sel distance 17.01 > color zone #2 near sel distance 18.32 > color zone #2 near sel distance 18.3 > color zone #2 near sel distance 18 > color zone #2 near sel distance 19 [Repeated 1 time(s)] > undo > hide #5.1 models > hide #!5 models > show #!5 models > hide #!2 models > hide #5.6 models > show #5.6 models > hide #5.4 models > show #5.4 models > color #5.4 #008f00 > color #5.4 #9437ff > color #5.4 #0433ff > show #5.1 models > color #5.4 #0096ff > select clear Drag select of 1789 residues, 8 pseudobonds > select down 13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected > select down 13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected > select down 13608 atoms, 8 pseudobonds, 1789 residues, 5 models selected > select up 14349 atoms, 14654 bonds, 8 pseudobonds, 1883 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > show #!1 models > color zone #1 near sel distance 9.96 > color single #1 > hide #!1 models > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > select up 56388 atoms, 54556 bonds, 8 pseudobonds, 9938 residues, 9 models selected > select down 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > select down 900 atoms, 913 bonds, 8 pseudobonds, 118 residues, 3 models selected > select down 14349 atoms, 14654 bonds, 8 pseudobonds, 1883 residues, 5 models selected > show #!1 models > color zone #1 near sel distance 9.96 > volume #1 level 0.01787 > color zone #1 near sel distance 12 > color zone #1 near sel distance 13 > color zone #1 near sel distance 14 > color zone #1 near sel distance 15 > hide #!5 models > volume splitbyzone #1 Opened whole-j532post copy.mrc 0 as #6.1, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 Opened whole-j532post copy.mrc 1 as #6.2, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 Opened whole-j532post copy.mrc 2 as #6.3, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 Opened whole-j532post copy.mrc 3 as #6.4, grid size 210,210,210, pixel 1.66, shown at level 0.0179, step 1, values float32 > volume #6.3 level 0.01596 > volume #6.4 level 0.016 > volume #6.2 level 0.016 > show #!2 models > show #!3 models > volume #6.2 level 0.014 > color #5.4 #805c93 > color #5.4 #f5affe [Repeated 1 time(s)] > volume #6.2 color #0096ff > volume #6.2 color #e3a2fe > volume #6.3 level 0.01531 > volume #6.4 level 0.0153 > color #2 #00f900 models > color #2 #8efa00 models > color #2 #fffb00 models > color #2 #d4fb79 models > color #2 #8efa00 models > color #2 #4f8f00 models > color #2 #8efa00 models > color #2 #fffb00 models > color #2 #00fdff models > color #2 #0096ff models > color #2 #005493 models > color #2 #0096ff models > lighting soft > volume #6.2 color #fffb00 > volume #6.2 color #fffc79 > volume #6.2 color #ffd479 > volume #6.2 color #fffc79 > undo [Repeated 1 time(s)] > redo [Repeated 2 time(s)]No redo action is available > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.6 Nothing selected > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.6 Nothing selected > hide #5.6 models > show #5.6 models > hide #5.6 models > hide #5.4 models > show #5.4 models > hide #5.4 models > show #5.4 models > hide #5.4 models > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.4 Nothing selected > hide #!3 models > show #5.6 models > color #5.6 #fffc79 > select clear > hide #!5.3 models > hide #!5.2 models > show #!5.2 models > show #!5.3 models > hide #5.1 models > show #!3 models > hide #!3 models Drag select of 6.1 whole-j532post copy.mrc 0 , 1798 residues, 8 pseudobonds > hide #!2 models > select clear > select #5.2 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > select clear Drag select of 6.1 whole-j532post copy.mrc 0 , 1861 residues, 8 pseudobonds > select clear > hide #!5 models > show #!5 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > close #6.1 Drag select of 1907 residues, 8 pseudobonds > select up 14615 atoms, 883 bonds, 8 pseudobonds, 1919 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > show #!3 models > color zone #3 near sel distance 14 > hide #!5.2 models > hide #!5.3 models > ~select #5.2 8218 atoms, 7935 bonds, 4 pseudobonds, 1466 residues, 3 models selected > ~select #5.3 900 atoms, 913 bonds, 118 residues, 1 model selected > hide #5.6 models > hide #!5.5 models > hide #!5.7 models > hide #!6 models > ~select #5.6 Nothing selected > show #!2 models > hide #!3 models > show #!3 models > hide #!6.2 models > show #!6.2 models > save /Users/miao/Downloads/coot/Figs2021Apr/20210427_0_colorB.cxs > save /Users/miao/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/miao/Desktop/movie1.mp4 Movie saved to /Users/miao/Desktop/movie1.mp4 > hide #!2 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models No atoms selected for color zoning [Repeated 1 time(s)] > show #!5.2 models > show #5.1 models > hide #5.1 models > show #!5.3 models > show #5.6 models > hide #!3 models Drag select of 1907 residues, 8 pseudobonds > select up 14615 atoms, 883 bonds, 8 pseudobonds, 1919 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > show #!3 models > color zone #3 near sel distance 16.7 > color zone #3 near sel distance 15.7 > color zone #3 near sel distance 16 [Repeated 1 time(s)] > color zone #3 near sel distance 17 > color zone #3 near sel distance 16 > color zone #3 near sel distance 16.6 > color zone #3 near sel distance 16 > color zone #3 near sel distance 16.7 > color zone #3 near sel distance 16 > color zone #3 near sel distance 16.8 > ~select #5.3 8218 atoms, 7935 bonds, 4 pseudobonds, 1466 residues, 3 models selected > ~select #5.2 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.6 Nothing selected > hide #5.6 models > hide #!5.3 models > hide #!5.2 models > hide #!5 models > show #!6 models > show #!2 models > save /Users/miao/Desktop/image2.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/miao/Desktop/movie1.mp4 Movie saved to /Users/miao/Desktop/movie1.mp4 > volume #3 level 0.0237 > volume #3 level 0.02302 > save /Users/miao/Downloads/coot/Figs2021Apr/20210427_0_colorB.cxs > save /Users/miao/Desktop/image3.png supersample 3 > marker segment #7 position 126.6,166.9,172.9 toPosition 122.2,172.1,180.9 > color yellow radius 0.415 label 10.46 labelHeight 1.046 labelColor yellow > save /Users/miao/Desktop/image4.png supersample 3 > save /Users/miao/Desktop/image5.png supersample 3 > save /Users/miao/Desktop/image6.png supersample 3 > open /Users/miao/Downloads/coot/Figs2021Apr/built.pdb Chain information for built.pdb #8 --- Chain | Description a | No description available b | No description available d | No description available e | No description available > hide #!6 models > hide #!6.2 models > show #!6 models > show #!6.2 models > hide #!3 models > select #8 325 atoms, 321 bonds, 65 residues, 1 model selected > hide #!7 models > close #7 > color #8 #ff2600 > hide #!2 models > show #!2 models > color zone #2 near #8 distance 9.96 > volume #!2#!6.2-4 style image > volume #!2#!6.2-4 style surface > volume #2 change image level -0.004278,0 level 0.0168,0.8 level 0.1241,1 > transparency #2.1#6.2.1#6.3.1#6.4.1 50 > volume #!2#!6.2-4 style surface [Repeated 1 time(s)] > volume #2 > undo [Repeated 2 time(s)] > volume #!2#!6.2-4 showOutlineBox true > volume #2 color #0096ff13 > volume #2 color #0096ffe6 > volume #2 color #0096ff > volume #2 color #0096ffc9 > color zone #2 near #8 distance 9.96 > volume #2 color #0096ff > volume #2 color #0096fff2 > volume #2 color #0096ff > color zone #2 near #8 distance 9.96 > color zone #2 near #8 distance 4.85 [Repeated 1 time(s)] > color zone #2 near #8 distance 3.41 [Repeated 1 time(s)] > ~select #8 Nothing selected > hide #8 models > volume #!2#!6.2-4 showOutlineBox false > show #!3 models > save /Users/miao/Downloads/coot/Figs2021Apr/20210427_colorB_1.cxs ——— End of log from Tue Apr 27 22:25:14 2021 ——— opened ChimeraX session > hide #!3 models > open ""/Users/miao/Desktop/paper/Figs2021Apr/Earsj669post copy.mrc"" Opened Earsj669post copy.mrc as #7, grid size 420,420,420, pixel 0.83, shown at level 0.00553, step 2, values float32 > hide #!2 models > hide #!6 models > hide #!6.2 models > hide #!6.3 models > hide #!6.4 models > select #7 2 models selected > show #!4 models > fitmap #7 inMap #4 Fit map Earsj669post copy.mrc in map C2E-j542post copy.mrc using 92433 points correlation = 0.9753, correlation about mean = 0.5301, overlap = 15.78 steps = 2000, shift = 0.787, angle = 1.69 degrees Position of Earsj669post copy.mrc (#7) relative to C2E-j542post copy.mrc (#4) coordinates: Matrix rotation and translation 0.99971969 -0.01913513 0.01394199 0.90271890 0.01888777 0.99966558 0.01766304 -5.00550361 -0.01427531 -0.01739476 0.99974679 5.23562545 Axis -0.59505469 0.47894741 0.64538306 Axis point 277.29100614 56.93511692 0.00000000 Rotation angle (degrees) 1.68804185 Shift along axis 0.44444389 > ~select #7 Nothing selected > hide #!4 models > show #!6.4 models > hide #!6.4 models > show #!6.3 models > hide #!6.3 models > show #!5.7 models > hide #!5.7 models > show #!5.5 models > show #!5.7 models > hide #!5.7 models > hide #!5.5 models > show #!5.3 models > show #!5.2 models > transparency #7 50 > lighting simple > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!5.3 models > show #!5.3 models > hide #!5.3 models > hide #!5.2 models > show #!5.2 models > show #!5.3 models > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > ~select #5.3 Nothing selected > select #5.2 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5.2,0.99041,-0.075512,-0.11566,24.224,0.092914,0.9838,0.15334,-26.555,0.10221,-0.16262,0.98138,11.092 > ui mousemode right ""translate selected models"" > view matrix models > #5.2,0.99041,-0.075512,-0.11566,25.76,0.092914,0.9838,0.15334,-35.378,0.10221,-0.16262,0.98138,14.12 > view matrix models > #5.2,0.99041,-0.075512,-0.11566,25.142,0.092914,0.9838,0.15334,-37.472,0.10221,-0.16262,0.98138,15.546 > ui mousemode right ""rotate selected models"" > view matrix models > #5.2,0.97247,-0.12405,0.19726,2.9512,-0.18158,-0.93395,0.30784,267.22,0.14604,-0.33519,-0.93076,229.35 > view matrix models > #5.2,0.86501,0.00048599,0.50176,-30.928,-0.31526,-0.77743,0.54425,239.34,0.39035,-0.62896,-0.67233,211.09 > view matrix models > #5.2,0.01246,0.77212,0.63535,-35.514,0.78178,-0.40368,0.47525,34.433,0.62343,0.49078,-0.60866,7.0741 > view matrix models > #5.2,-0.18397,0.46231,0.86742,14.397,0.50505,-0.71262,0.48692,118.17,0.84326,0.52767,-0.10239,-81.396 > view matrix models > #5.2,-0.67734,0.28346,0.67887,130.5,0.38395,-0.65094,0.65488,109.37,0.62753,0.70422,0.33207,-120.63 > view matrix models > #5.2,-0.95484,0.017624,0.2966,248.16,0.20161,-0.69484,0.69033,138.31,0.21826,0.71895,0.65991,-97.553 > view matrix models > #5.2,-0.9982,-0.02772,0.053127,285.82,0.059007,-0.60923,0.79079,135.96,0.010446,0.79251,0.60977,-73.459 > ui mousemode right ""translate selected models"" > view matrix models > #5.2,-0.9982,-0.02772,0.053127,284.37,0.059007,-0.60923,0.79079,135.41,0.010446,0.79251,0.60977,-72.158 > view matrix models > #5.2,-0.9982,-0.02772,0.053127,280.99,0.059007,-0.60923,0.79079,137.65,0.010446,0.79251,0.60977,-70.773 > fitmap #5.2 inMap #7 Fit molecule j532_fitall copy.pdb (#5.2) to map Earsj669post copy.mrc (#7) using 7318 atoms average map value = 0.007925, steps = 220 shifted from previous position = 4.86 rotated from previous position = 52.8 degrees atoms outside contour = 1402, contour level = 0.0055322 Position of j532_fitall copy.pdb (#5.2) relative to Earsj669post copy.mrc (#7) coordinates: Matrix rotation and translation -0.59833008 0.28261688 0.74975250 105.27324219 0.26528541 -0.81307900 0.51819512 168.13494361 0.75605871 0.50895012 0.41151549 -117.51792216 Axis -0.44812243 -0.30567365 -0.84008923 Axis point 84.49625073 105.12404280 0.00000000 Rotation angle (degrees) 179.40896873 Shift along axis 0.15581790 > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > fitmap #5.3 inMap #7 Fit molecule j532_fitall copy.pdb (#5.3) to map Earsj669post copy.mrc (#7) using 7318 atoms average map value = 0.007608, steps = 164 shifted from previous position = 9.63 rotated from previous position = 24.5 degrees atoms outside contour = 1545, contour level = 0.0055322 Position of j532_fitall copy.pdb (#5.3) relative to Earsj669post copy.mrc (#7) coordinates: Matrix rotation and translation 0.92058150 0.36352835 0.14274745 -43.22779944 -0.33016311 0.91963356 -0.21275909 114.29464103 -0.20861931 0.14873214 0.96662130 26.23285224 Axis 0.42155378 0.40974710 -0.80894977 Axis point 290.52764782 190.94936224 0.00000000 Rotation angle (degrees) 25.38892569 Shift along axis 7.38799622 > select clear > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs > show #!1 models > hide #!1 models > show #!6 models > hide #!6 models > show #!6 models > show #!6.2 models > show #!6.3 models > show #!6.4 models > hide #!5.2 models > hide #!5.3 models > show #5.1 models > select #5.1 25316 atoms, 24642 bonds, 4310 residues, 1 model selected > ~select #5.1 Nothing selected > hide #5.1 models > show #5.6 models > hide #!6 models > hide #!6.2 models > hide #!6.3 models > hide #!6.4 models > hide #!7 models > show #!7 models > fitmap #5.6 inMap #7 Fit molecule j532_fitall copy.pdb (#5.6) to map Earsj669post copy.mrc (#7) using 900 atoms average map value = 0.006734, steps = 112 shifted from previous position = 1.18 rotated from previous position = 33.2 degrees atoms outside contour = 307, contour level = 0.0055322 Position of j532_fitall copy.pdb (#5.6) relative to Earsj669post copy.mrc (#7) coordinates: Matrix rotation and translation 0.85031961 -0.48668234 0.20024198 72.96422939 0.49867852 0.86671607 -0.01109017 -66.86527886 -0.16815555 0.10928656 0.97968370 15.17413794 Axis 0.11368731 0.34792540 0.93060363 Axis point 160.42908477 100.77936831 0.00000000 Rotation angle (degrees) 31.96629376 Shift along axis -0.84791442 > hide #!7 models > show #!7 models > hide #5.6 models > show #!6 models > show #!6.2 models > show #!6.3 models > show #!6.4 models > show #5.4 models > hide #5.4 models > show #!5.3 models > hide #!5.3 models > show #!5.2 models > hide #!5.2 models > show #!5.5 models > show #!5.7 models > hide #!5.7 models > show #!5.7 models > select #5.7 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5.7,0.97853,0.024066,0.2047,-57.595,0.029953,0.96601,-0.25675,72.451,-0.20392,0.25737,0.94455,0.92223 > view matrix models > #5.7,-0.85141,-0.35492,0.38618,291.38,0.3557,-0.93181,-0.072179,336.76,0.38546,0.07591,0.9196,-61.061 > view matrix models > #5.7,-0.77013,-0.63784,-0.0073969,441.56,0.11852,-0.15447,0.98086,-65.554,-0.62678,0.75452,0.19456,185.82 > view matrix models > #5.7,-0.32035,-0.88134,0.34729,311.44,-0.73878,0.46191,0.49076,101.03,-0.59295,-0.099357,-0.79909,622.82 > view matrix models > #5.7,-0.14657,-0.79177,0.59297,194.98,-0.95239,-0.049055,-0.30092,458.59,0.26735,-0.60884,-0.74688,555.92 > view matrix models > #5.7,-0.16062,-0.74682,0.64533,174.13,-0.95827,-0.038649,-0.28324,452.69,0.23647,-0.6639,-0.70945,561.86 > ui mousemode right ""translate selected models"" > view matrix models > #5.7,-0.16062,-0.74682,0.64533,180.2,-0.95827,-0.038649,-0.28324,458.7,0.23647,-0.6639,-0.70945,561.78 > ui mousemode right ""rotate selected models"" > view matrix models > #5.7,-0.46816,-0.16224,0.86862,57.986,-0.69229,-0.54356,-0.47464,563.79,0.54915,-0.82354,0.14216,301.93 > view matrix models > #5.7,-0.70891,0.15677,0.68765,88.074,-0.38705,-0.90153,-0.19349,502.19,0.58961,-0.40332,0.69978,57.736 > view matrix models > #5.7,-0.96699,0.25469,-0.0075131,307.06,-0.23436,-0.87746,0.41849,300.94,0.099995,0.40644,0.90819,-72.327 > view matrix models > #5.7,-0.87809,-0.16588,-0.44883,496.17,-0.34996,-0.41706,0.8388,114.55,-0.32633,0.89361,0.30816,73.632 > view matrix models > #5.7,-0.60551,-0.66919,-0.43075,541.78,-0.58828,0.011843,0.80857,80.861,-0.53598,0.743,-0.40085,336.74 > view matrix models > #5.7,-0.49063,-0.81702,-0.30292,515.08,-0.69961,0.16212,0.69589,102.26,-0.51945,0.55335,-0.65113,440.39 > ui mousemode right ""translate selected models"" > view matrix models > #5.7,-0.49063,-0.81702,-0.30292,515.06,-0.69961,0.16212,0.69589,100.37,-0.51945,0.55335,-0.65113,440.43 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 4 maps. > hide #!5.5 models > hide #!7 models > hide #!6.4 models > show #!6.4 models > hide #!6.3 models > show #!6.3 models > hide #!6.2 models > show #!6.2 models > hide #!6.2 models > hide #!6 models > show #!6 models > hide #!6.3 models > hide #!6.4 models > show #!6.4 models > hide #!6.4 models > show #!6.3 models > hide #!6.3 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!5.7 models > show #!5.7 models > show #!6 models > show #!6.2 models > hide #!6.2 models > show #!6.3 models > show #!6.4 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!6.3 models > hide #!6.4 models > show #!1 models > fitmap #5.7 inMap #1 Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1) using 7318 atoms average map value = 0.01909, steps = 420 shifted from previous position = 2.21 rotated from previous position = 91.9 degrees atoms outside contour = 2525, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation -0.96963736 -0.08046323 -0.23093086 431.05259150 -0.08166871 -0.78355827 0.61592747 194.91585061 -0.23050730 0.61608611 0.75319604 -11.75435461 Axis 0.12321197 -0.32896944 -0.93626808 Axis point 214.78637025 99.44884749 0.00000000 Rotation angle (degrees) 179.96311468 Shift along axis -0.00529075 > view matrix models > #5.7,-0.97435,0.0056364,-0.22499,420.51,-0.15119,-0.7569,0.6358,201.02,-0.16671,0.6535,0.73834,-28.717 > ui mousemode right ""rotate selected models"" > view matrix models > #5.7,-0.98226,0.098546,0.15957,297.18,-0.075338,-0.98649,0.14548,368.45,0.17175,0.13087,0.97641,-51.905 > view matrix models > #5.7,-0.83679,-0.069724,0.54306,198.29,-0.20691,-0.87804,-0.43155,530.22,0.50692,-0.47348,0.72031,78.37 > view matrix models > #5.7,-0.65849,-0.35483,0.66369,189.32,-0.48379,-0.47594,-0.73445,584.13,0.57649,-0.80472,0.14174,291.34 > view matrix models > #5.7,-0.62452,-0.4786,0.61718,220.51,-0.6163,-0.18341,-0.76586,558.81,0.47974,-0.85866,-0.18041,408.3 > view matrix models > #5.7,-0.55875,-0.78232,0.27526,363.23,-0.80969,0.44278,-0.38516,364.59,0.17944,-0.43809,-0.88084,572.79 > view matrix models > #5.7,-0.45466,-0.8568,-0.24326,502.96,-0.86973,0.48596,-0.086078,283.95,0.19197,0.17243,-0.96613,474.13 > view matrix models > #5.7,-0.60797,-0.75669,-0.24039,509.68,-0.74609,0.44095,0.49891,108.91,-0.27152,0.48268,-0.83265,458.4 > fitmap #5.7 inMap #1 Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1) using 7318 atoms average map value = 0.01909, steps = 500 shifted from previous position = 4.41 rotated from previous position = 105 degrees atoms outside contour = 2528, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation -0.97004321 -0.07975247 -0.22946834 430.58007595 -0.08086523 -0.78470474 0.61457243 195.37143057 -0.22907856 0.61471783 0.75474830 -12.17547658 Axis 0.12238584 -0.32809726 -0.93668239 Axis point 214.52559461 99.74984071 0.00000000 Rotation angle (degrees) 179.96596673 Shift along axis 0.00062730 > transparency #1 50 > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs > hide #!6 models > show #!6 models > show #!6.2 models > hide #!6.2 models > show #!6.3 models > hide #!6.3 models > show #!6.3 models > hide #!6.3 models > show #!6.3 models > close #6.3 > show #!6.4 models > hide #!6.4 models > show #!6.4 models > close #6.4 > show #!6.2 models > hide #!6.2 models > close #6 > show #5.6 models > hide #5.6 models > show #!5.5 models > hide #!5.7 models > ~select #5.7 Nothing selected > select #5.5 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > fitmap #5.5 inMap #1 Fit molecule j532_fitall copy.pdb (#5.5) to map whole-j532post copy.mrc (#1) using 7318 atoms average map value = 0.01913, steps = 72 shifted from previous position = 0.423 rotated from previous position = 5.6 degrees atoms outside contour = 2342, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.5) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation 0.99999661 0.00017116 -0.00259673 0.57418855 -0.00016236 0.99999424 0.00338905 -0.78923841 0.00259730 -0.00338861 0.99999089 0.46028784 Axis -0.79312452 -0.60780773 -0.03902901 Axis point 0.00000000 135.28274606 231.97235454 Rotation angle (degrees) 0.24481179 Shift along axis 0.00633761 > show #!5.7 models > select #5.7 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > hide #!1 models Drag select of 783 residues, 2 pseudobonds > select clear Drag select of 1793 residues, 8 pseudobonds > select up 13744 atoms, 14044 bonds, 8 pseudobonds, 1804 residues, 4 models selected > show #5.1 models > hide #5.1 models > show #5.1 models > hide #5.1 models > show #5.6 models > hide #5.6 models > show #5.1 models > hide #5.1 models > show #5.4 models > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > show #!1 models > fitmap #5.4 inMap #1 Fit molecule j532_fitall copy.pdb (#5.4) to map whole-j532post copy.mrc (#1) using 900 atoms average map value = 0.02006, steps = 52 shifted from previous position = 2.91 rotated from previous position = 5.59 degrees atoms outside contour = 226, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.4) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation 0.99999991 0.00040715 0.00014933 -0.11963845 -0.00040716 0.99999991 0.00010627 0.03987865 -0.00014928 -0.00010633 0.99999998 0.04608935 Axis -0.23807271 0.33438276 -0.91187146 Axis point 98.05121057 293.99070369 0.00000000 Rotation angle (degrees) 0.02558290 Shift along axis -0.00021018 > color #5.4 #fffc79 > color #5.4 #fffb00 > show #5.1 models > color #5.1 #0096ff > hide sel cartoons > show sel cartoons > ~select #5.4 Nothing selected > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.4 Nothing selected > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > select #5.1 25316 atoms, 24642 bonds, 4310 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > hide sel surfaces > hide sel atoms > show sel surfaces > hide sel surfaces > style sel sphere Changed 25316 atom styles > show sel cartoons > show sel atoms > hide sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > style sel stick Changed 25316 atom styles > style sel sphere Changed 25316 atom styles > style sel ball Changed 25316 atom styles > hide sel atoms > hide #!5.1 models > ~select #5.1 6 models selected > hide #5.4 models > show #5.4 models > hide #!1 models Drag select of 1915 residues, 8 pseudobonds > select up 14644 atoms, 7022 bonds, 8 pseudobonds, 1922 residues, 5 models selected > select up 15536 atoms, 14044 bonds, 8 pseudobonds, 2814 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near sel distance 10 > transparency #1 50 > hide #!5.5 models > show #!5.5 models > view matrix models > #5.4,0.97722,0.076555,0.19794,-61.387,-0.046814,0.98746,-0.15079,51.477,-0.207,0.13808,0.96855,9.2568,#5.5,0.97778,0.075674,0.1955,-60.69,-0.046987,0.98796,-0.14742,50.563,-0.20431,0.13495,0.96956,9.3998,#5.7,-0.99947,-0.016135,-0.02816,371.99,-0.00024311,-0.86391,0.50364,226.2,-0.032454,0.50338,0.86345,-64.64 > view matrix models > #5.4,0.99572,-0.08866,0.026102,16.022,0.086095,0.99249,0.086877,-31.51,-0.033609,-0.084258,0.99588,23.73,#5.5,0.99577,-0.08898,0.023076,16.797,0.086576,0.99218,0.089897,-32.237,-0.030894,-0.087518,0.99568,24.189,#5.7,-0.96461,0.0064394,-0.26362,427.15,-0.18405,-0.73236,0.65557,198.55,-0.18884,0.68089,0.70762,-19.302 > hide #!5.5 models > hide #5.4 models > ~select #5.4 14636 atoms, 14044 bonds, 8 pseudobonds, 2696 residues, 4 models selected > ~select #5.5 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > fitmap #5.7 inMap #1 Fit molecule j532_fitall copy.pdb (#5.7) to map whole-j532post copy.mrc (#1) using 7318 atoms average map value = 0.01909, steps = 68 shifted from previous position = 2.12 rotated from previous position = 3.26 degrees atoms outside contour = 2527, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.7) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation -0.97010540 -0.07963360 -0.22924658 430.51178970 -0.08073779 -0.78491803 0.61431677 195.45352357 -0.22886003 0.61446088 0.75502378 -12.25717216 Axis 0.12225873 -0.32793471 -0.93675591 Axis point 214.48677904 99.80451132 0.00000000 Rotation angle (degrees) 179.96623180 Shift along axis 0.01981034 > hide #!5.7 models > show #!5.5 models > fitmap #5.5 inMap #1 Fit molecule j532_fitall copy.pdb (#5.5) to map whole-j532post copy.mrc (#1) using 7318 atoms average map value = 0.01913, steps = 88 shifted from previous position = 2.48 rotated from previous position = 2.95 degrees atoms outside contour = 2343, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.5) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation 0.99998311 -0.00050226 -0.00578991 1.47082238 0.00054555 0.99997189 0.00747826 -1.80906649 0.00578599 -0.00748129 0.99995528 1.05657988 Axis -0.78965862 -0.61104833 0.05531000 Axis point 0.00000000 139.76351743 242.23773702 Rotation angle (degrees) 0.54272333 Shift along axis 0.00241893 > hide #!5.5 models > show #5.6 models > hide #5.6 models > show #5.4 models > fitmap #5.4 inMap #1 Fit molecule j532_fitall copy.pdb (#5.4) to map whole-j532post copy.mrc (#1) using 900 atoms average map value = 0.02006, steps = 44 shifted from previous position = 1.32 rotated from previous position = 3.22 degrees atoms outside contour = 226, contour level = 0.017871 Position of j532_fitall copy.pdb (#5.4) relative to whole-j532post copy.mrc (#1) coordinates: Matrix rotation and translation 0.99999993 -0.00034182 -0.00016782 0.09944828 0.00034179 0.99999993 -0.00016596 -0.01577008 0.00016788 0.00016590 0.99999997 -0.06501357 Axis 0.39947768 -0.40408887 0.82287895 Axis point 54.95007303 299.57521035 0.00000000 Rotation angle (degrees) 0.02379919 Shift along axis -0.00739842 > select #5.4 900 atoms, 913 bonds, 118 residues, 1 model selected > show #!5.5 models > hide #!5.5 models > show #!5.5 models > show #!5.3 models > hide #!5.3 models > show #5.6 models > hide #5.6 models > show #!5.3 models > hide #!5.3 models > show #!5.7 models > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs > show #!5.3 models > show #!5.2 models > ui mousemode right select > show #!5.1 models > hide #!5.1 models > hide #!5.2 models > show #!5.2 models > hide #!5.3 models > show #!5.3 models > hide #!5.5 models > show #!5.5 models > hide #!5.7 models > show #!5.7 models > hide #!5.7 models > hide #!5.5 models > hide #5.4 models > ~select #5.4 Nothing selected > hide #!5.3 models > show #!5.3 models > save /Users/miao/Desktop/paper/Figs2021Apr/5.3fitsum.pdb relModel #7 > hide #!5.3 models > hide #!5.2 models > show #!5.2 models > show #!7 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!5 models > show #!5 models > hide #!5.2 models > show #!5.2 models > hide #!5 models > hide #!5.2 models > show #!5.2 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!1 models > fitmap #5.2 inMap #7 Fit molecule j532_fitall copy.pdb (#5.2) to map Earsj669post copy.mrc (#7) using 7318 atoms average map value = 0.007925, steps = 28 shifted from previous position = 0.0153 rotated from previous position = 0.0138 degrees atoms outside contour = 1397, contour level = 0.0055322 Position of j532_fitall copy.pdb (#5.2) relative to Earsj669post copy.mrc (#7) coordinates: Matrix rotation and translation -0.59836780 0.28274589 0.74967375 105.26779962 0.26505309 -0.81312864 0.51823612 168.15902185 0.75611033 0.50879915 0.41160732 -117.52190001 Axis -0.44810038 -0.30563139 -0.84011636 Axis point 84.50285188 105.12644030 0.00000000 Rotation angle (degrees) 179.39666609 Shift along axis 0.16685388 > save /Users/miao/Desktop/paper/Figs2021Apr/5.2fitsum.pdb relModel #7 > show #5.4 models > hide #5.4 models > show #5.4 models > save /Users/miao/Desktop/paper/Figs2021Apr/5.4fitsum.pdb relModel #7 > hide #5.4 models > show #5.6 models > save /Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum.pdb relModel #7 > close #3 > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs ——— End of log from Sun May 16 01:36:06 2021 ——— opened ChimeraX session > color #7 #929292 models > color #7 darkgrey models > volume #1 level 0.01807 > volume #7 level 0.005889 > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs > show #!5.7 models > hide #!5.7 models > show #!5.7 models > hide #!5.7 models > show #!5.5 models > hide #!5.5 models > show #5.4 models > hide #5.4 models > show #!5.3 models > surface dust #7 size 8.3 > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > hide #!7 models Drag select of 1678 residues, 8 pseudobonds > select up 13893 atoms, 14180 bonds, 8 pseudobonds, 1822 residues, 5 models selected > select up 15536 atoms, 14957 bonds, 8 pseudobonds, 2814 residues, 5 models selected > ui tool show ""Color Zone"" > color zone #7 near sel distance 4.98 > show #!7 models > color zone #7 near sel distance 6 > color zone #7 near sel distance 1 > color zone #7 near sel distance 10 > color zone #7 near sel distance 1 > color zone #7 near sel distance 8 > color single #7 > select down 13893 atoms, 14180 bonds, 8 pseudobonds, 1822 residues, 5 models selected > color zone #7 near sel distance 8 > color zone #7 near sel distance 1 > color zone #7 near sel distance 10 > color single #7 > hide #!7 models > select clear Drag select of 1912 residues, 8 pseudobonds > show #!7 models > color zone #7 near sel distance 10 > hide #7.1 models > hide #!7 models > show #!7 models > show #7.1 models > transparency #7 50 > transparency #7 80 > transparency #7 20 > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > select #5 56388 atoms, 54556 bonds, 16 pseudobonds, 9938 residues, 12 models selected > ~select #5 6 models selected > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB.cxs ——— End of log from Mon May 17 03:37:02 2021 ——— opened ChimeraX session > ui mousemode right ""map eraser"" > volume erase #7 center 174.29,174.12,181.36 radius 40.882 Opened Earsj669post copy.mrc copy as #6, grid size 420,420,420, pixel 0.83, shown at step 1, values float32 > volume erase #6 center 187.07,184.64,187.49 radius 40.786 > volume erase #6 center 155.85,162.89,182.48 radius 40.786 > volume erase #6 center 193.07,175.65,196.29 radius 40.786 > volume erase #6 center 160.09,214,176.05 radius 40.786 > volume erase #6 center 164.98,200.54,164.01 radius 40.786 > volume erase #6 center 137.84,203.92,176.11 radius 40.786 > surface dust #6 size 8.3 > ui mousemode right select > save /Users/miao/Desktop/paper/Figs2021Apr/Earsj669post_erased.mrc models #6 > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > select #5.3 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > select #5.2 7318 atoms, 7022 bonds, 4 pseudobonds, 1348 residues, 2 models selected > ~select #5.2 Nothing selected > hide #!6 models Drag select of 180 residues, 2 pseudobonds > select clear Drag select of 1912 residues, 8 pseudobonds > ui tool show ""Color Zone"" > color zone #6 near sel distance 4.98 > show #!6 models > color zone #6 near sel distance 4.9 > color zone #6 near sel distance 4 > color zone #6 near sel distance 1 > color zone #6 near sel distance 10 > color zone #6 near sel distance 1 > color zone #6 near sel distance 8 > color zone #6 near sel distance 1 > color zone #6 near sel distance 10 > transparency #7 20 > transparency #6 20 > select #5.6 900 atoms, 913 bonds, 118 residues, 1 model selected > ~select #5.6 Nothing selected > hide #!5.3 models > show #!5.3 models > hide #!5.3 models > hide #!5.2 models > hide #5.6 models > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs ——— End of log from Mon May 17 03:52:16 2021 ——— opened ChimeraX session > open /Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum-coot-2.pdb Summary of feedback from opening /Users/miao/Desktop/paper/Figs2021Apr/5.6fitsum-coot-2.pdb --- warning | End residue of secondary structure not found: HELIX 2 2 ARG 540 ARG 542 1 3 5.6fitsum-coot-2.pdb title: Crystal structure of the acyl-coa carboxylase, ACCD5, from mycobacterium tuberculosis [more info...] Chain information for 5.6fitsum-coot-2.pdb #3 --- Chain | Description ? | No description available > open /Users/miao/Desktop/paper/Figs2021Apr/Earsj669post_erased.mrc Opened Earsj669post_erased.mrc as #9, grid size 420,420,420, pixel 0.83, shown at level 0.00315, step 2, values float32 > volume #9 level 0.005719 > hide #!6 models > color #9 #ebebeb models > color #9 #d6d6d6 models > color #9 silver models > transparency #9 40 > transparency #9 50 > show #!5.2 models > show #!5.3 models > color #3 #ffd479 > color #3 #ff7e79 > color #3 #ffd479 > surface dust #9 size 8.3 > volume #9 step 1 > volume #9 level 0.00623 > surface dust #9 size 8.3 [Repeated 1 time(s)] > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs > transparency #9 80 > transparency #9 60 > transparency #9 90 > transparency #9 80 > volume #9 color darkgrey > volume #9 color silver > transparency #9 80 > volume #9 color darkgrey > transparency #9 80 > volume #9 color #929292 > transparency #9 80 > volume #9 color #919191 > transparency #9 80 > volume #9 color #929292 > transparency #9 80 > volume #9 color #919191 > transparency #9 80 > show #!3#!5.2-3 atoms > hide #!3#!5.2-3 atoms > show #!3#!5.2-3 atoms > nucleotides #!3#!5.2-3 atoms > style nucleic & #!3#!5.2-3 stick Changed 0 atom styles > style #!3#!5.2-3 stick Changed 15418 atom styles > style #!3#!5.2-3 sphere Changed 15418 atom styles > style #!3#!5.2-3 ball Changed 15418 atom styles > style #!3#!5.2-3 stick Changed 15418 atom styles > hide #!3#!5.2-3 atoms > show #!3#!5.2-3 cartoons > nucleotides #!3#!5.2-3 atoms > style nucleic & #!3#!5.2-3 stick Changed 0 atom styles > style #!3#!5.2-3 stick Changed 15418 atom styles > style #!3#!5.2-3 sphere Changed 15418 atom styles > style #!3#!5.2-3 ball Changed 15418 atom styles > show #!3#!5.2-3 surfaces > hide #!3#!5.2-3 surfaces > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs > transparency #3.2#9.1#5.2.2-3#5.3.2-3 0 > transparency #3.2#9.1#5.2.2-3#5.3.2-3 50 > transparency #9 80 > volume #!9 style image > volume #!9 style mesh > volume #!9 style surface > ui mousemode right ""contour level"" > volume #9 level 0.007048 > volume #9 level 0.006338 > hide #!5.3 models > show #!5.3 models > hide #!5.2 models > hide #!3 models > show #!3 models > show #!5.2 models > hide #!5.3 models > show #!5.3 models > hide #!5.2 models > save /Users/miao/Desktop/image10.png supersample 3 > turn x 90 > turn x -90 > save /Users/miao/Desktop/image11.png supersample 3 > save /Users/miao/Desktop/paper/Figs2021Apr/20210516_mergeB_ears.cxs ——— End of log from Mon May 17 05:23:44 2021 ——— opened ChimeraX session > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.01372 > show #!5.2 models > show #!5.5 models > show #!5.7 models > hide #!5.7 models > show #!4 models > hide #!1 models > hide #!5.5 models > hide #!5.3 models > hide #!5.2 models > hide #!5 models > show #!1 models > hide #!3 models > select #1 2 models selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 3 maps. > hide #!9 models > fitmap #1 inMap #4 Fit map whole-j532post copy.mrc in map C2E-j542post copy.mrc using 267974 points correlation = 0.8925, correlation about mean = 0.233, overlap = 88.55 steps = 52, shift = 0.0745, angle = 0.823 degrees Position of whole-j532post copy.mrc (#1) relative to C2E-j542post copy.mrc (#4) coordinates: Matrix rotation and translation 0.99605318 -0.06260193 0.06292113 1.10025049 0.06056904 0.99759447 0.03371449 -15.97237620 -0.06488036 -0.02977035 0.99744888 16.83278718 Axis -0.33677830 0.67796924 0.65340500 Axis point 261.46509857 0.00000000 -0.01120204 Rotation angle (degrees) 5.40833613 Shift along axis -0.20069295 > hide #!4 models > hide #!1 models > ~select #1 Nothing selected > show #!1 models > show #!4 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > hide #!1 models > hide #!4 models > show #!1 models > show #8 models > hide #8 models > show #!9 models > show #!6 models > hide #!6 models > show #!6 models > hide #!9 models > hide #!1 models > hide #!6 models > show #!9 models > show #!5.7 models > hide #!5.7 models > show #!5.5 models > hide #!5.5 models > show #!5.3 models > show #!5.2 models > show #5.4 models > hide #5.4 models > show #5.6 models > hide #5.6 models > show #!3 models > save /Users/miao/Desktop/paper/Figs2021Apr/20210518_mergeB_ears.cxs ——— End of log from Tue May 18 20:24:40 2021 ——— opened ChimeraX session > show #!4 models > hide #!9 models > color #4 silver models > transparency #4 50 > save /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears-BT.cxs ——— End of log from Wed May 19 14:45:04 2021 ——— opened ChimeraX session > open /Users/miao/Desktop/paper/Figs2021Apr/AccA_Phyre.pdb Chain information for AccA_Phyre.pdb #10 --- Chain | Description ? | No description available > ui tool show Matchmaker > matchmaker #10 to #5.2 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 j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain (blank) (#10), sequence alignment score = 1919.8 RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs: 6.902) [Repeated 1 time(s)] > select #10 4440 atoms, 4522 bonds, 597 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #10,0.51245,0.38099,0.76957,236.6,0.52009,-0.85082,0.074882,85.912,0.6833,0.36188,-0.63416,110.19 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.49506,-0.23949,0.8352,188.08,0.63051,-0.56235,-0.53499,93.526,0.5978,0.79146,-0.12739,158.02 > view matrix models > #10,0.30136,-0.57379,-0.76154,114.73,0.38514,0.80388,-0.45327,203.55,0.87227,-0.1567,0.46324,100.73 > view matrix models > #10,0.27538,-0.38807,-0.87953,126.19,0.396,0.87947,-0.26405,215.01,0.87598,-0.27558,0.39586,89.297 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.27538,-0.38807,-0.87953,99.696,0.396,0.87947,-0.26405,223.68,0.87598,-0.27558,0.39586,100.45 > view matrix models > #10,0.27538,-0.38807,-0.87953,98.938,0.396,0.87947,-0.26405,223.18,0.87598,-0.27558,0.39586,99.648 > view matrix models > #10,0.27538,-0.38807,-0.87953,99.074,0.396,0.87947,-0.26405,223.31,0.87598,-0.27558,0.39586,99.854 > matchmaker #10 to #5.2 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 j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain (blank) (#10), sequence alignment score = 1919.8 RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs: 6.902) [Repeated 1 time(s)] > save /Users/miao/Desktop/paper/Figs2021Apr/20210518_ears'-discard.cxs ——— End of log from Sun May 23 03:46:49 2021 ——— opened ChimeraX session > open /Users/miao/Desktop/paper/Figs2021Apr/AccA_Phyre.pdb Chain information for AccA_Phyre.pdb #11 --- Chain | Description ? | No description available > ui tool show Matchmaker > matchmaker #11/? to #5.2/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker j532_fitall copy.pdb, chain A (#5.2) with AccA_Phyre.pdb, chain (blank) (#11), sequence alignment score = 1919.8 RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs: 6.902) [Repeated 1 time(s)]No reference and/or match structure/chain chosen > matchmaker #11/? to #5.2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker j532_fitall copy.pdb, chain B (#5.2) with AccA_Phyre.pdb, chain (blank) (#11), sequence alignment score = 1919.8 RMSD between 312 pruned atom pairs is 0.993 angstroms; (across all 451 pairs: 6.902) [Repeated 1 time(s)]Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.14 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 203.0.0.0.0 SMC Version (system): 2.43f6 Software: System Software Overview: System Version: macOS 10.14.6 (18G2022) Kernel Version: Darwin 18.7.0 Time since boot: 1 day 1:39 Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No U28D590: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.1.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.18 ChimeraX-AtomicLibrary: 3.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.3 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202104240152 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.2.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.3 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.5 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.8 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.7 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}} " defect closed normal Structure Comparison duplicate all ChimeraX