id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18613 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x000000020abb20c0 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=16.8G written=352.7M(2%) resident=7614K(0%) swapped_out=345.2M(2%) unallocated=16.5G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 3168K 72 \nCG raster data 480K 10 \nColorSync 704K 38 \nCoreAnimation 3568K 165 \nCoreGraphics 48K 3 \nCoreImage 64K 2 \nCoreServices 624K 2 \nCoreUI image data 4720K 38 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 15.4G 242 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 39 \nStack 207.8M 39 \nVM_ALLOCATE 810.8M 710 \nVM_ALLOCATE (reserved) 384.0M 3 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 36.4M 1160 \n__DATA_CONST 38.0M 1169 \n__DATA_DIRTY 2777K 343 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 654.8M 220 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1153 \n__TEXT (graphics) 6304K 37 \n__TPRO_CONST 128K 2 \ndyld private memory 10.5M 86 \nmapped file 623.0M 115 \npage table in kernel 7614K 1 \nshared memory 3328K 34 \n=========== ======= ======= \nTOTAL 19.7G 7359 \nTOTAL, minus reserved VM space 19.3G 7359 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""127103aa6144a871a8c1969393be6d55507741e2"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/chenxi/Desktop/0817_lipf/7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb > format pdb Chain information for 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1 --- Chain | Description A B C | No description available > open /Users/chenxi/Desktop/PDB/7wlt.pdb format pdb 7wlt.pdb title: The curved structure of MPIEZO1 In lipid bilayer [more info...] Chain information for 7wlt.pdb #2 --- Chain | Description | UniProt A C E | protein FAM38A | PIEZ1_MOUSE 1-2547 Non-standard residues in 7wlt.pdb #2 --- P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE) PLX — (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol > open > /Users/chenxi/Desktop/0817_lipf/rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb > format pdb Chain information for rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3 --- Chain | Description A B C | No description available > open > /Users/chenxi/Desktop/0808rhlip_all/rhlipc0808/rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb > format pdb Chain information for rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4 --- Chain | Description A B C | No description available > open /Users/chenxi/Desktop/PDB/8ixo.pdb format pdb 8ixo.pdb title: Intermediate structure of MPIEZO1-S2472E [more info...] Chain information for 8ixo.pdb #5 --- Chain | Description | UniProt A B F | protein FAM38A | PIEZ1_MOUSE 1-2547 Non-standard residues in 8ixo.pdb #5 --- P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE) PLX — (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > select #1-8: 2501-2547 6207 atoms, 6297 bonds, 705 residues, 5 models selected > ui tool show Matchmaker > matchmaker #!2-5 & sel to #1 & sel Computing secondary structure 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 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 233.4 RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs: 0.953) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 215.4 RMSD between 45 pruned atom pairs is 1.182 angstroms; (across all 47 pairs: 1.253) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4), sequence alignment score = 232.8 RMSD between 44 pruned atom pairs is 0.736 angstroms; (across all 47 pairs: 1.064) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 8ixo.pdb, chain A (#5), sequence alignment score = 230.4 RMSD between 44 pruned atom pairs is 0.727 angstroms; (across all 47 pairs: 1.079) > cartoon style sel modeHelix tube sides 20 > set bgColor white > color #1 #ffb48cff > color #1 #ffca8cff > color #1 #ffca80ff > color #2 #90ceebff > color #2 #90b3ebff > color #2 #90b3ffff > select add #1 39729 atoms, 40584 bonds, 39 pseudobonds, 5061 residues, 6 models selected > select subtract #1 4968 atoms, 5040 bonds, 564 residues, 4 models selected > select add #2 37632 atoms, 38481 bonds, 33 pseudobonds, 4509 residues, 6 models selected > select subtract #2 3720 atoms, 3774 bonds, 423 residues, 3 models selected > select add #3 36756 atoms, 37572 bonds, 45 pseudobonds, 4728 residues, 4 models selected > select subtract #3 2481 atoms, 2517 bonds, 282 residues, 2 models selected > select add #4 38838 atoms, 39771 bonds, 36 pseudobonds, 4680 residues, 3 models selected > select subtract #4 1233 atoms, 1251 bonds, 141 residues, 1 model selected > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > select subtract #5 Nothing selected > color #2 #29b3ffff > color #2 #299dffff > color #2 #299d8fff > color #2 #29728fff > color #2 #297270ff > color #2 #299d70ff > color #2 #299d8fff > color #2 #309d8fff > color #2 #3a9d8fff > color #2 #759d8fff > color #2 #209d8fff > color #2 #20918fff > color #2 #20919cff > color #2 #209182ff > color #3 #90a0ddff > color #3 #90b3ddff > color #3 #90b3ffff > color #4 #20ee90ff > color #4 #209190ff > color #4 #209182ff > color #2 #9e9a9aff > color #2 #c6c2c1ff > color #2 #b6b1b1ff > color #2 #ada9a8ff > color #5 #f28072ff > color #5 #f2a772ff > color #5 #f2a7bcff > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > view orient > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5.1 models > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > select #3: 2116-2492 8721 atoms, 8946 bonds, 9 pseudobonds, 1089 residues, 2 models selected > select ~sel & ##selected 25554 atoms, 26109 bonds, 36 pseudobonds, 3357 residues, 2 models selected > hide sel cartoons > show #!1 models > hide #!3 models > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > select #1: 2116-2492 8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected > select ~sel & ##selected 26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected > hide sel cartoons > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > show #!3 models > select #1: 2476 21 atoms, 18 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color sel indian red > select #3: 2476 21 atoms, 18 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color sel indian red > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > lighting soft > lighting full > lighting simple > lighting shadows true > lighting flat > graphics silhouettes false > graphics silhouettes true > hide #!1,3 atoms > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > lighting full > lighting soft > view orient > turn z 50 > turn y 50 > view orient > turn y 90 > turn z 90 > turn x 5 > turn x -5 > turn y 5 > select #1 and #3 2185-2213 Expected a keyword > select #1, #3: 2185-2213 Expected an objects specifier or a keyword > select #1 and #3: 2185-2213 Expected a keyword > select #1: 2185-2213 702 atoms, 720 bonds, 87 residues, 1 model selected > transparency 50 > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > turn y 5 > ui tool show ""Side View"" > ui dockable false ""Side View"" > save /Users/chenxi/Desktop/RH-figure/change/rhlf-wtlf.png width 2000 height > 1468 supersample 3 transparentBackground true > hide #!1 models > show #!5 models > select #5: 2116-2492 8814 atoms, 9045 bonds, 3 pseudobonds, 1101 residues, 2 models selected > select ~sel & ##selected 23298 atoms, 23754 bonds, 36 pseudobonds, 3099 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #5: 2476 21 atoms, 18 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color sel indian red > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > select subtract #5 Nothing selected > save /Users/chenxi/Desktop/RH-figure/change/rhlf-se.png width 2000 height > 1468 supersample 3 transparentBackground true > turn z 90 > turn z -90 > turn x 90 > ui tool show ""Side View"" > save /Users/chenxi/Desktop/RH-figure/change/rhlf-se-cap.png width 2000 > height 1468 supersample 3 transparentBackground true > hide #!5 models > show #!1 models > save /Users/chenxi/Desktop/RH-figure/change/rhlf-wtlf-cap.png width 2000 > height 1468 supersample 3 transparentBackground true > ui tool show ""Side View"" > turn x -90 > ui tool show ""Side View"" > show #!5 models > hide #!3 models > hide #!1 models > show #!1 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > hide #!5 models > ui mousemode right select Drag select of 1155 residues, 6 pseudobonds > select ~sel & ##selected 26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected > select ~sel & ##selected 8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected > hide sel atoms > hide sel cartoons > select ~sel & ##selected 26037 atoms, 26595 bonds, 33 pseudobonds, 3408 residues, 2 models selected > hide sel cartoons > show sel cartoons > ui tool show ""Side View"" > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > show #!5 models > ui tool show ""Side View"" > view orient > turn x -90 > turn y 5 > turn y -5 > turn y 5 > show #!2 models > hide #!2 models > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting soft > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting simple > lighting soft > save ""/Users/chenxi/Desktop/RH-figure/model align/sehole+rhlf.png"" width > 2000 height 1468 supersample 3 transparentBackground true > log metadata #5 Metadata for 8ixo.pdb #5 --- Title | Intermediate structure of MPIEZO1-S2472E Citation | AN intermediate open structure reveals the gating transitionof the mechanically activated PIEZO1 channel. PMID: 39719701 Non-standard residues | P5S — O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine (phosphatidyl serine) PEE — 1,2-dioleoyl-Sn-glycero-3-phosphoethanolamine (DOPE) PLX — (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol Gene source | Mus musculus (house mouse) Experimental method | Electron microscopy Resolution | 4.00Å > log chains #5 Chain information for 8ixo.pdb #5 --- Chain | Description | UniProt A B F | protein FAM38A | PIEZ1_MOUSE 1-2547 > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!5 models > hide #!2.1 models > hide #!2 atoms > show #!1 models > hide #!1 models > show #!1 models > hide #1.1 models > hide #3.1 models > hide #4.1 models > hide #!1 models > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlt.png"" width 894 height > 656 supersample 3 > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlt.png"" width 2000 > height 1468 supersample 3 transparentBackground true > open /Users/chenxi/Desktop/PDB/8yfg_hp1_RH_mdfic.pdb 8yfg_hp1_RH_mdfic.pdb title: Human PIEZO1-R2456H_mdfic [more info...] Chain information for 8yfg_hp1_RH_mdfic.pdb #6 --- Chain | Description | UniProt A B D | piezo-type mechanosensitive ion channel component 1 | PIEZ1_HUMAN 1-2521 C E F | myod family inhibitor domain-containing protein | MDFIC_HUMAN 2-247 > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > hide sel surfaces > hide (#!6 & sel) target a > show sel cartoons > hide sel atoms > cartoon style (#!6 & sel) modeHelix tube sides 20 > select #1-6: 2116-2492 52605 atoms, 53946 bonds, 27 pseudobonds, 6609 residues, 12 models selected > ui tool show Matchmaker > matchmaker #!2-6 & sel to #1 & sel Computing secondary structure 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 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 1801.5 RMSD between 254 pruned atom pairs is 0.701 angstroms; (across all 363 pairs: 2.467) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 1756.8 RMSD between 203 pruned atom pairs is 0.938 angstroms; (across all 363 pairs: 15.989) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4), sequence alignment score = 1798.8 RMSD between 239 pruned atom pairs is 1.053 angstroms; (across all 363 pairs: 2.319) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 8ixo.pdb, chain B (#5), sequence alignment score = 1754.3 RMSD between 220 pruned atom pairs is 0.715 angstroms; (across all 361 pairs: 9.420) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 1473.7 RMSD between 164 pruned atom pairs is 1.284 angstroms; (across all 340 pairs: 11.113) > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #1-6: 2501-2547 6762 atoms, 6864 bonds, 768 residues, 6 models selected > ui tool show Matchmaker > matchmaker #!1,3-6 & sel to #2 & sel Computing secondary structure 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 7wlt.pdb, chain A (#2) with 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1), sequence alignment score = 233.4 RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs: 0.953) Matchmaker 7wlt.pdb, chain A (#2) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 229.8 RMSD between 42 pruned atom pairs is 0.993 angstroms; (across all 47 pairs: 1.286) Matchmaker 7wlt.pdb, chain A (#2) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4), sequence alignment score = 240.6 RMSD between 47 pruned atom pairs is 0.343 angstroms; (across all 47 pairs: 0.343) Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence alignment score = 244.8 RMSD between 47 pruned atom pairs is 0.506 angstroms; (across all 47 pairs: 0.506) Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 101.9 RMSD between 20 pruned atom pairs is 0.385 angstroms; (across all 21 pairs: 1.216) > select add #1 40284 atoms, 41151 bonds, 39 pseudobonds, 5124 residues, 7 models selected > select add #2 72948 atoms, 74592 bonds, 72 pseudobonds, 9069 residues, 9 models selected > select subtract #1 38187 atoms, 39048 bonds, 33 pseudobonds, 4572 residues, 7 models selected > select subtract #2 4275 atoms, 4341 bonds, 486 residues, 4 models selected > select add #2 38187 atoms, 39048 bonds, 33 pseudobonds, 4572 residues, 7 models selected > select subtract #2 4275 atoms, 4341 bonds, 486 residues, 4 models selected > select add #3 37311 atoms, 38139 bonds, 45 pseudobonds, 4791 residues, 5 models selected > select subtract #3 3036 atoms, 3084 bonds, 345 residues, 3 models selected > select add #4 39393 atoms, 40338 bonds, 36 pseudobonds, 4743 residues, 4 models selected > select subtract #4 1788 atoms, 1818 bonds, 204 residues, 2 models selected > select add #5 32667 atoms, 33366 bonds, 39 pseudobonds, 4263 residues, 4 models selected > select subtract #5 555 atoms, 567 bonds, 63 residues, 1 model selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > color #6 #ffdbcaff > color #6 #fcd9c8ff > show #!5 models > hide #!2 models > color #6 #fcbca1ff > color #6 #fc6f9aff > color #6 #fc7e6dff > color #6 #d76b5dff > color #6 #c76356ff > color #6 #c75851ff > color #6 #c74d47ff > color #6 #c7708eff > color #6 #c75655ff > color #6 #c74743ff > color #6 #c74f5cff > color #6 #c74641ff > color #6 #853ac7ff > color #6 #6f41c7ff > color #6 #ac76c7ff > color #6 #c7605dff > color #6 #c75956ff > color #6 #c7565bff > color #6 #52c7b0ff > show #!4 models > hide #!4 models > color #6 #72c7bdff > show #!4 models > hide #!4 models > color #6 #c75e59ff > color #6 #c74142ff > color #6 #c74e58ff > color #6 #c74738ff > show #!4 models > hide #!4 models > color #6 #c7c5c1ff > color #6 #bfc7c1ff > show #!2 models > hide #!2 models > color #6 #c4c7c2ff > color #6 #cdd0cbff > color #6 #fcfff9ff > show #!2 models > hide #!2 models > color #6 #73ff77ff > color #6 #b5ffbeff > color #6 #c7ffb3ff > color #6 #c1ffc0ff > color #6 #acffa3ff > color #6 #fa6956ff > color #6 #faf3acff > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > ui tool show ""Color Actions"" > color sel indian red > color sel dim gray > color sel dark goldenrod > color sel rosy brown > color sel burly wood > color sel blue violet > color sel yellow green > color sel olive > color sel chartreuse > color sel yellow green > color sel dark khaki > color sel indian red > color sel saddle brown > color sel sienna > color sel coral > color sel cornflower blue > color sel peru > color sel yellow green > color sel dark goldenrod > color sel salmon > color sel indian red > color sel salmon > color sel indian red > color sel sea green > color sel dark sea green > show #!4 models > color sel gainsboro > show #!2 models > color #2 #7b7a7aff > color #2 #939292ff > hide #!5 models > hide #!4 models > select subtract #6 Nothing selected > color #6 #fdffffff > hide #6.1 models > show #!5 models > hide #!5 models > hide #!6 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > color #2 #b1b1b1ff > show #!6 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!6 models > show #!6 models > hide #!2 models > show #!2 models > hide #!6 models > show #!6 models > hide #!2 models > show #!2 models > show #!4 models > show #!5 models > hide #!5 models > color #4 #54ada4ff > hide #!4 models > hide #!2 models > show #!3 models > hide #!6 models > show #!6 models > view orient > turn z 90 > turn x 90 > turn x 180 > turn y 5 > hide #!6 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > show #!5 models > show #!1 models > hide #!1 models > show #!1 models > turn y -5 > hide #!1 models > show #!2 models > hide #!5 models > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlt.png"" width 2000 > height 1468 supersample 3 transparentBackground true > show #!6 models > color #6 #bfffbaff > color #6 #64ffa6ff > color #6 #cfff46ff > color #6 #ecff78ff > color #6 #ff7e75ff > color #6 #ff847eff > color #6 #ff7c7bff > show #!5 models > hide #!5 models > color #6 #e87070ff > color #6 #df6c6cff > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > ui tool show ""Color Actions"" > color sel indian red > select subtract #6 Nothing selected > color #2 #ccccccff > color #2 silver > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!6 models > show #!5 models > show #!1 models > save ""/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png"" width > 2000 height 1468 supersample 3 transparentBackground true > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!5 models Drag select of 1140 residues > undo > hide #!5 models > hide #!3 models > show #!5 models > show #!1 models > select #1-6: 2476 138 atoms, 120 bonds, 18 residues, 6 models selected > color (#!1,5 & sel) red > select add #1 34878 atoms, 35646 bonds, 39 pseudobonds, 4512 residues, 7 models selected > select subtract #1 117 atoms, 102 bonds, 15 residues, 5 models selected > select clear > save ""/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png"" width > 2000 height 1468 supersample 3 transparentBackground true > hide #!1 models > hide #!5 models > show #!3 models Drag select of 1155 residues > hide sel cartoons > select ~sel & ##selected 25554 atoms, 26109 bonds, 36 pseudobonds, 3357 residues, 2 models selected > show sel cartoons > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > show #!5 models > save ""/Users/chenxi/Desktop/RH-figure/model align/sehole+rhlf.png"" width > 2000 height 1468 supersample 3 transparentBackground true > hide #!3 models > hide #!5 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > select #1-6: 2476 138 atoms, 120 bonds, 18 residues, 6 models selected > color sel red > select clear > hide #!1 models > hide #!3 models > hide #!2 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > show #!6 models > show #!2 models > hide #!6 models > show #!6 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!6 models > show #!6 models > show #!3 models > hide #!3 models > hide #!6 models > show #!4 models > show #!6 models > hide #!6 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!6 models > save ""/Users/chenxi/Desktop/RH-figure/model align/8yfg+7wlt.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!6 models > show #!6 models > hide #!6 models > hide #!2 models > show #!2 models > hide #!2 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > show #!1 models > show sel cartoons > select subtract #1 Nothing selected > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlu.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!1 models > show #!3 models > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > show sel cartoons > select subtract #3 Nothing selected > hide #!3 models > show #!3 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 atoms > show #!5 models > hide #!5 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlc.png"" width 894 height > 656 supersample 3 > hide #!4 models > show #!4 models > show #!2 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlc+7wlt.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!4 models > hide #!2 models > show #!1 models > show #!3 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!1 models > show #!5 models > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > show sel cartoons > select subtract #5 Nothing selected > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png"" width 2000 > height 1468 supersample 3 transparentBackground true > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > show #!6 models > hide #!3 models > hide #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > open /Users/chenxi/Desktop/mP1-RH-detergent/RH-full- > length/RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb > format pdb Chain information for RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7 --- Chain | Description A B C | No description available > hide #!7 models > show #!7 models > hide #!3 models > hide #!5 models > hide #!7 surfaces > hide #7 target a > show #!7 cartoons > cartoon style #7 modeHelix tube sides 20 > hide #7.1 models > hide #!7 models > show #!7 models > select add #7 45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected > ui tool show ""Color Actions"" > color sel thistle > color sel plum > color sel gainsboro > color sel medium purple > color sel purple > color sel thistle > color #7 #cfb1deff > color #7 #c69fdeff > color #7 #c5afdeff > color #7 #c1abdaff > color #7 #b399daff > color #7 #b4a0daff > color #7 #ad96daff > color #7 #ad98daff > select subtract #7 Nothing selected > hide #!7 models > select #1-7: 2501-2547 8010 atoms, 8130 bonds, 909 residues, 7 models selected > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > view orient > ui tool show Matchmaker > matchmaker #!1,3-7 & sel to #2 & sel Computing secondary structure 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 7wlt.pdb, chain A (#2) with 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1), sequence alignment score = 233.4 RMSD between 44 pruned atom pairs is 0.675 angstroms; (across all 47 pairs: 0.953) Matchmaker 7wlt.pdb, chain A (#2) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 229.8 RMSD between 42 pruned atom pairs is 0.993 angstroms; (across all 47 pairs: 1.286) Matchmaker 7wlt.pdb, chain A (#2) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4), sequence alignment score = 240.6 RMSD between 47 pruned atom pairs is 0.343 angstroms; (across all 47 pairs: 0.343) Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence alignment score = 244.8 RMSD between 47 pruned atom pairs is 0.506 angstroms; (across all 47 pairs: 0.506) Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 101.9 RMSD between 20 pruned atom pairs is 0.385 angstroms; (across all 21 pairs: 1.216) Matchmaker 7wlt.pdb, chain A (#2) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb, chain A (#7), sequence alignment score = 233.4 RMSD between 47 pruned atom pairs is 0.329 angstroms; (across all 47 pairs: 0.329) > select clear > hide #!1 models > hide #!2 models > hide #!4 models > hide #!6 models > hide #!7 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!5 models > show #!5 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > view orient > turn x 90 > turn x 180 > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > turn y -20 > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!5 models > hide #!3 models > show #!3 models > turn y 5 > show #!2 models > hide #!3 models > show #!3 models > turn y -5 > hide #!5 models > hide #!3 models > hide #!2 models > show #!3 models > show #!2 models > show #!5 models > hide #!2 models > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > select clear > ui mousemode right ""rotate selected models"" > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > view matrix models > #5,0.6268,-0.77847,0.033399,220.59,-0.77721,-0.62768,-0.044291,490.46,0.055443,0.0018034,-0.99846,424.49 > select subtract #5 Nothing selected > select #1-7: 2490-2547 9909 atoms, 10086 bonds, 1140 residues, 7 models selected > ui tool show Matchmaker > matchmaker #!2-7 & sel to #1 & sel ssFraction false Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 301 RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs: 1.091) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 301 RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs: 1.301) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4), sequence alignment score = 301 RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs: 1.170) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 8ixo.pdb, chain A (#5), sequence alignment score = 301 RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs: 1.216) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 161 RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs: 1.523) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb, chain A (#1) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb, chain A (#7), sequence alignment score = 301 RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs: 1.062) > hide #!3 models > show #!3 models > ui tool show Matchmaker > matchmaker #!2-7 & sel to #1 & sel alg Smith-Waterman ssFraction false > showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Smith-Waterman Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with 7wlt.pdb (#2), sequence alignment score = 301 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 7wlt.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs: 1.091) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb (#3), sequence alignment score = 301 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs: 1.301) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb (#4), sequence alignment score = 301 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs: 1.170) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with 8ixo.pdb (#5), sequence alignment score = 301 Alignment identifier is 4 Showing conservation header (""seq_conservation"" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 8ixo.pdb #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs: 1.216) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with 8yfg_hp1_RH_mdfic.pdb (#6), sequence alignment score = 161 Alignment identifier is 5 Showing conservation header (""seq_conservation"" residue attribute) for alignment 5 Hiding conservation header for alignment 5 Chains used in RMSD evaluation for alignment 5: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, 8yfg_hp1_RH_mdfic.pdb #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs: 1.523) Matchmaker 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb (#1) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb (#7), sequence alignment score = 301 Alignment identifier is 6 Showing conservation header (""seq_conservation"" residue attribute) for alignment 6 Hiding conservation header for alignment 6 Chains used in RMSD evaluation for alignment 6: 7wlu0815_ncs74-coot-1-ref75-withlipid-2.pdb #1/A, RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 6 RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs: 1.062) > select #1/A:2541 #7/A:2541 18 atoms, 16 bonds, 2 residues, 2 models selected > show #!1 models > show #!2 models > show #!4 models > show #!6 models > show #!7 models > select add #1 34770 atoms, 35552 bonds, 39 pseudobonds, 4498 residues, 3 models selected > select subtract #1 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7 45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected > select subtract #7 Nothing selected > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > show #!7 models > show #!6 models > hide #!6 models > hide #!7 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!3 models > hide #!5 models > show #!4 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > show #!3 models > show #!5 models > show #!6 models > show #!7 models > select #1-7: 2490-2547 9909 atoms, 10086 bonds, 1140 residues, 7 models selected > ui tool show ""Similar Structures"" > ui tool show Matchmaker > select add #1 43164 atoms, 44097 bonds, 39 pseudobonds, 5463 residues, 8 models selected > select add #2 75561 atoms, 77262 bonds, 72 pseudobonds, 9375 residues, 10 models selected > select add #3 108330 atoms, 110784 bonds, 117 pseudobonds, 13647 residues, 11 models selected > select subtract #3 74055 atoms, 75729 bonds, 72 pseudobonds, 9201 residues, 9 models selected > select clear > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > rename chain C to B #1 Missing or invalid ""models"" argument: invalid models specifier > rename #1 chain C to B Expected a keyword > rename #1 chainC to B Expected a keyword > rename #1 chainC B Expected a keyword > ui tool show ""Change Chain IDs"" > changechains #* B Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (B/576/) > rename #1 chainC > ui tool show ""Change Chain IDs"" > select #1/C 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > changechains sel B Proposed chainID change conflicts with existing residue chainC #1/B GLU 576 > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > show #!1 models > select #1/B 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > show #!2 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > hide #!2 models > changechains C D Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (D/576/) > select #1/ B 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel D Chain IDs of 1499 residues changed > select #1/ C 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 1499 residues changed > select #1/ D 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1499 residues changed > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!5 models > show #!6 models > hide #!6 models > show #!2 models > hide #!2 models > show #!3 models > select #3/ B 11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel D Chain IDs of 1482 residues changed > select #3/ C 11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 1482 residues changed > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 0 residues changed > select #3/ D 11425 atoms, 11685 bonds, 15 pseudobonds, 1482 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1482 residues changed > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > select #5/ F 10704 atoms, 10933 bonds, 13 pseudobonds, 1400 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1400 residues changed > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > hide #!5 models > select subtract #5 Nothing selected > show #!6 models > select #6/ D 10394 atoms, 10647 bonds, 15 pseudobonds, 1280 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1280 residues changed > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > hide #!6 models > show #!7 models > select #7/ B 14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel D Chain IDs of 1848 residues changed > select #7/ B Nothing selected > select #7/ C 14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected > ui tool show ""Renumber Residues"" > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 1848 residues changed > select #7/ D 14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1848 residues changed > select add #7 45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected > select subtract #7 Nothing selected > hide #!7 models > show #!1 models > rename #1 7wlu-rechain > matchmaker #2-7 to #1 :2490-2547 Computing secondary structure 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 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 280.3 RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs: 1.091) Matchmaker 7wlu-rechain, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 268.3 RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs: 1.301) Matchmaker 7wlu-rechain, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4), sequence alignment score = 288.7 RMSD between 55 pruned atom pairs is 0.970 angstroms; (across all 58 pairs: 1.172) Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence alignment score = 277.3 RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs: 1.216) Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 273.4 RMSD between 50 pruned atom pairs is 0.747 angstroms; (across all 58 pairs: 1.460) Matchmaker 7wlu-rechain, chain A (#1) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb, chain A (#7), sequence alignment score = 272.5 RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs: 1.062) > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > hide #!3 models > show #!1 models > show #!3 models > select #1: 2490-2547 1506 atoms, 1533 bonds, 174 residues, 1 model selected > select #1-7: 2490-2547 9909 atoms, 10086 bonds, 1140 residues, 7 models selected > ui tool show Matchmaker > matchmaker #!2-7 & sel to #1 & sel ssFraction false showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 301 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: 7wlu-rechain #1/A, 7wlt.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs: 1.091) Matchmaker 7wlu-rechain, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 301 Alignment identifier is 5 Showing conservation header (""seq_conservation"" residue attribute) for alignment 5 Hiding conservation header for alignment 5 Chains used in RMSD evaluation for alignment 5: 7wlu-rechain #1/A, rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs: 1.301) Matchmaker 7wlu-rechain, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain A (#4), sequence alignment score = 301 Alignment identifier is 6 Showing conservation header (""seq_conservation"" residue attribute) for alignment 6 Hiding conservation header for alignment 6 Chains used in RMSD evaluation for alignment 6: 7wlu-rechain #1/A, rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 6 RMSD between 54 pruned atom pairs is 0.933 angstroms; (across all 58 pairs: 1.170) Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence alignment score = 301 Alignment identifier is 7 Showing conservation header (""seq_conservation"" residue attribute) for alignment 7 Hiding conservation header for alignment 7 Chains used in RMSD evaluation for alignment 7: 7wlu-rechain #1/A, 8ixo.pdb #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 7 RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs: 1.216) Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 161 Alignment identifier is 8 Showing conservation header (""seq_conservation"" residue attribute) for alignment 8 Hiding conservation header for alignment 8 Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A, 8yfg_hp1_RH_mdfic.pdb #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 8 RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs: 1.523) Matchmaker 7wlu-rechain, chain A (#1) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb, chain A (#7), sequence alignment score = 301 Alignment identifier is 9 Showing conservation header (""seq_conservation"" residue attribute) for alignment 9 Hiding conservation header for alignment 9 Chains used in RMSD evaluation for alignment 9: 7wlu-rechain #1/A, RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #7/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 9 RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs: 1.062) > matchmaker #2-7/A,B,C:50-100 to #1/A,B,C:50-100 No 'to' model specified > matchmaker #2-7 /A,B,C: 2490-2547 to #1/ A,B,C: 2490-2547 Computing secondary structure 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 7wlu-rechain, chain A (#1) with 7wlt.pdb, chain A (#2), sequence alignment score = 280.3 RMSD between 55 pruned atom pairs is 0.927 angstroms; (across all 58 pairs: 1.091) Matchmaker 7wlu-rechain, chain A (#1) with rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb, chain A (#3), sequence alignment score = 268.3 RMSD between 52 pruned atom pairs is 1.076 angstroms; (across all 58 pairs: 1.301) Matchmaker 7wlu-rechain, chain A (#1) with rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb, chain C (#4), sequence alignment score = 288.7 RMSD between 55 pruned atom pairs is 0.970 angstroms; (across all 58 pairs: 1.172) Matchmaker 7wlu-rechain, chain A (#1) with 8ixo.pdb, chain A (#5), sequence alignment score = 277.3 RMSD between 51 pruned atom pairs is 0.764 angstroms; (across all 58 pairs: 1.216) Matchmaker 7wlu-rechain, chain A (#1) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 140.3 RMSD between 29 pruned atom pairs is 0.658 angstroms; (across all 32 pairs: 1.523) Matchmaker 7wlu-rechain, chain A (#1) with RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb, chain A (#7), sequence alignment score = 272.5 RMSD between 56 pruned atom pairs is 0.951 angstroms; (across all 58 pairs: 1.062) > show #!4 models > hide #!3 models > select #1-7: 2490-2547 9909 atoms, 10086 bonds, 1140 residues, 7 models selected > select ~sel 239871 atoms, 245531 bonds, 288 pseudobonds, 30102 residues, 16 models selected > hide sel & #!1,4 cartoons > view orient > hide #!4 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > show #!3 models > show #!2 models > show #!5 models > show #!6 models > show #!7 models > select #1-7: 2490-2547 9909 atoms, 10086 bonds, 1140 residues, 7 models selected > select ~sel 239871 atoms, 245531 bonds, 288 pseudobonds, 30102 residues, 16 models selected > hide sel cartoons > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > show #!3 models > show #!1 models > view orient > select add #1 241377 atoms, 247067 bonds, 288 pseudobonds, 30276 residues, 16 models selected > select add #2 242892 atoms, 248612 bonds, 288 pseudobonds, 30450 residues, 16 models selected > select subtract #2 208980 atoms, 213905 bonds, 255 pseudobonds, 26364 residues, 13 models selected > select clear Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > ui tool show Matchmaker > hide #!1 models > hide #!3 models > show #!2 models > show #!4 models > hide #!4 models > select #1/C 11587 atoms, 11848 bonds, 13 pseudobonds, 1499 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel B Proposed chainID change conflicts with existing residue 7wlu-rechain #1/B GLU 576 > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > select #2/C 11304 atoms, 11569 bonds, 11 pseudobonds, 1362 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 1362 residues changed > select #2/E 11304 atoms, 11569 bonds, 11 pseudobonds, 1362 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 1362 residues changed > select add #2 33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected > select subtract #2 Nothing selected > rename #3 rhlf-0814 > rename #4 rhlc > rename #7 rhdc > show #!3 models > hide #!3 models > hide #!2 models > show #!1 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > ui tool show Matchmaker > matchmaker #1/A#1/B#1/C to #2/A#2/B#2/C pairing ss ssFraction false > showAlignment true Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with 7wlu-rechain, chain A (#1), sequence alignment score = 7177 Alignment identifier is 10 Showing conservation header (""seq_conservation"" residue attribute) for alignment 10 Hiding conservation header for alignment 10 Chains used in RMSD evaluation for alignment 10: 7wlu-rechain #1/A, 7wlt.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 10 Matchmaker 7wlt.pdb, chain B (#2) with 7wlu-rechain, chain B (#1), sequence alignment score = 7177 Alignment identifier is 11 Showing conservation header (""seq_conservation"" residue attribute) for alignment 11 Hiding conservation header for alignment 11 Chains used in RMSD evaluation for alignment 11: 7wlu-rechain #1/B, 7wlt.pdb #2/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 11 Matchmaker 7wlt.pdb, chain C (#2) with 7wlu-rechain, chain C (#1), sequence alignment score = 7177 Alignment identifier is 12 Showing conservation header (""seq_conservation"" residue attribute) for alignment 12 Hiding conservation header for alignment 12 Chains used in RMSD evaluation for alignment 12: 7wlu-rechain #1/C, 7wlt.pdb #2/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 12 RMSD between 750 pruned atom pairs is 0.634 angstroms; (across all 3822 pairs: 24.058) > select clear > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > show #!2 models > hide #!1 models > ui tool show Matchmaker > matchmaker #3/A#3/B#3/C to #2/A#2/B#2/C pairing ss ssFraction false > showAlignment true Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with rhlf-0814, chain A (#3), sequence alignment score = 7066 Alignment identifier is 10 Showing conservation header (""seq_conservation"" residue attribute) for alignment 10 Hiding conservation header for alignment 10 Chains used in RMSD evaluation for alignment 10: 7wlt.pdb #2/A, rhlf-0814 #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 10 Matchmaker 7wlt.pdb, chain B (#2) with rhlf-0814, chain B (#3), sequence alignment score = 7066 Alignment identifier is 11 Showing conservation header (""seq_conservation"" residue attribute) for alignment 11 Hiding conservation header for alignment 11 Chains used in RMSD evaluation for alignment 11: 7wlt.pdb #2/B, rhlf-0814 #3/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 11 Matchmaker 7wlt.pdb, chain C (#2) with rhlf-0814, chain C (#3), sequence alignment score = 7066 Alignment identifier is 12 Showing conservation header (""seq_conservation"" residue attribute) for alignment 12 Hiding conservation header for alignment 12 Chains used in RMSD evaluation for alignment 12: 7wlt.pdb #2/C, rhlf-0814 #3/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 12 RMSD between 303 pruned atom pairs is 1.225 angstroms; (across all 3822 pairs: 30.759) > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > ui tool show Matchmaker > matchmaker #4/A#4/B#4/C to #2/A#2/B#2/C pairing ss ssFraction false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with rhlc, chain A (#4), sequence alignment score = 7252 Matchmaker 7wlt.pdb, chain B (#2) with rhlc, chain B (#4), sequence alignment score = 7252 Matchmaker 7wlt.pdb, chain C (#2) with rhlc, chain C (#4), sequence alignment score = 7252 RMSD between 1532 pruned atom pairs is 1.144 angstroms; (across all 4059 pairs: 6.889) > hide #!4 models > show #!5 models > ui tool show Matchmaker > matchmaker #5/A#5/B#5/C to #2/A#2/B#2/C pairing ss ssFraction false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with 8ixo.pdb, chain A (#5), sequence alignment score = 13421 Matchmaker 7wlt.pdb, chain B (#2) with 8ixo.pdb, chain B (#5), sequence alignment score = 13421 Matchmaker 7wlt.pdb, chain C (#2) with 8ixo.pdb, chain C (#5), sequence alignment score = 13421 RMSD between 453 pruned atom pairs is 0.925 angstroms; (across all 3747 pairs: 20.776) > ui tool show Matchmaker > show #!6 models > hide #!5 models > matchmaker #6/A#6/B#6/C to #2/A#2/B#2/C pairing ss ssFraction false Different number of reference/match chains (3 ref, 4 match) > select add #6.1 45 pseudobonds, 1 model selected > select subtract #6.1 Nothing selected > show #6.1 models > hide #6.1 models > select #6/ E 141 atoms, 141 bonds, 21 residues, 1 model selected > show sel cartoons > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > show sel cartoons > select subtract #6.1 31599 atoms, 32357 bonds, 3903 residues, 1 model selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > select #6/ E 141 atoms, 141 bonds, 21 residues, 1 model selected > select #6 : 2490-2547 852 atoms, 867 bonds, 96 residues, 1 model selected > select ~sel & ##selected 30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected > hide sel cartoons > view orient > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > matchmaker #6/A#6/B#6/C to #2/A#2/B#2/C pairing ss ssFraction false Different number of reference/match chains (3 ref, 4 match) > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > show sel cartoons > select subtract #6 Nothing selected > select #6/C 10535 atoms, 10788 bonds, 15 pseudobonds, 1301 residues, 2 models selected > ui tool show ""Side View"" > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > ui mousemode right select Drag select of 21 residues Drag select of 7 residues Drag select of 10 residues > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > select #6: 227-247 423 atoms, 423 bonds, 63 residues, 1 model selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected Drag select of 8 residues > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected Drag select of 23 residues Drag select of 5 residues > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected Drag select of 23 residues > select #6/E 141 atoms, 141 bonds, 21 residues, 1 model selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected Drag select of 23 residues > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > hide #!6 models > show #!6 models > close #6 > open /Users/chenxi/Desktop/PDB/8yfg_hp1_RH_mdfic.pdb 8yfg_hp1_RH_mdfic.pdb title: Human PIEZO1-R2456H_mdfic [more info...] Chain information for 8yfg_hp1_RH_mdfic.pdb #6 --- Chain | Description | UniProt A B D | piezo-type mechanosensitive ion channel component 1 | PIEZ1_HUMAN 1-2521 C E F | myod family inhibitor domain-containing protein | MDFIC_HUMAN 2-247 Associated 8yfg_hp1_RH_mdfic.pdb chain A to 7wlt.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain B to 7wlt.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain D to 7wlt.pdb with 1 mismatch Chains used in RMSD evaluation for alignment 1: 7wlu-rechain #1/A, 7wlt.pdb #2/A, 8yfg_hp1_RH_mdfic.pdb #6/D Associated 8yfg_hp1_RH_mdfic.pdb chain A to rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain B to rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain D to rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb with 1 mismatch Chains used in RMSD evaluation for alignment 2: 7wlu-rechain #1/A, rhlf-0814 #3/A, 8yfg_hp1_RH_mdfic.pdb #6/D Associated 8yfg_hp1_RH_mdfic.pdb chain A to 8ixo.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain B to 8ixo.pdb with 1 mismatch Associated 8yfg_hp1_RH_mdfic.pdb chain D to 8ixo.pdb with 1 mismatch Chains used in RMSD evaluation for alignment 4: 7wlu-rechain #1/A, 8ixo.pdb #5/A, 8yfg_hp1_RH_mdfic.pdb #6/D Associated 8yfg_hp1_RH_mdfic.pdb chain A to 8yfg_hp1_RH_mdfic.pdb, chain A with 0 mismatches Associated 8yfg_hp1_RH_mdfic.pdb chain B to 8yfg_hp1_RH_mdfic.pdb, chain A with 0 mismatches Associated 8yfg_hp1_RH_mdfic.pdb chain D to 8yfg_hp1_RH_mdfic.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A, 8yfg_hp1_RH_mdfic.pdb #6/D > view > ui tool show ""Side View"" > view orient > show #!2,6 cartoons > hide #!2 models > show #!6 cartoons > hide #6 target a > cartoon style #6 modeHelix tube sides 20 > ui tool show ""Color Actions"" > color indian red > undo > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > ui tool show ""Color Actions"" > color sel indian red > hide #6.1 models > select subtract #6.1 31599 atoms, 32357 bonds, 3903 residues, 1 model selected > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > select #6: 2490-2547 852 atoms, 867 bonds, 96 residues, 1 model selected > select ~sel & ##selected 30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected > hide sel cartoons > select subtract #6.1 30747 atoms, 31490 bonds, 3807 residues, 1 model selected > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!3 models > show #!4 models > hide #!4 models > show #!2 models > select #2: 2490-2547 1515 atoms, 1542 bonds, 174 residues, 1 model selected > select ~sel & ##selected 32397 atoms, 33165 bonds, 33 pseudobonds, 3912 residues, 2 models selected > hide sel cartoons > hide #!6 models > select add #2 33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected > select subtract #2 Nothing selected > show #!6 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > select #6: 2490-2547 852 atoms, 867 bonds, 96 residues, 1 model selected > show sel cartoons > select #2: 2490-2547 1515 atoms, 1542 bonds, 174 residues, 1 model selected > select add #2 33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected > select subtract #2 Nothing selected > hide #!3 models > select #6: 2490-2547 852 atoms, 867 bonds, 96 residues, 1 model selected > select ~sel & ##selected 30747 atoms, 31490 bonds, 45 pseudobonds, 3807 residues, 2 models selected > show sel cartoons > hide sel cartoons > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > select subtract #6 Nothing selected > matchmaker #6/A#6/B#6/D to #2/A#2/B#2/C pairing ss ssFraction false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with 8yfg_hp1_RH_mdfic.pdb, chain A (#6), sequence alignment score = 10759 Matchmaker 7wlt.pdb, chain B (#2) with 8yfg_hp1_RH_mdfic.pdb, chain B (#6), sequence alignment score = 10759 Matchmaker 7wlt.pdb, chain C (#2) with 8yfg_hp1_RH_mdfic.pdb, chain D (#6), sequence alignment score = 10759 RMSD between 800 pruned atom pairs is 1.358 angstroms; (across all 3504 pairs: 10.161) Chains used in RMSD evaluation for alignment 1: 7wlu-rechain #1/A, 7wlt.pdb #2/A, 8yfg_hp1_RH_mdfic.pdb #6/A Chains used in RMSD evaluation for alignment 2: 7wlu-rechain #1/A, rhlf-0814 #3/A, 8yfg_hp1_RH_mdfic.pdb #6/A Chains used in RMSD evaluation for alignment 4: 7wlu-rechain #1/A, 8ixo.pdb #5/A, 8yfg_hp1_RH_mdfic.pdb #6/A Chains used in RMSD evaluation for alignment 8: 7wlu-rechain #1/A, 8yfg_hp1_RH_mdfic.pdb #6/A > hide #!6 models > show #!7 models > view orient > ui tool show Matchmaker > matchmaker #7/A#7/B#7/C to #2/A#2/B#2/C pairing ss ssFraction false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlt.pdb, chain A (#2) with rhdc, chain A (#7), sequence alignment score = 8828 Matchmaker 7wlt.pdb, chain B (#2) with rhdc, chain B (#7), sequence alignment score = 8828 Matchmaker 7wlt.pdb, chain C (#2) with rhdc, chain C (#7), sequence alignment score = 8828 RMSD between 1801 pruned atom pairs is 1.163 angstroms; (across all 4059 pairs: 4.567) > hide #!7 models > hide #!2 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select add #2 68673 atoms, 70251 bonds, 72 pseudobonds, 8583 residues, 5 models selected > select add #3 102948 atoms, 105306 bonds, 117 pseudobonds, 13029 residues, 7 models selected > select add #4 140553 atoms, 143826 bonds, 153 pseudobonds, 17568 residues, 9 models selected > select add #5 172665 atoms, 176625 bonds, 192 pseudobonds, 21768 residues, 12 models selected > select add #6 204264 atoms, 208982 bonds, 237 pseudobonds, 25671 residues, 14 models selected > select add #7 249780 atoms, 255638 bonds, 288 pseudobonds, 31242 residues, 16 models selected > select subtract #1 215019 atoms, 220094 bonds, 249 pseudobonds, 26745 residues, 14 models selected > select subtract #2 181107 atoms, 185387 bonds, 216 pseudobonds, 22659 residues, 11 models selected > select subtract #3 146832 atoms, 150332 bonds, 171 pseudobonds, 18213 residues, 9 models selected > select subtract #5 114720 atoms, 117533 bonds, 132 pseudobonds, 14013 residues, 6 models selected > select subtract #6 83121 atoms, 85176 bonds, 87 pseudobonds, 10110 residues, 4 models selected > select subtract #7 37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected > select subtract #4 Nothing selected > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > show sel cartoons > select subtract #1 Nothing selected > hide #!1 models > select add #2 33912 atoms, 34707 bonds, 33 pseudobonds, 4086 residues, 3 models selected > show sel cartoons > select subtract #2 Nothing selected > hide #!2 models > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > show sel cartoons > select subtract #3 Nothing selected > hide #!3 models > select add #4 37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected > show sel cartoons > select subtract #4 Nothing selected > hide #!4 models > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > show sel cartoons > select subtract #5 Nothing selected > hide #!5 models > select add #6 31599 atoms, 32357 bonds, 45 pseudobonds, 3903 residues, 2 models selected > show sel cartoons > select subtract #6 Nothing selected > hide #!6 models > select add #7 45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected > show sel cartoons > select subtract #7 Nothing selected > hide #!7 models > show #!2 models > show #!3 models > view orient > turn x 90 > turn x 180 > turn y -20 > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > show #!1 models > view > ui tool show ""Side View"" > show #!4 models > show #!5 models > show #!6 models > show #!7 models > select #1-7: 2476 159 atoms, 138 bonds, 21 residues, 7 models selected > color sel red > select clear > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > show #!2 models > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlt.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!2 models > show #!1 models > save ""/Users/chenxi/Desktop/RH-figure/model align/7wlt.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!1 models > show #!3 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!3 models > show #!4 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlc.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!4 models > show #!6 models > hide #!6 models > show #!7 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhdc.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!7 models > show #!7 models > hide #!7 models > show #!5 models > select #5: 2116-2492 8814 atoms, 9045 bonds, 3 pseudobonds, 1101 residues, 2 models selected > select ~sel & ##selected 23298 atoms, 23754 bonds, 36 pseudobonds, 3099 residues, 2 models selected > hide sel cartoons > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > select subtract #5 Nothing selected > show #!1 models > select #1: 2116-2492 8724 atoms, 8949 bonds, 6 pseudobonds, 1089 residues, 2 models selected > hide sel cartoons > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png"" width 2000 > height 1237 supersample 3 transparentBackground true > save ""/Users/chenxi/Desktop/RH-figure/model align/sehole+wtlf.png"" width > 2000 height 1237 supersample 3 transparentBackground true > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > show #!1 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!1 models > show #!3 models > show #!1 models > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > show sel cartoons > select subtract #1 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!5 models > select add #5 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > show sel cartoons > select subtract #5 Nothing selected > hide #!5 models > show #!1 models > hide #!1 models > show #!5 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > show #!6 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!2 models > save ""/Users/chenxi/Desktop/RH-figure/model align/8yfg+7wlt.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!7 models > hide #!7 models > hide #!6 models > show #!7 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > save ""/Users/chenxi/Desktop/RH-figure/model align/rhdc+7wlt.png"" width 2000 > height 1237 supersample 3 transparentBackground true > save ""/Users/chenxi/Desktop/RH-figure/model align/model-align.cxs"" > includeMaps true > hide #!2 models > show #!1 models > hide #!7 models > show #!3 models > select #1,3: 2490-2547 3012 atoms, 3066 bonds, 348 residues, 2 models selected > ui tool show Matchmaker > matchmaker #3/A#3/B#3/C & sel to #1/A#1/B#1/C & sel pairing ss ssFraction > false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker 7wlu-rechain, chain A (#1) with rhlf-0814, chain A (#3), sequence alignment score = 301 Matchmaker 7wlu-rechain, chain C (#1) with rhlf-0814, chain C (#3), sequence alignment score = 301 Matchmaker 7wlu-rechain, chain B (#1) with rhlf-0814, chain B (#3), sequence alignment score = 301 RMSD between 159 pruned atom pairs is 1.210 angstroms; (across all 174 pairs: 1.320) > select add #1 36267 atoms, 37077 bonds, 39 pseudobonds, 4671 residues, 3 models selected > select add #3 69036 atoms, 70599 bonds, 84 pseudobonds, 8943 residues, 4 models selected > select subtract #1 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select add #1 69036 atoms, 70599 bonds, 84 pseudobonds, 8943 residues, 4 models selected > select subtract #1 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > lighting simple > lighting soft > ui tool show ""Side View"" > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+7wlu.png"" width 2000 > height 1237 supersample 3 transparentBackground true > hide #!1 models > show #!5 models > hide #!5 models > show #!5 models > lighting soft > lighting full > lighting soft > lighting flat > lighting soft > ui tool show ""Side View"" > select #3,5: 2490-2547 3006 atoms, 3060 bonds, 348 residues, 2 models selected > ui tool show Matchmaker > matchmaker #5/A#5/B#5/C & sel to #3/A#3/B#3/C & sel pairing ss ssFraction > false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker rhlf-0814, chain A (#3) with 8ixo.pdb, chain C (#5), sequence alignment score = 301 Matchmaker rhlf-0814, chain C (#3) with 8ixo.pdb, chain A (#5), sequence alignment score = 301 Matchmaker rhlf-0814, chain B (#3) with 8ixo.pdb, chain B (#5), sequence alignment score = 301 RMSD between 7 pruned atom pairs is 0.900 angstroms; (across all 174 pairs: 20.592) > select ~sel & ##selected 63381 atoms, 64794 bonds, 84 pseudobonds, 8298 residues, 4 models selected > hide sel cartoons > select clear > ui tool show Matchmaker > matchmaker #5/A#5/B#5/C to #3/A#3/B#3/C pairing ss ssFraction false Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 No secondary-structure guidance used Gap open | 12 Gap extend | 1 Iteration cutoff | 2 Matchmaker rhlf-0814, chain A (#3) with 8ixo.pdb, chain A (#5), sequence alignment score = 7062 Matchmaker rhlf-0814, chain B (#3) with 8ixo.pdb, chain B (#5), sequence alignment score = 7062 Matchmaker rhlf-0814, chain C (#3) with 8ixo.pdb, chain C (#5), sequence alignment score = 7062 RMSD between 255 pruned atom pairs is 1.217 angstroms; (across all 4116 pairs: 23.493) > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select add #5 66387 atoms, 67854 bonds, 84 pseudobonds, 8646 residues, 5 models selected > show sel cartoons > select subtract #3 32112 atoms, 32799 bonds, 39 pseudobonds, 4200 residues, 3 models selected > select subtract #5 Nothing selected > view > ui tool show ""Side View"" > view orient > turn x 90 > turn y -20 > turn y -5 > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png"" width 2000 > height 1237 supersample 3 transparentBackground true > ui tool show ""Side View"" > save ""/Users/chenxi/Desktop/RH-figure/model align/rhlf+8ixo.png"" width 2000 > height 1237 supersample 3 transparentBackground true > show #!1 models > hide #!5 models > select #1,3: 2116-2213 4872 atoms, 5010 bonds, 588 residues, 2 models selected > select ~sel & ##selected 64164 atoms, 65589 bonds, 84 pseudobonds, 8355 residues, 4 models selected > hide sel cartoons > select #1,3: 2417-2492 3165 atoms, 3246 bonds, 6 pseudobonds, 408 residues, 4 models selected > show sel cartoons > hide sel cartoons > select #1,3: 2465-2492 1281 atoms, 1308 bonds, 168 residues, 2 models selected > select #1,3: 2476 42 atoms, 36 bonds, 6 residues, 2 models selected Drag select of 9 residues > select clear > select #1,3: 2476 42 atoms, 36 bonds, 6 residues, 2 models selected > show sel cartoons > hide sel cartoons > select #1,3: 2465-2492 1281 atoms, 1308 bonds, 168 residues, 2 models selected > show sel cartoons > select clear > ui tool show ""Side View"" Drag select of 3 residues > select add #3 34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected > select subtract #3 Nothing selected > select #1,3: 2417-2492 3165 atoms, 3246 bonds, 6 pseudobonds, 408 residues, 4 models selected > show sel cartoons > select clear > show #3.1 models > show #1.1 models > ui tool show ""Side View"" > select #1,3/A 23012 atoms, 23533 bonds, 28 pseudobonds, 2981 residues, 4 models selected > hide sel cartoons > show sel cartoons > hide sel cartoons > undo > select #1,3/A,B 46024 atoms, 47066 bonds, 56 pseudobonds, 5962 residues, 4 models selected > color (#!1,3 & sel) dark gray > color (#!1,3 & sel) white > lighting flat > select clear > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting simple > lighting soft > select #1/C:2475 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1 34761 atoms, 35544 bonds, 39 pseudobonds, 4497 residues, 2 models selected > select subtract #1 Nothing selected > ui tool show ""Side View"" > save ""/Users/chenxi/Desktop/RH-figure/model align/IH-OH-rhlf-7wlu.png"" width > 2000 height 1237 supersample 3 transparentBackground true > select #1,3: 2214-2465 11316 atoms, 11589 bonds, 15 pseudobonds, 1428 residues, 4 models selected > select ~sel & ##selected 57720 atoms, 59010 bonds, 69 pseudobonds, 7515 residues, 4 models selected > hide sel cartoons > select #1,3: 2214-2465 11316 atoms, 11589 bonds, 15 pseudobonds, 1428 residues, 4 models selected > show sel cartoons > select #1,3: 2200-2470 12258 atoms, 12567 bonds, 15 pseudobonds, 1542 residues, 4 models selected > show sel cartoons > select #1,3: 2200-2476 12516 atoms, 12825 bonds, 15 pseudobonds, 1578 residues, 4 models selected > show sel cartoons > select clear > select #1,3: 2185-2492 13977 atoms, 14325 bonds, 15 pseudobonds, 1764 residues, 4 models selected > show sel cartoons > select clear > save ""/Users/chenxi/Desktop/RH-figure/model align/capside-rhlf-7wlu.png"" > width 2000 height 1237 supersample 3 transparentBackground true > view orient > turn y 90 > turn z 90 > turn y 90 > turn x 90 > turn z 90 > view orient > turn z 90 > view orient > turn x 90 > turn y 90 > turn x 90 > ui tool show ""Side View"" > save ""/Users/chenxi/Desktop/RH-figure/model align/captop-rhlf-7wlu.png"" > width 2000 height 1237 supersample 3 transparentBackground true > hide #1.1 models > hide #3.1 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: MLXY3CH/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 17天13小时28分钟 Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: YOGA27_APH8: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 1280 x 720 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX