id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16373 Crash in Sequence::rname3to1 drawing ribbons after restoring session chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003513ab000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000320f77000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py"", line 1134 in read File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py"", line 1278 in recv_into File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 706 in readinto File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 279 in _read_status File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 318 in begin File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1378 in getresponse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1352 in do_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1391 in https_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 496 in _call_chain File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 536 in _open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 519 in open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 216 in urlopen File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/available.py"", line 62 in load File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 465 in reload_available File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fffc4c00 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1897 in polymers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 53 in _make_ribbon_graphics File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 630 in compute_ribbons File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 667 in _create_ribbon_graphics File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 357 in update_graphics_if_needed File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1906 in _update_graphics_if_needed File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 295 in check_for_drawing_change File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 76 in draw_new_frame File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 323 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1030 in init File 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""deploymentId"" : 240000012 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9.dev202407020250 (2024-07-02) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/sramonabarua/Library/CloudStorage/GoogleDrive- > sramona.barua@gmail.com/.shortcut-targets-by- > id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cxs Log from Mon Nov 25 16:32:30 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sramonabarua/Library/CloudStorage/GoogleDrive- > sramona.barua@gmail.com/.shortcut-targets-by- > id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif Summary of feedback from opening /Users/sramonabarua/Library/CloudStorage/GoogleDrive- sramona.barua@gmail.com/.shortcut-targets-by- id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV- Full/cryosparc_P31_J281_004_volume_map_sharp--VC- Conf1/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif #1 --- Chain | Description 0 BX Bf CP | No description available 1 Bi CE DG | No description available 4 | No description available 5 | No description available 6 | No description available 8 | No description available 9 | No description available A | No description available A0 AA | No description available A3 | No description available A4 | No description available A5 | No description available A9 | No description available AB AN Bg | No description available AC | No description available AF | No description available AG DX | No description available AI | No description available AJ | No description available AK AQ Ba | No description available AL | No description available AM | No description available AO Bn El | No description available AP | No description available AS | No description available AT | No description available AU B7 | No description available AX Cx | No description available AY Dz a | No description available Aa | No description available Ab | No description available Ad | No description available Ae Ds | No description available Ai | No description available Al | No description available An | No description available Ap | No description available Ar | No description available At | No description available Au | No description available Av | No description available Aw CB | No description available Ax | No description available Az | No description available B | No description available B0 | No description available B1 D6 DJ EC | No description available B4 | No description available B8 | No description available B9 | No description available BB | No description available BC Cl | No description available BD | No description available BE | No description available BG | No description available BI | No description available BM | No description available BN | No description available BO | No description available BQ Cm ES | No description available BR | No description available BZ | No description available Be | No description available Bh | No description available Bk | No description available Bp | No description available Br | No description available Bs CF | No description available Bt | No description available Bv C6 | No description available Bw | No description available C | No description available C4 | No description available C8 | No description available C9 | No description available CL | No description available CO FF | No description available CQ | No description available CR | No description available CY DM | No description available Ce | No description available Ch | No description available Ck | No description available Cu | No description available D | No description available D0 | No description available D2 | No description available D4 i | No description available DO | No description available DR | No description available DT | No description available DZ | No description available Di | No description available Dm | No description available Dp | No description available Dy | No description available E | No description available ET | No description available EW | No description available EY | No description available Ea | No description available Eh | No description available Em | No description available F | No description available F0 | No description available F1 | No description available F2 | No description available F3 | No description available F4 | No description available F5 | No description available F6 | No description available F7 | No description available F8 | No description available F9 | No description available FB | No description available FZ | No description available Fa | No description available Fb | No description available Fh | No description available Fi | No description available Fj | No description available Fk | No description available Fl | No description available Fm | No description available Fn | No description available Fo | No description available Fp | No description available Fq | No description available Fr | No description available Fs | No description available Ft | No description available Fu | No description available Fv | No description available Fw | No description available Fx | No description available Fy | No description available Fz | No description available G | No description available G0 | No description available G1 | No description available G2 | No description available G3 | No description available G4 | No description available G5 | No description available G6 | No description available G7 | No description available G8 | No description available G9 | No description available GA | No description available GB | No description available GC | No description available GD | No description available GE | No description available GF | No description available GG | No description available GH | No description available GI | No description available GJ | No description available GK | No description available GL | No description available GM | No description available GN | No description available GO | No description available GP | No description available GQ | No description available GR | No description available GS | No description available GT | No description available GU | No description available GV | No description available GW | No description available GX | No description available GY | No description available GZ | No description available Ga | No description available Gb | No description available Gc | No description available Gd | No description available Ge | No description available Gf | No description available Gg | No description available Gh | No description available Gi | No description available Gj | No description available Gk | No description available Gl | No description available Gm | No description available Gn | No description available Go | No description available Gp | No description available Gq | No description available Gr | No description available Gs | No description available Gt | No description available Gu | No description available Gv | No description available Gw | No description available Gx | No description available Gy | No description available Gz | No description available H | No description available H0 | No description available H1 | No description available H2 | No description available H3 | No description available H4 | No description available H5 | No description available H6 | No description available H7 | No description available H8 | No description available H9 | No description available HA | No description available HB | No description available HC | No description available HD | No description available HE | No description available HF | No description available HG | No description available HH | No description available HI | No description available HJ | No description available HK | No description available HL | No description available HM | No description available HN | No description available HO | No description available HP | No description available HQ | No description available HR | No description available HS | No description available HT | No description available HU | No description available HV | No description available HW | No description available HX | No description available HY | No description available HZ | No description available Ha | No description available Hb | No description available Hc | No description available Hd | No description available He | No description available Hf | No description available Hg | No description available Hh | No description available Hi | No description available Hj | No description available Hk | No description available Hl | No description available Hm | No description available Hn | No description available Ho | No description available Hp | No description available Hq | No description available Hr | No description available Hs | No description available Ht | No description available Hu | No description available Hv | No description available Hw | No description available Hx | No description available Hy | No description available Hz | No description available I | No description available I0 | No description available I1 | No description available I2 | No description available I3 | No description available I4 | No description available I5 | No description available I6 | No description available I7 | No description available I8 | No description available I9 | No description available IA | No description available IB | No description available IC | No description available ID | No description available IE | No description available IF | No description available IG | No description available IH | No description available II | No description available IJ | No description available IK | No description available IL | No description available IM | No description available IN | No description available IO | No description available IP | No description available IQ | No description available IR | No description available IS | No description available IT | No description available IU | No description available IV | No description available IW | No description available IX | No description available IY | No description available IZ | No description available Ia | No description available Ib | No description available Ic | No description available Id | No description available Ie | No description available If | No description available Ig | No description available Ih | No description available Ii | No description available Ij | No description available Ik | No description available Il | No description available Im | No description available In | No description available Io | No description available Ip | No description available Iq | No description available Ir | No description available Is | No description available It | No description available Iu | No description available Iv | No description available Iw | No description available Ix | No description available Iy | No description available Iz | No description available J | No description available JA | No description available JB | No description available JC | No description available JD | No description available JE | No description available JF | No description available JG | No description available JH | No description available JI | No description available JJ | No description available JK | No description available JL | No description available JM | No description available JN | No description available JO | No description available JP | No description available JQ | No description available JR | No description available JS | No description available JT | No description available JU | No description available JV | No description available K | No description available L | No description available M | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available j | No description available k | No description available l | No description available m | No description available n | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available w | No description available x | No description available y | No description available z | No description available > cd /Users/sramonabarua/Library/CloudStorage/GoogleDrive- > sramona.barua@gmail.com/.shortcut-targets-by- > id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1 Current working directory is: /Users/sramonabarua/Library/CloudStorage/GoogleDrive- sramona.barua@gmail.com/.shortcut-targets-by- id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV- Full/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1 > runscript ../../scripts/renameAndRenumberChainsChimeraX.py #1 > ./central_stalk/Mod_copy.txt ['7', '58'] ['7', '58'] ['1', '9'] ['1', '9'] ['12'] ['1', '2'] ['1', '18'] ['1', '18'] ['12'] ['1', '2'] ['1', '21'] ['1', '21'] ['1', '3'] ['1', '3'] ['1', '3'] ['1', '3'] ['1', '29'] ['1', '29'] ['1', '8'] ['1', '8'] ['1', '8'] ['1', '8'] ['1', '8'] ['1', '8'] ['2', '28'] ['2', '28'] ['1', '53'] ['1', '53'] ['1', '8'] ['1', '8'] ['1', '5'] ['1', '5'] ['1', '8'] ['1', '8'] ['4', '22'] ['4', '22'] ['12'] ['1', '2'] ['1', '18'] ['1', '18'] ['1', '3'] ['1', '3'] ['1', '8'] ['1', '8'] ['1', '10'] ['1', '10'] ['1', '5'] ['1', '5'] ['2', '23'] ['2', '23'] ['1', '15'] ['1', '15'] ['1', '4'] ['1', '4'] ['1', '4'] ['1', '4'] ['12'] ['1', '2'] ['1', '4'] ['1', '4'] ['12'] ['1', '2'] ['1', '24'] ['1', '24'] ['12'] ['1', '2'] ['1', '3'] ['1', '3'] ['6', '13'] ['6', '13'] ['1', '3'] ['1', '3'] ['12'] ['1', '2'] ['1', '4'] ['1', '4'] ['1', '3'] ['1', '3'] ['12'] ['1', '2'] ['1', '6'] ['1', '6'] LtaP21.2100.mRNA LtaP30.3640.mRNA LtaP36.0640.mRNA > combine #1 close false name renamedAndRenumberedModel Renumering chain LtaP21.2100.mRNA > delete #2/IY:14 > delete #2/IY:37 > renumber #2/IY:15-9999999 start 14 50 residues renumbered > renumber #2/IY:37-9999999 start 36 28 residues renumbered > renumber #2/IY:18-9999999 start 19 46 residues renumbered > ~bond #2/IY:17@C #2/IY:19@N ['7', '55'] > select #2/IY 523 atoms, 530 bonds, 3 pseudobonds, 63 residues, 2 models selected 0 2 >2 > renumber #2/IY start 2 63 residues renumbered ['1', '9'] > select #2/GE 71 atoms, 72 bonds, 9 residues, 1 model selected 65 64 >-1 > delete #2/GE:2 > delete #2/GE:1 > renumber #2/GE start 66 7 residues renumbered > changechains #2/GE IY Chain IDs of 7 residues changed ['1', '2'] > select #2/DT 15 atoms, 14 bonds, 2 residues, 1 model selected 72 76 >4 > renumber #2/DT start 76 2 residues renumbered > changechains #2/DT IY Chain IDs of 2 residues changed ['1', '18'] > select #2/H2 128 atoms, 129 bonds, 18 residues, 1 model selected 77 78 >1 > renumber #2/H2 start 78 18 residues renumbered > changechains #2/H2 IY Chain IDs of 18 residues changed ['1', '2'] > select #2/DJ 8 atoms, 7 bonds, 2 residues, 1 model selected 95 96 >1 > renumber #2/DJ start 96 2 residues renumbered > changechains #2/DJ IY Chain IDs of 2 residues changed ['1', '21'] > select #2/Iw 170 atoms, 172 bonds, 21 residues, 1 model selected 97 98 >1 > renumber #2/Iw start 98 21 residues renumbered > changechains #2/Iw IY Chain IDs of 21 residues changed ['1', '3'] > select #2/t 25 atoms, 24 bonds, 3 residues, 1 model selected 118 119 >1 > renumber #2/t start 119 3 residues renumbered > changechains #2/t IY Chain IDs of 3 residues changed ['1', '3'] > select #2/IZ 24 atoms, 24 bonds, 3 residues, 1 model selected 121 122 >1 > renumber #2/IZ start 122 3 residues renumbered > changechains #2/IZ IY Chain IDs of 3 residues changed ['1', '29'] > select #2/G6 231 atoms, 236 bonds, 29 residues, 1 model selected 124 125 >1 > renumber #2/G6 start 125 29 residues renumbered > changechains #2/G6 IY Chain IDs of 29 residues changed ['1', '8'] > select #2/L 77 atoms, 79 bonds, 8 residues, 1 model selected 153 154 >1 > renumber #2/L start 154 8 residues renumbered > changechains #2/L IY Chain IDs of 8 residues changed ['1', '8'] > select #2/GN 57 atoms, 57 bonds, 8 residues, 1 model selected 161 162 >1 > renumber #2/GN start 162 8 residues renumbered > changechains #2/GN IY Chain IDs of 8 residues changed ['1', '8'] > select #2/Z 69 atoms, 72 bonds, 8 residues, 1 model selected 169 171 >2 > renumber #2/Z start 171 8 residues renumbered > changechains #2/Z IY Chain IDs of 8 residues changed ['2', '28'] > select #2/Fy 319 atoms, 324 bonds, 38 residues, 1 model selected 178 178 >0 > delete #2/Fy:1 > renumber #2/Fy start 179 37 residues renumbered > changechains #2/Fy IY Chain IDs of 37 residues changed ['1', '53'] > select #2/V 564 atoms, 567 bonds, 70 residues, 1 model selected 215 216 >1 > renumber #2/V start 216 70 residues renumbered > changechains #2/V IY Chain IDs of 70 residues changed ['1', '8'] > select #2/Iv 69 atoms, 69 bonds, 8 residues, 1 model selected 285 288 >3 > renumber #2/Iv start 288 8 residues renumbered > changechains #2/Iv IY Chain IDs of 8 residues changed Renumering chain LtaP30.3640.mRNA ['1', '5'] > select #2/JC 43 atoms, 44 bonds, 5 residues, 1 model selected 0 22 >22 > renumber #2/JC start 22 5 residues renumbered ['1', '8'] > select #2/R 63 atoms, 63 bonds, 8 residues, 1 model selected 26 26 >0 > delete #2/R:1 > renumber #2/R start 27 7 residues renumbered > changechains #2/R JC Chain IDs of 7 residues changed ['4', '22'] > select #2/G9 197 atoms, 201 bonds, 24 residues, 1 model selected 33 34 >1 > renumber #2/G9 start 34 24 residues renumbered > changechains #2/G9 JC Chain IDs of 24 residues changed ['1', '2'] > select #2/B1 8 atoms, 7 bonds, 2 residues, 1 model selected 57 58 >1 > renumber #2/B1 start 58 2 residues renumbered > changechains #2/B1 JC Chain IDs of 2 residues changed ['1', '18'] > select #2/I3 143 atoms, 145 bonds, 18 residues, 1 model selected 59 60 >1 > renumber #2/I3 start 60 18 residues renumbered > changechains #2/I3 JC Chain IDs of 18 residues changed ['1', '3'] > select #2/r 20 atoms, 19 bonds, 3 residues, 1 model selected 77 77 >0 > delete #2/r:1 > renumber #2/r start 78 2 residues renumbered > changechains #2/r JC Chain IDs of 2 residues changed ['1', '8'] > select #2/HX 62 atoms, 61 bonds, 8 residues, 1 model selected 79 80 >1 > renumber #2/HX start 80 8 residues renumbered > changechains #2/HX JC Chain IDs of 8 residues changed ['1', '10'] > select #2/P 79 atoms, 80 bonds, 10 residues, 1 model selected 87 88 >1 > renumber #2/P start 88 10 residues renumbered > changechains #2/P JC Chain IDs of 10 residues changed ['1', '5'] > select #2/Q 38 atoms, 37 bonds, 5 residues, 1 model selected 97 98 >1 > renumber #2/Q start 98 5 residues renumbered > changechains #2/Q JC Chain IDs of 5 residues changed ['2', '23'] > select #2/He 206 atoms, 210 bonds, 26 residues, 1 model selected 102 101 >-1 > delete #2/He:2 > delete #2/He:1 > renumber #2/He start 103 24 residues renumbered > changechains #2/He JC Chain IDs of 24 residues changed ['1', '15'] > select #2/IE 116 atoms, 118 bonds, 15 residues, 1 model selected 126 127 >1 > renumber #2/IE start 127 15 residues renumbered > changechains #2/IE JC Chain IDs of 15 residues changed ['1', '4'] > select #2/GZ 30 atoms, 29 bonds, 4 residues, 1 model selected 141 143 >2 > renumber #2/GZ start 143 4 residues renumbered > changechains #2/GZ JC Chain IDs of 4 residues changed ['1', '4'] > select #2/I 28 atoms, 27 bonds, 4 residues, 1 model selected 146 148 >2 > renumber #2/I start 148 4 residues renumbered > changechains #2/I JC Chain IDs of 4 residues changed ['1', '2'] > select #2/BC 17 atoms, 16 bonds, 2 residues, 1 model selected 151 152 >1 > renumber #2/BC start 152 2 residues renumbered > changechains #2/BC JC Chain IDs of 2 residues changed ['1', '4'] > select #2/AM 28 atoms, 27 bonds, 4 residues, 1 model selected 153 154 >1 > renumber #2/AM start 154 4 residues renumbered > changechains #2/AM JC Chain IDs of 4 residues changed ['1', '2'] > select #2/B9 10 atoms, 9 bonds, 2 residues, 1 model selected 157 158 >1 > renumber #2/B9 start 158 2 residues renumbered > changechains #2/B9 JC Chain IDs of 2 residues changed ['1', '24'] > select #2/H7 196 atoms, 195 bonds, 24 residues, 1 model selected 159 160 >1 > renumber #2/H7 start 160 24 residues renumbered > changechains #2/H7 JC Chain IDs of 24 residues changed Renumering chain LtaP36.0640.mRNA ['1', '2'] > select #2/D6 8 atoms, 7 bonds, 2 residues, 1 model selected 0 7 >7 > renumber #2/D6 start 7 2 residues renumbered ['1', '3'] > select #2/C8 23 atoms, 22 bonds, 3 residues, 1 model selected 8 9 >1 > renumber #2/C8 start 9 3 residues renumbered > changechains #2/C8 D6 Chain IDs of 3 residues changed ['6', '13'] > select #2/Hd 202 atoms, 201 bonds, 26 residues, 1 model selected 11 14 >3 > renumber #2/Hd start 14 26 residues renumbered > changechains #2/Hd D6 Chain IDs of 26 residues changed ['1', '3'] > select #2/JV 25 atoms, 24 bonds, 3 residues, 1 model selected 39 41 >2 > renumber #2/JV start 41 3 residues renumbered > changechains #2/JV D6 Chain IDs of 3 residues changed ['1', '2'] > select #2/At 16 atoms, 15 bonds, 2 residues, 1 model selected 43 44 >1 > renumber #2/At start 44 2 residues renumbered > changechains #2/At D6 Chain IDs of 2 residues changed ['1', '4'] > select #2/6 33 atoms, 34 bonds, 4 residues, 1 model selected 45 46 >1 > renumber #2/6 start 46 4 residues renumbered > changechains #2/6 D6 Chain IDs of 4 residues changed ['1', '3'] > select #2/Io 20 atoms, 20 bonds, 3 residues, 1 model selected 49 50 >1 > renumber #2/Io start 50 3 residues renumbered > changechains #2/Io D6 Chain IDs of 3 residues changed ['1', '2'] > select #2/BN 16 atoms, 15 bonds, 2 residues, 1 model selected 52 63 >11 > renumber #2/BN start 63 2 residues renumbered > changechains #2/BN D6 Chain IDs of 2 residues changed ['1', '6'] > select #2/I5 44 atoms, 43 bonds, 6 residues, 1 model selected 64 65 >1 > renumber #2/I5 start 65 6 residues renumbered > changechains #2/I5 D6 Chain IDs of 6 residues changed > hide #1 models > select add #2 48037 atoms, 48351 bonds, 3 pseudobonds, 6078 residues, 2 models selected > hide sel atoms > show sel cartoons > runscript ../../scripts/bondFragmentsAndFillGapsMultipleChains.py #2 3 > ./central_stalk/Mod_copy.txt > combine #2 close false name gapsFilledModel > color #3 gray > select #3/IY 2331 atoms, 2357 bonds, 3 pseudobonds, 287 residues, 2 models selected -*****************-*****************************************************---**********************************************************************************************-*******************************************************************************************************************--********-------- FYI: command is replacing existing command: ""build invert"" FYI: command is replacing existing command: ""build join peptide"" FYI: command is replacing existing command: ""build join bond"" FYI: command is replacing existing command: ""build modify"" FYI: command is replacing existing command: ""build start"" FYI: command is replacing existing command: ""bond"" FYI: command is replacing existing command: ""~bond"" FYI: command is replacing existing command: ""bond length"" > build start peptide #3 Y 1,1 position > 283.6507980671056,299.2096922474093,284.9317073958794 chainId zz > delete #3/zz:1@OXT > renumber #3/zz start 19 1 residues renumbered > changechains #3/zz IY Chain IDs of 1 residues changed > bond #3/IY:19@C #3/IY:20@N reasonable false Created 1 bond > bond #3/IY:18@C #3/IY:19@N reasonable false Created 1 bond > color #3/IY:19-19@C* red > build start peptide #3 PVM 1,1 1,1 1,1 position > 268.4778101337697,293.5020375253132,299.18008777153227 chainId zz > delete #3/zz:3@OXT > renumber #3/zz start 73 3 residues renumbered > changechains #3/zz IY Chain IDs of 3 residues changed > bond #3/IY:75@C #3/IY:76@N reasonable false Created 1 bond > bond #3/IY:72@C #3/IY:73@N reasonable false Created 1 bond > color #3/IY:73-75@C* red > build start peptide #3 Q 1,1 position > 277.8905614257111,284.7191156752,312.0360418859748 chainId zz > delete #3/zz:1@OXT > renumber #3/zz start 170 1 residues renumbered > changechains #3/zz IY Chain IDs of 1 residues changed > bond #3/IY:170@C #3/IY:171@N reasonable false Created 1 bond > bond #3/IY:169@C #3/IY:170@N reasonable false Created 1 bond > color #3/IY:170-170@C* red > build start peptide #3 NA 1,1 1,1 position > 303.7947658745627,282.8651265547019,230.76316856057028 chainId zz > delete #3/zz:2@OXT > renumber #3/zz start 286 2 residues renumbered > changechains #3/zz IY Chain IDs of 2 residues changed > bond #3/IY:287@C #3/IY:288@N reasonable false Created 1 bond > bond #3/IY:285@C #3/IY:286@N reasonable false Created 1 bond > color #3/IY:286-287@C* red > bond #3/IY:154@C #3/IY:155@N reasonable false Created 0 bonds > bond #3/IY:155@C #3/IY:156@N reasonable false Created 0 bonds > bond #3/IY:156@C #3/IY:157@N reasonable false Created 0 bonds > bond #3/IY:157@C #3/IY:158@N reasonable false Created 0 bonds > bond #3/IY:158@C #3/IY:159@N reasonable false Created 0 bonds > bond #3/IY:159@C #3/IY:160@N reasonable false Created 0 bonds > bond #3/IY:160@C #3/IY:161@N reasonable false Created 0 bonds > bond #3/IY:161@C #3/IY:162@N reasonable false Created 1 bond > bond #3/IY:216@C #3/IY:217@N reasonable false Created 0 bonds > bond #3/IY:217@C #3/IY:218@N reasonable false Created 0 bonds > bond #3/IY:218@C #3/IY:219@N reasonable false Created 0 bonds > bond #3/IY:219@C #3/IY:220@N reasonable false Created 0 bonds > bond #3/IY:220@C #3/IY:221@N reasonable false Created 0 bonds > bond #3/IY:221@C #3/IY:222@N reasonable false Created 0 bonds > bond #3/IY:222@C #3/IY:223@N reasonable false Created 0 bonds > bond #3/IY:223@C #3/IY:224@N reasonable false Created 0 bonds > bond #3/IY:224@C #3/IY:225@N reasonable false Created 0 bonds > bond #3/IY:225@C #3/IY:226@N reasonable false Created 0 bonds > bond #3/IY:226@C #3/IY:227@N reasonable false Created 0 bonds > bond #3/IY:227@C #3/IY:228@N reasonable false Created 0 bonds > bond #3/IY:228@C #3/IY:229@N reasonable false Created 0 bonds > bond #3/IY:229@C #3/IY:230@N reasonable false Created 0 bonds > bond #3/IY:230@C #3/IY:231@N reasonable false Created 0 bonds > bond #3/IY:231@C #3/IY:232@N reasonable false Created 0 bonds > bond #3/IY:232@C #3/IY:233@N reasonable false Created 0 bonds > bond #3/IY:233@C #3/IY:234@N reasonable false Created 0 bonds > bond #3/IY:234@C #3/IY:235@N reasonable false Created 0 bonds > bond #3/IY:235@C #3/IY:236@N reasonable false Created 0 bonds > bond #3/IY:236@C #3/IY:237@N reasonable false Created 0 bonds > bond #3/IY:237@C #3/IY:238@N reasonable false Created 0 bonds > bond #3/IY:238@C #3/IY:239@N reasonable false Created 0 bonds > bond #3/IY:239@C #3/IY:240@N reasonable false Created 0 bonds > bond #3/IY:240@C #3/IY:241@N reasonable false Created 0 bonds > bond #3/IY:241@C #3/IY:242@N reasonable false Created 0 bonds > bond #3/IY:242@C #3/IY:243@N reasonable false Created 0 bonds > bond #3/IY:243@C #3/IY:244@N reasonable false Created 0 bonds > bond #3/IY:244@C #3/IY:245@N reasonable false Created 0 bonds > bond #3/IY:245@C #3/IY:246@N reasonable false Created 0 bonds > bond #3/IY:246@C #3/IY:247@N reasonable false Created 0 bonds > bond #3/IY:247@C #3/IY:248@N reasonable false Created 0 bonds > bond #3/IY:248@C #3/IY:249@N reasonable false Created 0 bonds > bond #3/IY:249@C #3/IY:250@N reasonable false Created 0 bonds > bond #3/IY:250@C #3/IY:251@N reasonable false Created 0 bonds > bond #3/IY:251@C #3/IY:252@N reasonable false Created 0 bonds > bond #3/IY:252@C #3/IY:253@N reasonable false Created 0 bonds > bond #3/IY:253@C #3/IY:254@N reasonable false Created 0 bonds > bond #3/IY:254@C #3/IY:255@N reasonable false Created 0 bonds > bond #3/IY:255@C #3/IY:256@N reasonable false Created 0 bonds > bond #3/IY:256@C #3/IY:257@N reasonable false Created 0 bonds > bond #3/IY:257@C #3/IY:258@N reasonable false Created 0 bonds > bond #3/IY:258@C #3/IY:259@N reasonable false Created 0 bonds > bond #3/IY:259@C #3/IY:260@N reasonable false Created 0 bonds > bond #3/IY:260@C #3/IY:261@N reasonable false Created 0 bonds > bond #3/IY:261@C #3/IY:262@N reasonable false Created 0 bonds > bond #3/IY:262@C #3/IY:263@N reasonable false Created 0 bonds > bond #3/IY:263@C #3/IY:264@N reasonable false Created 0 bonds > bond #3/IY:264@C #3/IY:265@N reasonable false Created 0 bonds > bond #3/IY:265@C #3/IY:266@N reasonable false Created 0 bonds > bond #3/IY:266@C #3/IY:267@N reasonable false Created 0 bonds > bond #3/IY:267@C #3/IY:268@N reasonable false Created 0 bonds > bond #3/IY:268@C #3/IY:269@N reasonable false Created 0 bonds > bond #3/IY:269@C #3/IY:270@N reasonable false Created 0 bonds > bond #3/IY:270@C #3/IY:271@N reasonable false Created 0 bonds > bond #3/IY:271@C #3/IY:272@N reasonable false Created 0 bonds > bond #3/IY:272@C #3/IY:273@N reasonable false Created 0 bonds > bond #3/IY:273@C #3/IY:274@N reasonable false Created 0 bonds > bond #3/IY:274@C #3/IY:275@N reasonable false Created 0 bonds > bond #3/IY:275@C #3/IY:276@N reasonable false Created 0 bonds > bond #3/IY:276@C #3/IY:277@N reasonable false Created 0 bonds > bond #3/IY:277@C #3/IY:278@N reasonable false Created 0 bonds > bond #3/IY:278@C #3/IY:279@N reasonable false Created 0 bonds > bond #3/IY:279@C #3/IY:280@N reasonable false Created 0 bonds > bond #3/IY:280@C #3/IY:281@N reasonable false Created 0 bonds > bond #3/IY:281@C #3/IY:282@N reasonable false Created 0 bonds > bond #3/IY:282@C #3/IY:283@N reasonable false Created 0 bonds > bond #3/IY:283@C #3/IY:284@N reasonable false Created 0 bonds > bond #3/IY:284@C #3/IY:285@N reasonable false Created 0 bonds > bond #3/IY:171@C #3/IY:172@N reasonable false Created 0 bonds > bond #3/IY:172@C #3/IY:173@N reasonable false Created 0 bonds > bond #3/IY:173@C #3/IY:174@N reasonable false Created 0 bonds > bond #3/IY:174@C #3/IY:175@N reasonable false Created 0 bonds > bond #3/IY:175@C #3/IY:176@N reasonable false Created 0 bonds > bond #3/IY:176@C #3/IY:177@N reasonable false Created 0 bonds > bond #3/IY:177@C #3/IY:178@N reasonable false Created 0 bonds > bond #3/IY:178@C #3/IY:179@N reasonable false Created 1 bond > bond #3/IY:119@C #3/IY:120@N reasonable false Created 0 bonds > bond #3/IY:120@C #3/IY:121@N reasonable false Created 0 bonds > bond #3/IY:121@C #3/IY:122@N reasonable false Created 1 bond > bond #3/IY:96@C #3/IY:97@N reasonable false Created 0 bonds > bond #3/IY:97@C #3/IY:98@N reasonable false Created 1 bond > bond #3/IY:76@C #3/IY:77@N reasonable false Created 0 bonds > bond #3/IY:77@C #3/IY:78@N reasonable false Created 1 bond > bond #3/IY:179@C #3/IY:180@N reasonable false Created 0 bonds > bond #3/IY:180@C #3/IY:181@N reasonable false Created 0 bonds > bond #3/IY:181@C #3/IY:182@N reasonable false Created 0 bonds > bond #3/IY:182@C #3/IY:183@N reasonable false Created 0 bonds > bond #3/IY:183@C #3/IY:184@N reasonable false Created 0 bonds > bond #3/IY:184@C #3/IY:185@N reasonable false Created 0 bonds > bond #3/IY:185@C #3/IY:186@N reasonable false Created 0 bonds > bond #3/IY:186@C #3/IY:187@N reasonable false Created 0 bonds > bond #3/IY:187@C #3/IY:188@N reasonable false Created 0 bonds > bond #3/IY:188@C #3/IY:189@N reasonable false Created 0 bonds > bond #3/IY:189@C #3/IY:190@N reasonable false Created 0 bonds > bond #3/IY:190@C #3/IY:191@N reasonable false Created 0 bonds > bond #3/IY:191@C #3/IY:192@N reasonable false Created 0 bonds > bond #3/IY:192@C #3/IY:193@N reasonable false Created 0 bonds > bond #3/IY:193@C #3/IY:194@N reasonable false Created 0 bonds > bond #3/IY:194@C #3/IY:195@N reasonable false Created 0 bonds > bond #3/IY:195@C #3/IY:196@N reasonable false Created 0 bonds > bond #3/IY:196@C #3/IY:197@N reasonable false Created 0 bonds > bond #3/IY:197@C #3/IY:198@N reasonable false Created 0 bonds > bond #3/IY:198@C #3/IY:199@N reasonable false Created 0 bonds > bond #3/IY:199@C #3/IY:200@N reasonable false Created 0 bonds > bond #3/IY:200@C #3/IY:201@N reasonable false Created 0 bonds > bond #3/IY:201@C #3/IY:202@N reasonable false Created 0 bonds > bond #3/IY:202@C #3/IY:203@N reasonable false Created 0 bonds > bond #3/IY:203@C #3/IY:204@N reasonable false Created 0 bonds > bond #3/IY:204@C #3/IY:205@N reasonable false Created 0 bonds > bond #3/IY:205@C #3/IY:206@N reasonable false Created 0 bonds > bond #3/IY:206@C #3/IY:207@N reasonable false Created 0 bonds > bond #3/IY:207@C #3/IY:208@N reasonable false Created 0 bonds > bond #3/IY:208@C #3/IY:209@N reasonable false Created 0 bonds > bond #3/IY:209@C #3/IY:210@N reasonable false Created 0 bonds > bond #3/IY:210@C #3/IY:211@N reasonable false Created 0 bonds > bond #3/IY:211@C #3/IY:212@N reasonable false Created 0 bonds > bond #3/IY:212@C #3/IY:213@N reasonable false Created 0 bonds > bond #3/IY:213@C #3/IY:214@N reasonable false Created 0 bonds > bond #3/IY:214@C #3/IY:215@N reasonable false Created 0 bonds > bond #3/IY:215@C #3/IY:216@N reasonable false Created 1 bond > bond #3/IY:66@C #3/IY:67@N reasonable false Created 0 bonds > bond #3/IY:67@C #3/IY:68@N reasonable false Created 0 bonds > bond #3/IY:68@C #3/IY:69@N reasonable false Created 0 bonds > bond #3/IY:69@C #3/IY:70@N reasonable false Created 0 bonds > bond #3/IY:70@C #3/IY:71@N reasonable false Created 0 bonds > bond #3/IY:71@C #3/IY:72@N reasonable false Created 0 bonds > bond #3/IY:162@C #3/IY:163@N reasonable false Created 0 bonds > bond #3/IY:163@C #3/IY:164@N reasonable false Created 0 bonds > bond #3/IY:164@C #3/IY:165@N reasonable false Created 0 bonds > bond #3/IY:165@C #3/IY:166@N reasonable false Created 0 bonds > bond #3/IY:166@C #3/IY:167@N reasonable false Created 0 bonds > bond #3/IY:167@C #3/IY:168@N reasonable false Created 0 bonds > bond #3/IY:168@C #3/IY:169@N reasonable false Created 0 bonds > bond #3/IY:125@C #3/IY:126@N reasonable false Created 0 bonds > bond #3/IY:126@C #3/IY:127@N reasonable false Created 0 bonds > bond #3/IY:127@C #3/IY:128@N reasonable false Created 0 bonds > bond #3/IY:128@C #3/IY:129@N reasonable false Created 0 bonds > bond #3/IY:129@C #3/IY:130@N reasonable false Created 0 bonds > bond #3/IY:130@C #3/IY:131@N reasonable false Created 0 bonds > bond #3/IY:131@C #3/IY:132@N reasonable false Created 0 bonds > bond #3/IY:132@C #3/IY:133@N reasonable false Created 0 bonds > bond #3/IY:133@C #3/IY:134@N reasonable false Created 0 bonds > bond #3/IY:134@C #3/IY:135@N reasonable false Created 0 bonds > bond #3/IY:135@C #3/IY:136@N reasonable false Created 0 bonds > bond #3/IY:136@C #3/IY:137@N reasonable false Created 0 bonds > bond #3/IY:137@C #3/IY:138@N reasonable false Created 0 bonds > bond #3/IY:138@C #3/IY:139@N reasonable false Created 0 bonds > bond #3/IY:139@C #3/IY:140@N reasonable false Created 0 bonds > bond #3/IY:140@C #3/IY:141@N reasonable false Created 0 bonds > bond #3/IY:141@C #3/IY:142@N reasonable false Created 0 bonds > bond #3/IY:142@C #3/IY:143@N reasonable false Created 0 bonds > bond #3/IY:143@C #3/IY:144@N reasonable false Created 0 bonds > bond #3/IY:144@C #3/IY:145@N reasonable false Created 0 bonds > bond #3/IY:145@C #3/IY:146@N reasonable false Created 0 bonds > bond #3/IY:146@C #3/IY:147@N reasonable false Created 0 bonds > bond #3/IY:147@C #3/IY:148@N reasonable false Created 0 bonds > bond #3/IY:148@C #3/IY:149@N reasonable false Created 0 bonds > bond #3/IY:149@C #3/IY:150@N reasonable false Created 0 bonds > bond #3/IY:150@C #3/IY:151@N reasonable false Created 0 bonds > bond #3/IY:151@C #3/IY:152@N reasonable false Created 0 bonds > bond #3/IY:152@C #3/IY:153@N reasonable false Created 0 bonds > bond #3/IY:153@C #3/IY:154@N reasonable false Created 1 bond > bond #3/IY:78@C #3/IY:79@N reasonable false Created 0 bonds > bond #3/IY:79@C #3/IY:80@N reasonable false Created 0 bonds > bond #3/IY:80@C #3/IY:81@N reasonable false Created 0 bonds > bond #3/IY:81@C #3/IY:82@N reasonable false Created 0 bonds > bond #3/IY:82@C #3/IY:83@N reasonable false Created 0 bonds > bond #3/IY:83@C #3/IY:84@N reasonable false Created 0 bonds > bond #3/IY:84@C #3/IY:85@N reasonable false Created 0 bonds > bond #3/IY:85@C #3/IY:86@N reasonable false Created 0 bonds > bond #3/IY:86@C #3/IY:87@N reasonable false Created 0 bonds > bond #3/IY:87@C #3/IY:88@N reasonable false Created 0 bonds > bond #3/IY:88@C #3/IY:89@N reasonable false Created 0 bonds > bond #3/IY:89@C #3/IY:90@N reasonable false Created 0 bonds > bond #3/IY:90@C #3/IY:91@N reasonable false Created 0 bonds > bond #3/IY:91@C #3/IY:92@N reasonable false Created 0 bonds > bond #3/IY:92@C #3/IY:93@N reasonable false Created 0 bonds > bond #3/IY:93@C #3/IY:94@N reasonable false Created 0 bonds > bond #3/IY:94@C #3/IY:95@N reasonable false Created 0 bonds > bond #3/IY:95@C #3/IY:96@N reasonable false Created 1 bond > bond #3/IY:2@C #3/IY:3@N reasonable false Created 0 bonds > bond #3/IY:3@C #3/IY:4@N reasonable false Created 0 bonds > bond #3/IY:4@C #3/IY:5@N reasonable false Created 0 bonds > bond #3/IY:5@C #3/IY:6@N reasonable false Created 0 bonds > bond #3/IY:6@C #3/IY:7@N reasonable false Created 0 bonds > bond #3/IY:7@C #3/IY:8@N reasonable false Created 0 bonds > bond #3/IY:8@C #3/IY:9@N reasonable false Created 0 bonds > bond #3/IY:9@C #3/IY:10@N reasonable false Created 0 bonds > bond #3/IY:10@C #3/IY:11@N reasonable false Created 0 bonds > bond #3/IY:11@C #3/IY:12@N reasonable false Created 0 bonds > bond #3/IY:12@C #3/IY:13@N reasonable false Created 0 bonds > bond #3/IY:13@C #3/IY:14@N reasonable false Created 0 bonds > bond #3/IY:14@C #3/IY:15@N reasonable false Created 1 bond > bond #3/IY:15@C #3/IY:16@N reasonable false Created 0 bonds > bond #3/IY:16@C #3/IY:17@N reasonable false Created 0 bonds > bond #3/IY:17@C #3/IY:18@N reasonable false Created 0 bonds > bond #3/IY:20@C #3/IY:21@N reasonable false Created 0 bonds > bond #3/IY:21@C #3/IY:22@N reasonable false Created 0 bonds > bond #3/IY:22@C #3/IY:23@N reasonable false Created 0 bonds > bond #3/IY:23@C #3/IY:24@N reasonable false Created 0 bonds > bond #3/IY:24@C #3/IY:25@N reasonable false Created 0 bonds > bond #3/IY:25@C #3/IY:26@N reasonable false Created 0 bonds > bond #3/IY:26@C #3/IY:27@N reasonable false Created 0 bonds > bond #3/IY:27@C #3/IY:28@N reasonable false Created 0 bonds > bond #3/IY:28@C #3/IY:29@N reasonable false Created 0 bonds > bond #3/IY:29@C #3/IY:30@N reasonable false Created 0 bonds > bond #3/IY:30@C #3/IY:31@N reasonable false Created 0 bonds > bond #3/IY:31@C #3/IY:32@N reasonable false Created 0 bonds > bond #3/IY:32@C #3/IY:33@N reasonable false Created 0 bonds > bond #3/IY:33@C #3/IY:34@N reasonable false Created 0 bonds > bond #3/IY:34@C #3/IY:35@N reasonable false Created 0 bonds > bond #3/IY:35@C #3/IY:36@N reasonable false Created 0 bonds > bond #3/IY:36@C #3/IY:37@N reasonable false Created 0 bonds > bond #3/IY:37@C #3/IY:38@N reasonable false Created 1 bond > bond #3/IY:38@C #3/IY:39@N reasonable false Created 0 bonds > bond #3/IY:39@C #3/IY:40@N reasonable false Created 0 bonds > bond #3/IY:40@C #3/IY:41@N reasonable false Created 0 bonds > bond #3/IY:41@C #3/IY:42@N reasonable false Created 0 bonds > bond #3/IY:42@C #3/IY:43@N reasonable false Created 0 bonds > bond #3/IY:43@C #3/IY:44@N reasonable false Created 0 bonds > bond #3/IY:44@C #3/IY:45@N reasonable false Created 0 bonds > bond #3/IY:45@C #3/IY:46@N reasonable false Created 0 bonds > bond #3/IY:46@C #3/IY:47@N reasonable false Created 0 bonds > bond #3/IY:47@C #3/IY:48@N reasonable false Created 0 bonds > bond #3/IY:48@C #3/IY:49@N reasonable false Created 0 bonds > bond #3/IY:49@C #3/IY:50@N reasonable false Created 0 bonds > bond #3/IY:50@C #3/IY:51@N reasonable false Created 0 bonds > bond #3/IY:51@C #3/IY:52@N reasonable false Created 0 bonds > bond #3/IY:52@C #3/IY:53@N reasonable false Created 0 bonds > bond #3/IY:53@C #3/IY:54@N reasonable false Created 0 bonds > bond #3/IY:54@C #3/IY:55@N reasonable false Created 0 bonds > bond #3/IY:55@C #3/IY:56@N reasonable false Created 0 bonds > bond #3/IY:56@C #3/IY:57@N reasonable false Created 0 bonds > bond #3/IY:57@C #3/IY:58@N reasonable false Created 0 bonds > bond #3/IY:58@C #3/IY:59@N reasonable false Created 0 bonds > bond #3/IY:59@C #3/IY:60@N reasonable false Created 0 bonds > bond #3/IY:60@C #3/IY:61@N reasonable false Created 0 bonds > bond #3/IY:61@C #3/IY:62@N reasonable false Created 0 bonds > bond #3/IY:62@C #3/IY:63@N reasonable false Created 0 bonds > bond #3/IY:63@C #3/IY:64@N reasonable false Created 0 bonds > bond #3/IY:64@C #3/IY:65@N reasonable false Created 0 bonds > bond #3/IY:65@C #3/IY:66@N reasonable false Created 1 bond > bond #3/IY:122@C #3/IY:123@N reasonable false Created 0 bonds > bond #3/IY:123@C #3/IY:124@N reasonable false Created 0 bonds > bond #3/IY:124@C #3/IY:125@N reasonable false Created 1 bond > bond #3/IY:288@C #3/IY:289@N reasonable false Created 0 bonds > bond #3/IY:289@C #3/IY:290@N reasonable false Created 0 bonds > bond #3/IY:290@C #3/IY:291@N reasonable false Created 0 bonds > bond #3/IY:291@C #3/IY:292@N reasonable false Created 0 bonds > bond #3/IY:292@C #3/IY:293@N reasonable false Created 0 bonds > bond #3/IY:293@C #3/IY:294@N reasonable false Created 0 bonds > bond #3/IY:294@C #3/IY:295@N reasonable false Created 0 bonds > bond #3/IY:98@C #3/IY:99@N reasonable false Created 0 bonds > bond #3/IY:99@C #3/IY:100@N reasonable false Created 0 bonds > bond #3/IY:100@C #3/IY:101@N reasonable false Created 0 bonds > bond #3/IY:101@C #3/IY:102@N reasonable false Created 0 bonds > bond #3/IY:102@C #3/IY:103@N reasonable false Created 0 bonds > bond #3/IY:103@C #3/IY:104@N reasonable false Created 0 bonds > bond #3/IY:104@C #3/IY:105@N reasonable false Created 0 bonds > bond #3/IY:105@C #3/IY:106@N reasonable false Created 0 bonds > bond #3/IY:106@C #3/IY:107@N reasonable false Created 0 bonds > bond #3/IY:107@C #3/IY:108@N reasonable false Created 0 bonds > bond #3/IY:108@C #3/IY:109@N reasonable false Created 0 bonds > bond #3/IY:109@C #3/IY:110@N reasonable false Created 0 bonds > bond #3/IY:110@C #3/IY:111@N reasonable false Created 0 bonds > bond #3/IY:111@C #3/IY:112@N reasonable false Created 0 bonds > bond #3/IY:112@C #3/IY:113@N reasonable false Created 0 bonds > bond #3/IY:113@C #3/IY:114@N reasonable false Created 0 bonds > bond #3/IY:114@C #3/IY:115@N reasonable false Created 0 bonds > bond #3/IY:115@C #3/IY:116@N reasonable false Created 0 bonds > bond #3/IY:116@C #3/IY:117@N reasonable false Created 0 bonds > bond #3/IY:117@C #3/IY:118@N reasonable false Created 0 bonds > bond #3/IY:118@C #3/IY:119@N reasonable false Created 1 bond > select #3/JC 1259 atoms, 1263 bonds, 160 residues, 1 model selected \---------------------************************************************************************************************************************-****-********************************** > build start peptide #3 E 1,1 position > 253.26145227640222,323.16895561049313,318.93294617572474 chainId zz > delete #3/zz:1@OXT > renumber #3/zz start 142 1 residues renumbered > changechains #3/zz JC Chain IDs of 1 residues changed > bond #3/JC:142@C #3/JC:143@N reasonable false Created 1 bond > bond #3/JC:141@C #3/JC:142@N reasonable false Created 1 bond > color #3/JC:142-142@C* red > build start peptide #3 Q 1,1 position > 245.88878959150833,318.9809337422343,316.345575943639 chainId zz > delete #3/zz:1@OXT > renumber #3/zz start 147 1 residues renumbered > changechains #3/zz JC Chain IDs of 1 residues changed > bond #3/JC:147@C #3/JC:148@N reasonable false Created 1 bond > bond #3/JC:146@C #3/JC:147@N reasonable false Created 1 bond > color #3/JC:147-147@C* red > bond #3/JC:148@C #3/JC:149@N reasonable false Created 0 bonds > bond #3/JC:149@C #3/JC:150@N reasonable false Created 0 bonds > bond #3/JC:150@C #3/JC:151@N reasonable false Created 0 bonds > bond #3/JC:151@C #3/JC:152@N reasonable false Created 1 bond > bond #3/JC:88@C #3/JC:89@N reasonable false Created 0 bonds > bond #3/JC:89@C #3/JC:90@N reasonable false Created 0 bonds > bond #3/JC:90@C #3/JC:91@N reasonable false Created 0 bonds > bond #3/JC:91@C #3/JC:92@N reasonable false Created 0 bonds > bond #3/JC:92@C #3/JC:93@N reasonable false Created 0 bonds > bond #3/JC:93@C #3/JC:94@N reasonable false Created 0 bonds > bond #3/JC:94@C #3/JC:95@N reasonable false Created 0 bonds > bond #3/JC:95@C #3/JC:96@N reasonable false Created 0 bonds > bond #3/JC:96@C #3/JC:97@N reasonable false Created 0 bonds > bond #3/JC:97@C #3/JC:98@N reasonable false Created 1 bond > bond #3/JC:98@C #3/JC:99@N reasonable false Created 0 bonds > bond #3/JC:99@C #3/JC:100@N reasonable false Created 0 bonds > bond #3/JC:100@C #3/JC:101@N reasonable false Created 0 bonds > bond #3/JC:101@C #3/JC:102@N reasonable false Created 0 bonds > bond #3/JC:102@C #3/JC:103@N reasonable false Created 1 bond > bond #3/JC:27@C #3/JC:28@N reasonable false Created 0 bonds > bond #3/JC:28@C #3/JC:29@N reasonable false Created 0 bonds > bond #3/JC:29@C #3/JC:30@N reasonable false Created 0 bonds > bond #3/JC:30@C #3/JC:31@N reasonable false Created 0 bonds > bond #3/JC:31@C #3/JC:32@N reasonable false Created 0 bonds > bond #3/JC:32@C #3/JC:33@N reasonable false Created 0 bonds > bond #3/JC:33@C #3/JC:34@N reasonable false Created 1 bond > bond #3/JC:78@C #3/JC:79@N reasonable false Created 0 bonds > bond #3/JC:79@C #3/JC:80@N reasonable false Created 1 bond > bond #3/JC:154@C #3/JC:155@N reasonable false Created 0 bonds > bond #3/JC:155@C #3/JC:156@N reasonable false Created 0 bonds > bond #3/JC:156@C #3/JC:157@N reasonable false Created 0 bonds > bond #3/JC:157@C #3/JC:158@N reasonable false Created 1 bond > bond #3/JC:152@C #3/JC:153@N reasonable false Created 0 bonds > bond #3/JC:153@C #3/JC:154@N reasonable false Created 1 bond > bond #3/JC:58@C #3/JC:59@N reasonable false Created 0 bonds > bond #3/JC:59@C #3/JC:60@N reasonable false Created 1 bond > bond #3/JC:158@C #3/JC:159@N reasonable false Created 0 bonds > bond #3/JC:159@C #3/JC:160@N reasonable false Created 1 bond > bond #3/JC:143@C #3/JC:144@N reasonable false Created 0 bonds > bond #3/JC:144@C #3/JC:145@N reasonable false Created 0 bonds > bond #3/JC:145@C #3/JC:146@N reasonable false Created 0 bonds > bond #3/JC:34@C #3/JC:35@N reasonable false Created 0 bonds > bond #3/JC:35@C #3/JC:36@N reasonable false Created 0 bonds > bond #3/JC:36@C #3/JC:37@N reasonable false Created 0 bonds > bond #3/JC:37@C #3/JC:38@N reasonable false Created 0 bonds > bond #3/JC:38@C #3/JC:39@N reasonable false Created 0 bonds > bond #3/JC:39@C #3/JC:40@N reasonable false Created 0 bonds > bond #3/JC:40@C #3/JC:41@N reasonable false Created 0 bonds > bond #3/JC:41@C #3/JC:42@N reasonable false Created 0 bonds > bond #3/JC:42@C #3/JC:43@N reasonable false Created 0 bonds > bond #3/JC:43@C #3/JC:44@N reasonable false Created 0 bonds > bond #3/JC:44@C #3/JC:45@N reasonable false Created 0 bonds > bond #3/JC:45@C #3/JC:46@N reasonable false Created 0 bonds > bond #3/JC:46@C #3/JC:47@N reasonable false Created 0 bonds > bond #3/JC:47@C #3/JC:48@N reasonable false Created 0 bonds > bond #3/JC:48@C #3/JC:49@N reasonable false Created 0 bonds > bond #3/JC:49@C #3/JC:50@N reasonable false Created 0 bonds > bond #3/JC:50@C #3/JC:51@N reasonable false Created 0 bonds > bond #3/JC:51@C #3/JC:52@N reasonable false Created 0 bonds > bond #3/JC:52@C #3/JC:53@N reasonable false Created 0 bonds > bond #3/JC:53@C #3/JC:54@N reasonable false Created 0 bonds > bond #3/JC:54@C #3/JC:55@N reasonable false Created 0 bonds > bond #3/JC:55@C #3/JC:56@N reasonable false Created 0 bonds > bond #3/JC:56@C #3/JC:57@N reasonable false Created 0 bonds > bond #3/JC:57@C #3/JC:58@N reasonable false Created 1 bond > bond #3/JC:80@C #3/JC:81@N reasonable false Created 0 bonds > bond #3/JC:81@C #3/JC:82@N reasonable false Created 0 bonds > bond #3/JC:82@C #3/JC:83@N reasonable false Created 0 bonds > bond #3/JC:83@C #3/JC:84@N reasonable false Created 0 bonds > bond #3/JC:84@C #3/JC:85@N reasonable false Created 0 bonds > bond #3/JC:85@C #3/JC:86@N reasonable false Created 0 bonds > bond #3/JC:86@C #3/JC:87@N reasonable false Created 0 bonds > bond #3/JC:87@C #3/JC:88@N reasonable false Created 1 bond > bond #3/JC:103@C #3/JC:104@N reasonable false Created 0 bonds > bond #3/JC:104@C #3/JC:105@N reasonable false Created 0 bonds > bond #3/JC:105@C #3/JC:106@N reasonable false Created 0 bonds > bond #3/JC:106@C #3/JC:107@N reasonable false Created 0 bonds > bond #3/JC:107@C #3/JC:108@N reasonable false Created 0 bonds > bond #3/JC:108@C #3/JC:109@N reasonable false Created 0 bonds > bond #3/JC:109@C #3/JC:110@N reasonable false Created 0 bonds > bond #3/JC:110@C #3/JC:111@N reasonable false Created 0 bonds > bond #3/JC:111@C #3/JC:112@N reasonable false Created 0 bonds > bond #3/JC:112@C #3/JC:113@N reasonable false Created 0 bonds > bond #3/JC:113@C #3/JC:114@N reasonable false Created 0 bonds > bond #3/JC:114@C #3/JC:115@N reasonable false Created 0 bonds > bond #3/JC:115@C #3/JC:116@N reasonable false Created 0 bonds > bond #3/JC:116@C #3/JC:117@N reasonable false Created 0 bonds > bond #3/JC:117@C #3/JC:118@N reasonable false Created 0 bonds > bond #3/JC:118@C #3/JC:119@N reasonable false Created 0 bonds > bond #3/JC:119@C #3/JC:120@N reasonable false Created 0 bonds > bond #3/JC:120@C #3/JC:121@N reasonable false Created 0 bonds > bond #3/JC:121@C #3/JC:122@N reasonable false Created 0 bonds > bond #3/JC:122@C #3/JC:123@N reasonable false Created 0 bonds > bond #3/JC:123@C #3/JC:124@N reasonable false Created 0 bonds > bond #3/JC:124@C #3/JC:125@N reasonable false Created 0 bonds > bond #3/JC:125@C #3/JC:126@N reasonable false Created 0 bonds > bond #3/JC:126@C #3/JC:127@N reasonable false Created 1 bond > bond #3/JC:160@C #3/JC:161@N reasonable false Created 0 bonds > bond #3/JC:161@C #3/JC:162@N reasonable false Created 0 bonds > bond #3/JC:162@C #3/JC:163@N reasonable false Created 0 bonds > bond #3/JC:163@C #3/JC:164@N reasonable false Created 0 bonds > bond #3/JC:164@C #3/JC:165@N reasonable false Created 0 bonds > bond #3/JC:165@C #3/JC:166@N reasonable false Created 0 bonds > bond #3/JC:166@C #3/JC:167@N reasonable false Created 0 bonds > bond #3/JC:167@C #3/JC:168@N reasonable false Created 0 bonds > bond #3/JC:168@C #3/JC:169@N reasonable false Created 0 bonds > bond #3/JC:169@C #3/JC:170@N reasonable false Created 0 bonds > bond #3/JC:170@C #3/JC:171@N reasonable false Created 0 bonds > bond #3/JC:171@C #3/JC:172@N reasonable false Created 0 bonds > bond #3/JC:172@C #3/JC:173@N reasonable false Created 0 bonds > bond #3/JC:173@C #3/JC:174@N reasonable false Created 0 bonds > bond #3/JC:174@C #3/JC:175@N reasonable false Created 0 bonds > bond #3/JC:175@C #3/JC:176@N reasonable false Created 0 bonds > bond #3/JC:176@C #3/JC:177@N reasonable false Created 0 bonds > bond #3/JC:177@C #3/JC:178@N reasonable false Created 0 bonds > bond #3/JC:178@C #3/JC:179@N reasonable false Created 0 bonds > bond #3/JC:179@C #3/JC:180@N reasonable false Created 0 bonds > bond #3/JC:180@C #3/JC:181@N reasonable false Created 0 bonds > bond #3/JC:181@C #3/JC:182@N reasonable false Created 0 bonds > bond #3/JC:182@C #3/JC:183@N reasonable false Created 0 bonds > bond #3/JC:127@C #3/JC:128@N reasonable false Created 0 bonds > bond #3/JC:128@C #3/JC:129@N reasonable false Created 0 bonds > bond #3/JC:129@C #3/JC:130@N reasonable false Created 0 bonds > bond #3/JC:130@C #3/JC:131@N reasonable false Created 0 bonds > bond #3/JC:131@C #3/JC:132@N reasonable false Created 0 bonds > bond #3/JC:132@C #3/JC:133@N reasonable false Created 0 bonds > bond #3/JC:133@C #3/JC:134@N reasonable false Created 0 bonds > bond #3/JC:134@C #3/JC:135@N reasonable false Created 0 bonds > bond #3/JC:135@C #3/JC:136@N reasonable false Created 0 bonds > bond #3/JC:136@C #3/JC:137@N reasonable false Created 0 bonds > bond #3/JC:137@C #3/JC:138@N reasonable false Created 0 bonds > bond #3/JC:138@C #3/JC:139@N reasonable false Created 0 bonds > bond #3/JC:139@C #3/JC:140@N reasonable false Created 0 bonds > bond #3/JC:140@C #3/JC:141@N reasonable false Created 0 bonds > bond #3/JC:60@C #3/JC:61@N reasonable false Created 0 bonds > bond #3/JC:61@C #3/JC:62@N reasonable false Created 0 bonds > bond #3/JC:62@C #3/JC:63@N reasonable false Created 0 bonds > bond #3/JC:63@C #3/JC:64@N reasonable false Created 0 bonds > bond #3/JC:64@C #3/JC:65@N reasonable false Created 0 bonds > bond #3/JC:65@C #3/JC:66@N reasonable false Created 0 bonds > bond #3/JC:66@C #3/JC:67@N reasonable false Created 0 bonds > bond #3/JC:67@C #3/JC:68@N reasonable false Created 0 bonds > bond #3/JC:68@C #3/JC:69@N reasonable false Created 0 bonds > bond #3/JC:69@C #3/JC:70@N reasonable false Created 0 bonds > bond #3/JC:70@C #3/JC:71@N reasonable false Created 0 bonds > bond #3/JC:71@C #3/JC:72@N reasonable false Created 0 bonds > bond #3/JC:72@C #3/JC:73@N reasonable false Created 0 bonds > bond #3/JC:73@C #3/JC:74@N reasonable false Created 0 bonds > bond #3/JC:74@C #3/JC:75@N reasonable false Created 0 bonds > bond #3/JC:75@C #3/JC:76@N reasonable false Created 0 bonds > bond #3/JC:76@C #3/JC:77@N reasonable false Created 0 bonds > bond #3/JC:77@C #3/JC:78@N reasonable false Created 1 bond > bond #3/JC:22@C #3/JC:23@N reasonable false Created 0 bonds > bond #3/JC:23@C #3/JC:24@N reasonable false Created 0 bonds > bond #3/JC:24@C #3/JC:25@N reasonable false Created 0 bonds > bond #3/JC:25@C #3/JC:26@N reasonable false Created 0 bonds > bond #3/JC:26@C #3/JC:27@N reasonable false Created 1 bond > select #3/D6 387 atoms, 381 bonds, 51 residues, 1 model selected \------*****--**************************-************----------********--- > build start peptide #3 RD 1,1 1,1 position > 240.95136576070178,300.84769718569873,326.9298774506158 chainId zz > delete #3/zz:2@OXT > renumber #3/zz start 12 2 residues renumbered > changechains #3/zz D6 Chain IDs of 2 residues changed > bond #3/D6:13@C #3/D6:14@N reasonable false Created 1 bond > bond #3/D6:11@C #3/D6:12@N reasonable false Created 1 bond > color #3/D6:12-13@C* red > build start peptide #3 K 1,1 position > 265.73153028549467,312.79277069016905,316.5874818354688 chainId zz > delete #3/zz:1@OXT > renumber #3/zz start 40 1 residues renumbered > changechains #3/zz D6 Chain IDs of 1 residues changed > bond #3/D6:40@C #3/D6:41@N reasonable false Created 1 bond > bond #3/D6:39@C #3/D6:40@N reasonable false Created 1 bond > color #3/D6:40-40@C* red > bond #3/D6:46@C #3/D6:47@N reasonable false Created 0 bonds > bond #3/D6:47@C #3/D6:48@N reasonable false Created 0 bonds > bond #3/D6:48@C #3/D6:49@N reasonable false Created 0 bonds > bond #3/D6:49@C #3/D6:50@N reasonable false Created 1 bond > bond #3/D6:44@C #3/D6:45@N reasonable false Created 0 bonds > bond #3/D6:45@C #3/D6:46@N reasonable false Created 1 bond > bond #3/D6:63@C #3/D6:64@N reasonable false Created 0 bonds > bond #3/D6:64@C #3/D6:65@N reasonable false Created 1 bond > bond #3/D6:9@C #3/D6:10@N reasonable false Created 0 bonds > bond #3/D6:10@C #3/D6:11@N reasonable false Created 0 bonds > bond #3/D6:7@C #3/D6:8@N reasonable false Created 0 bonds > bond #3/D6:8@C #3/D6:9@N reasonable false Created 1 bond > bond #3/D6:14@C #3/D6:15@N reasonable false Created 0 bonds > bond #3/D6:15@C #3/D6:16@N reasonable false Created 0 bonds > bond #3/D6:16@C #3/D6:17@N reasonable false Created 0 bonds > bond #3/D6:17@C #3/D6:18@N reasonable false Created 0 bonds > bond #3/D6:18@C #3/D6:19@N reasonable false Created 0 bonds > bond #3/D6:19@C #3/D6:20@N reasonable false Created 0 bonds > bond #3/D6:20@C #3/D6:21@N reasonable false Created 0 bonds > bond #3/D6:21@C #3/D6:22@N reasonable false Created 0 bonds > bond #3/D6:22@C #3/D6:23@N reasonable false Created 0 bonds > bond #3/D6:23@C #3/D6:24@N reasonable false Created 0 bonds > bond #3/D6:24@C #3/D6:25@N reasonable false Created 0 bonds > bond #3/D6:25@C #3/D6:26@N reasonable false Created 0 bonds > bond #3/D6:26@C #3/D6:27@N reasonable false Created 0 bonds > bond #3/D6:27@C #3/D6:28@N reasonable false Created 0 bonds > bond #3/D6:28@C #3/D6:29@N reasonable false Created 0 bonds > bond #3/D6:29@C #3/D6:30@N reasonable false Created 0 bonds > bond #3/D6:30@C #3/D6:31@N reasonable false Created 0 bonds > bond #3/D6:31@C #3/D6:32@N reasonable false Created 0 bonds > bond #3/D6:32@C #3/D6:33@N reasonable false Created 0 bonds > bond #3/D6:33@C #3/D6:34@N reasonable false Created 0 bonds > bond #3/D6:34@C #3/D6:35@N reasonable false Created 0 bonds > bond #3/D6:35@C #3/D6:36@N reasonable false Created 0 bonds > bond #3/D6:36@C #3/D6:37@N reasonable false Created 0 bonds > bond #3/D6:37@C #3/D6:38@N reasonable false Created 0 bonds > bond #3/D6:38@C #3/D6:39@N reasonable false Created 0 bonds > bond #3/D6:50@C #3/D6:51@N reasonable false Created 0 bonds > bond #3/D6:51@C #3/D6:52@N reasonable false Created 0 bonds > bond #3/D6:65@C #3/D6:66@N reasonable false Created 0 bonds > bond #3/D6:66@C #3/D6:67@N reasonable false Created 0 bonds > bond #3/D6:67@C #3/D6:68@N reasonable false Created 0 bonds > bond #3/D6:68@C #3/D6:69@N reasonable false Created 0 bonds > bond #3/D6:69@C #3/D6:70@N reasonable false Created 0 bonds > bond #3/D6:41@C #3/D6:42@N reasonable false Created 0 bonds > bond #3/D6:42@C #3/D6:43@N reasonable false Created 0 bonds > bond #3/D6:43@C #3/D6:44@N reasonable false Created 1 bond > save ""/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/central_stalk/centralstalk_protein_version1_renumbered model.cif"" > models #2 Not saving entity_poly_seq for non-authoritative sequences > save ""/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/central_stalk/centralstalk_protein_version1_renumbered model.cxs"" > save ""/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cif"" models > #3 Not saving entity_poly_seq for non-authoritative sequences > save ""/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV- > Full/cryosparc_P31_J281_004_volume_map_sharp--VC- > Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cxs"" ——— End of log from Mon Nov 25 16:32:30 2024 ——— opened ChimeraX session ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,3 Model Number: Z1C8000ANFN/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 5 days, 22 hours, 8 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2723QE: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.0 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX