Crash in background load of OpenMM forcefields

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.10.198-gentoo-x86_64-Intel-R-_Xeon-R-_Silver_4110_CPU_@_2.10GHz-with-glibc2.37
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
loaded pdb file then loaded cryoEM map.
Fatal Python error: Segmentation fault

Current thread 0x00007f83bedff6c0 (most recent call first):
  File "/home/pauline/.local/share/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/forcefields.py", line 67 in _background_load_ff
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/concurrent/futures/thread.py", line 58 in run
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/concurrent/futures/thread.py", line 83 in _worker
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f84f7d5a740 (most recent call first):
  File "", line 647 in _compile_bytecode
  File "", line 978 in get_code
  File "", line 846 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/home/pauline/.local/share/ChimeraX/1.6/site-packages/chimerax/isolde/validation/ramaplot/__init__.py", line 1 in 
  File "", line 228 in _call_with_frames_removed
  File "", line 850 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "", line 228 in _call_with_frames_removed
  File "", line 972 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/home/pauline/.local/share/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py", line 722 in register_next_frame
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 54 in draw_new_frame
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib64/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/pauline/Desktop/flipvol_maps/7lrf_3spirals.cxs format session

Opened cryosparc_P31_J316_010_volume_map_sharp.mrc as #1, grid size
900,900,900, pixel 0.485, shown at level 0.0115, step 4, values float32  
opened ChimeraX session  

> combine #2 #3 #4 close true

Remapping chain ID '0' in copy of combination #3 to 'A7'  
Remapping chain ID '1' in copy of combination #3 to 'A8'  
Remapping chain ID '2' in copy of combination #3 to 'A9'  
Remapping chain ID '3' in copy of combination #3 to 'A0'  
Remapping chain ID '4' in copy of combination #3 to 'BA'  
Remapping chain ID '5' in copy of combination #3 to 'BB'  
Remapping chain ID '6' in copy of combination #3 to 'BC'  
Remapping chain ID '7' in copy of combination #3 to 'BD'  
Remapping chain ID '8' in copy of combination #3 to 'BE'  
Remapping chain ID '9' in copy of combination #3 to 'BF'  
Remapping chain ID 'A' in copy of combination #3 to 'BG'  
Remapping chain ID 'A1' in copy of combination #3 to 'BH'  
Remapping chain ID 'A2' in copy of combination #3 to 'BI'  
Remapping chain ID 'A3' in copy of combination #3 to 'BJ'  
Remapping chain ID 'A4' in copy of combination #3 to 'BK'  
Remapping chain ID 'A5' in copy of combination #3 to 'BL'  
Remapping chain ID 'A6' in copy of combination #3 to 'BM'  
Remapping chain ID 'AA' in copy of combination #3 to 'BN'  
Remapping chain ID 'AB' in copy of combination #3 to 'BO'  
Remapping chain ID 'AC' in copy of combination #3 to 'BP'  
Remapping chain ID 'AD' in copy of combination #3 to 'BQ'  
Remapping chain ID 'AE' in copy of combination #3 to 'BR'  
Remapping chain ID 'AF' in copy of combination #3 to 'BS'  
Remapping chain ID 'AG' in copy of combination #3 to 'BT'  
Remapping chain ID 'AH' in copy of combination #3 to 'BU'  
Remapping chain ID 'AI' in copy of combination #3 to 'BV'  
Remapping chain ID 'AJ' in copy of combination #3 to 'BW'  
Remapping chain ID 'AK' in copy of combination #3 to 'BX'  
Remapping chain ID 'AL' in copy of combination #3 to 'BY'  
Remapping chain ID 'AM' in copy of combination #3 to 'BZ'  
Remapping chain ID 'AN' in copy of combination #3 to 'Ba'  
Remapping chain ID 'AO' in copy of combination #3 to 'Bb'  
Remapping chain ID 'AP' in copy of combination #3 to 'Bc'  
Remapping chain ID 'AQ' in copy of combination #3 to 'Bd'  
Remapping chain ID 'AR' in copy of combination #3 to 'Be'  
Remapping chain ID 'AS' in copy of combination #3 to 'Bf'  
Remapping chain ID 'AT' in copy of combination #3 to 'Bg'  
Remapping chain ID 'AU' in copy of combination #3 to 'Bh'  
Remapping chain ID 'AV' in copy of combination #3 to 'Bi'  
Remapping chain ID 'AW' in copy of combination #3 to 'Bj'  
Remapping chain ID 'AX' in copy of combination #3 to 'Bk'  
Remapping chain ID 'AY' in copy of combination #3 to 'Bl'  
Remapping chain ID 'AZ' in copy of combination #3 to 'Bm'  
Remapping chain ID 'Aa' in copy of combination #3 to 'Bn'  
Remapping chain ID 'Ab' in copy of combination #3 to 'Bo'  
Remapping chain ID 'Ac' in copy of combination #3 to 'Bp'  
Remapping chain ID 'Ad' in copy of combination #3 to 'Bq'  
Remapping chain ID 'Ae' in copy of combination #3 to 'Br'  
Remapping chain ID 'Af' in copy of combination #3 to 'Bs'  
Remapping chain ID 'Ag' in copy of combination #3 to 'Bt'  
Remapping chain ID 'Ah' in copy of combination #3 to 'Bu'  
Remapping chain ID 'Ai' in copy of combination #3 to 'Bv'  
Remapping chain ID 'Aj' in copy of combination #3 to 'Bw'  
Remapping chain ID 'Ak' in copy of combination #3 to 'Bx'  
Remapping chain ID 'Al' in copy of combination #3 to 'By'  
Remapping chain ID 'Am' in copy of combination #3 to 'Bz'  
Remapping chain ID 'An' in copy of combination #3 to 'B1'  
Remapping chain ID 'Ao' in copy of combination #3 to 'B2'  
Remapping chain ID 'Ap' in copy of combination #3 to 'B3'  
Remapping chain ID 'Aq' in copy of combination #3 to 'B4'  
Remapping chain ID 'Ar' in copy of combination #3 to 'B5'  
Remapping chain ID 'As' in copy of combination #3 to 'B6'  
Remapping chain ID 'At' in copy of combination #3 to 'B7'  
Remapping chain ID 'Au' in copy of combination #3 to 'B8'  
Remapping chain ID 'Av' in copy of combination #3 to 'B9'  
Remapping chain ID 'Aw' in copy of combination #3 to 'B0'  
Remapping chain ID 'Ax' in copy of combination #3 to 'CA'  
Remapping chain ID 'Ay' in copy of combination #3 to 'CB'  
Remapping chain ID 'Az' in copy of combination #3 to 'CC'  
Remapping chain ID 'B' in copy of combination #3 to 'CD'  
Remapping chain ID 'C' in copy of combination #3 to 'CE'  
Remapping chain ID 'D' in copy of combination #3 to 'CF'  
Remapping chain ID 'E' in copy of combination #3 to 'CG'  
Remapping chain ID 'F' in copy of combination #3 to 'CH'  
Remapping chain ID 'G' in copy of combination #3 to 'CI'  
Remapping chain ID 'H' in copy of combination #3 to 'CJ'  
Remapping chain ID 'I' in copy of combination #3 to 'CK'  
Remapping chain ID 'J' in copy of combination #3 to 'CL'  
Remapping chain ID 'K' in copy of combination #3 to 'CM'  
Remapping chain ID 'L' in copy of combination #3 to 'CN'  
Remapping chain ID 'M' in copy of combination #3 to 'CO'  
Remapping chain ID 'N' in copy of combination #3 to 'CP'  
Remapping chain ID 'O' in copy of combination #3 to 'CQ'  
Remapping chain ID 'P' in copy of combination #3 to 'CR'  
Remapping chain ID 'Q' in copy of combination #3 to 'CS'  
Remapping chain ID 'R' in copy of combination #3 to 'CT'  
Remapping chain ID 'S' in copy of combination #3 to 'CU'  
Remapping chain ID 'T' in copy of combination #3 to 'CV'  
Remapping chain ID 'U' in copy of combination #3 to 'CW'  
Remapping chain ID 'V' in copy of combination #3 to 'CX'  
Remapping chain ID 'W' in copy of combination #3 to 'CY'  
Remapping chain ID 'X' in copy of combination #3 to 'CZ'  
Remapping chain ID 'Y' in copy of combination #3 to 'Ca'  
Remapping chain ID 'Z' in copy of combination #3 to 'Cb'  
Remapping chain ID 'a' in copy of combination #3 to 'Cc'  
Remapping chain ID 'b' in copy of combination #3 to 'Cd'  
Remapping chain ID 'c' in copy of combination #3 to 'Ce'  
Remapping chain ID 'd' in copy of combination #3 to 'Cf'  
Remapping chain ID 'e' in copy of combination #3 to 'Cg'  
Remapping chain ID 'f' in copy of combination #3 to 'Ch'  
Remapping chain ID 'g' in copy of combination #3 to 'Ci'  
Remapping chain ID 'h' in copy of combination #3 to 'Cj'  
Remapping chain ID 'i' in copy of combination #3 to 'Ck'  
Remapping chain ID 'j' in copy of combination #3 to 'Cl'  
Remapping chain ID 'k' in copy of combination #3 to 'Cm'  
Remapping chain ID 'l' in copy of combination #3 to 'Cn'  
Remapping chain ID 'm' in copy of combination #3 to 'Co'  
Remapping chain ID 'n' in copy of combination #3 to 'Cp'  
Remapping chain ID 'o' in copy of combination #3 to 'Cq'  
Remapping chain ID 'p' in copy of combination #3 to 'Cr'  
Remapping chain ID 'q' in copy of combination #3 to 'Cs'  
Remapping chain ID 'r' in copy of combination #3 to 'Ct'  
Remapping chain ID 's' in copy of combination #3 to 'Cu'  
Remapping chain ID 't' in copy of combination #3 to 'Cv'  
Remapping chain ID 'u' in copy of combination #3 to 'Cw'  
Remapping chain ID 'v' in copy of combination #3 to 'Cx'  
Remapping chain ID 'w' in copy of combination #3 to 'Cy'  
Remapping chain ID 'x' in copy of combination #3 to 'Cz'  
Remapping chain ID 'y' in copy of combination #3 to 'C1'  
Remapping chain ID 'z' in copy of combination #3 to 'C2'  
Remapping chain ID '0' in copy of combination #4 to 'C3'  
Remapping chain ID '1' in copy of combination #4 to 'C4'  
Remapping chain ID '2' in copy of combination #4 to 'C5'  
Remapping chain ID '3' in copy of combination #4 to 'C6'  
Remapping chain ID '4' in copy of combination #4 to 'C7'  
Remapping chain ID '5' in copy of combination #4 to 'C8'  
Remapping chain ID '6' in copy of combination #4 to 'C9'  
Remapping chain ID '7' in copy of combination #4 to 'C0'  
Remapping chain ID '8' in copy of combination #4 to 'DA'  
Remapping chain ID '9' in copy of combination #4 to 'DB'  
Remapping chain ID 'A' in copy of combination #4 to 'DC'  
Remapping chain ID 'A1' in copy of combination #4 to 'DD'  
Remapping chain ID 'A2' in copy of combination #4 to 'DE'  
Remapping chain ID 'A3' in copy of combination #4 to 'DF'  
Remapping chain ID 'A4' in copy of combination #4 to 'DG'  
Remapping chain ID 'A5' in copy of combination #4 to 'DH'  
Remapping chain ID 'A6' in copy of combination #4 to 'DI'  
Remapping chain ID 'AA' in copy of combination #4 to 'DJ'  
Remapping chain ID 'AB' in copy of combination #4 to 'DK'  
Remapping chain ID 'AC' in copy of combination #4 to 'DL'  
Remapping chain ID 'AD' in copy of combination #4 to 'DM'  
Remapping chain ID 'AE' in copy of combination #4 to 'DN'  
Remapping chain ID 'AF' in copy of combination #4 to 'DO'  
Remapping chain ID 'AG' in copy of combination #4 to 'DP'  
Remapping chain ID 'AH' in copy of combination #4 to 'DQ'  
Remapping chain ID 'AI' in copy of combination #4 to 'DR'  
Remapping chain ID 'AJ' in copy of combination #4 to 'DS'  
Remapping chain ID 'AK' in copy of combination #4 to 'DT'  
Remapping chain ID 'AL' in copy of combination #4 to 'DU'  
Remapping chain ID 'AM' in copy of combination #4 to 'DV'  
Remapping chain ID 'AN' in copy of combination #4 to 'DW'  
Remapping chain ID 'AO' in copy of combination #4 to 'DX'  
Remapping chain ID 'AP' in copy of combination #4 to 'DY'  
Remapping chain ID 'AQ' in copy of combination #4 to 'DZ'  
Remapping chain ID 'AR' in copy of combination #4 to 'Da'  
Remapping chain ID 'AS' in copy of combination #4 to 'Db'  
Remapping chain ID 'AT' in copy of combination #4 to 'Dc'  
Remapping chain ID 'AU' in copy of combination #4 to 'Dd'  
Remapping chain ID 'AV' in copy of combination #4 to 'De'  
Remapping chain ID 'AW' in copy of combination #4 to 'Df'  
Remapping chain ID 'AX' in copy of combination #4 to 'Dg'  
Remapping chain ID 'AY' in copy of combination #4 to 'Dh'  
Remapping chain ID 'AZ' in copy of combination #4 to 'Di'  
Remapping chain ID 'Aa' in copy of combination #4 to 'Dj'  
Remapping chain ID 'Ab' in copy of combination #4 to 'Dk'  
Remapping chain ID 'Ac' in copy of combination #4 to 'Dl'  
Remapping chain ID 'Ad' in copy of combination #4 to 'Dm'  
Remapping chain ID 'Ae' in copy of combination #4 to 'Dn'  
Remapping chain ID 'Af' in copy of combination #4 to 'Do'  
Remapping chain ID 'Ag' in copy of combination #4 to 'Dp'  
Remapping chain ID 'Ah' in copy of combination #4 to 'Dq'  
Remapping chain ID 'Ai' in copy of combination #4 to 'Dr'  
Remapping chain ID 'Aj' in copy of combination #4 to 'Ds'  
Remapping chain ID 'Ak' in copy of combination #4 to 'Dt'  
Remapping chain ID 'Al' in copy of combination #4 to 'Du'  
Remapping chain ID 'Am' in copy of combination #4 to 'Dv'  
Remapping chain ID 'An' in copy of combination #4 to 'Dw'  
Remapping chain ID 'Ao' in copy of combination #4 to 'Dx'  
Remapping chain ID 'Ap' in copy of combination #4 to 'Dy'  
Remapping chain ID 'Aq' in copy of combination #4 to 'Dz'  
Remapping chain ID 'Ar' in copy of combination #4 to 'D1'  
Remapping chain ID 'As' in copy of combination #4 to 'D2'  
Remapping chain ID 'At' in copy of combination #4 to 'D3'  
Remapping chain ID 'Au' in copy of combination #4 to 'D4'  
Remapping chain ID 'Av' in copy of combination #4 to 'D5'  
Remapping chain ID 'Aw' in copy of combination #4 to 'D6'  
Remapping chain ID 'Ax' in copy of combination #4 to 'D7'  
Remapping chain ID 'Ay' in copy of combination #4 to 'D8'  
Remapping chain ID 'Az' in copy of combination #4 to 'D9'  
Remapping chain ID 'B' in copy of combination #4 to 'D0'  
Remapping chain ID 'C' in copy of combination #4 to 'EA'  
Remapping chain ID 'D' in copy of combination #4 to 'EB'  
Remapping chain ID 'E' in copy of combination #4 to 'EC'  
Remapping chain ID 'F' in copy of combination #4 to 'ED'  
Remapping chain ID 'G' in copy of combination #4 to 'EE'  
Remapping chain ID 'H' in copy of combination #4 to 'EF'  
Remapping chain ID 'I' in copy of combination #4 to 'EG'  
Remapping chain ID 'J' in copy of combination #4 to 'EH'  
Remapping chain ID 'K' in copy of combination #4 to 'EI'  
Remapping chain ID 'L' in copy of combination #4 to 'EJ'  
Remapping chain ID 'M' in copy of combination #4 to 'EK'  
Remapping chain ID 'N' in copy of combination #4 to 'EL'  
Remapping chain ID 'O' in copy of combination #4 to 'EM'  
Remapping chain ID 'P' in copy of combination #4 to 'EN'  
Remapping chain ID 'Q' in copy of combination #4 to 'EO'  
Remapping chain ID 'R' in copy of combination #4 to 'EP'  
Remapping chain ID 'S' in copy of combination #4 to 'EQ'  
Remapping chain ID 'T' in copy of combination #4 to 'ER'  
Remapping chain ID 'U' in copy of combination #4 to 'ES'  
Remapping chain ID 'V' in copy of combination #4 to 'ET'  
Remapping chain ID 'W' in copy of combination #4 to 'EU'  
Remapping chain ID 'X' in copy of combination #4 to 'EV'  
Remapping chain ID 'Y' in copy of combination #4 to 'EW'  
Remapping chain ID 'Z' in copy of combination #4 to 'EX'  
Remapping chain ID 'a' in copy of combination #4 to 'EY'  
Remapping chain ID 'b' in copy of combination #4 to 'EZ'  
Remapping chain ID 'c' in copy of combination #4 to 'Ea'  
Remapping chain ID 'd' in copy of combination #4 to 'Eb'  
Remapping chain ID 'e' in copy of combination #4 to 'Ec'  
Remapping chain ID 'f' in copy of combination #4 to 'Ed'  
Remapping chain ID 'g' in copy of combination #4 to 'Ee'  
Remapping chain ID 'h' in copy of combination #4 to 'Ef'  
Remapping chain ID 'i' in copy of combination #4 to 'Eg'  
Remapping chain ID 'j' in copy of combination #4 to 'Eh'  
Remapping chain ID 'k' in copy of combination #4 to 'Ei'  
Remapping chain ID 'l' in copy of combination #4 to 'Ej'  
Remapping chain ID 'm' in copy of combination #4 to 'Ek'  
Remapping chain ID 'n' in copy of combination #4 to 'El'  
Remapping chain ID 'o' in copy of combination #4 to 'Em'  
Remapping chain ID 'p' in copy of combination #4 to 'En'  
Remapping chain ID 'q' in copy of combination #4 to 'Eo'  
Remapping chain ID 'r' in copy of combination #4 to 'Ep'  
Remapping chain ID 's' in copy of combination #4 to 'Eq'  
Remapping chain ID 't' in copy of combination #4 to 'Er'  
Remapping chain ID 'u' in copy of combination #4 to 'Es'  
Remapping chain ID 'v' in copy of combination #4 to 'Et'  
Remapping chain ID 'w' in copy of combination #4 to 'Eu'  
Remapping chain ID 'x' in copy of combination #4 to 'Ev'  
Remapping chain ID 'y' in copy of combination #4 to 'Ew'  
Remapping chain ID 'z' in copy of combination #4 to 'Ex'  

> show cartoons

> show #!1 models

> hide #!1 models

> select add #2

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 3 models selected  

> save /home/pauline/Desktop/test.pdb selectedOnly true relModel #1

> close session

> open /home/pauline/Desktop/flipvol_maps/3spirals_7lrf.pdb format pdb

Summary of feedback from opening
/home/pauline/Desktop/flipvol_maps/3spirals_7lrf.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CA (505 )  
Cannot find LINK/SSBOND residue CA (505 )  
Cannot find LINK/SSBOND residue CA (505 )  
Cannot find LINK/SSBOND residue NA (506 )  
Cannot find LINK/SSBOND residue NA (506 )  
43 messages similar to the above omitted  
  
Chain information for 3spirals_7lrf.pdb  
---  
Chain | Description  
1.1/0 1.1/9 1.1/A 1.1/AK 1.1/AL 1.1/AW 1.1/AX 1.1/Ai 1.1/Aj 1.1/Au 1.1/Av
1.1/B 1.1/M 1.1/N 1.1/Y 1.1/Z 1.1/k 1.1/l 1.1/w 1.1/x | No description
available  
1.2/0 1.3/0 1.2/AL 1.3/AL 1.2/AX 1.3/AX 1.2/Aj 1.3/Aj 1.2/Av 1.3/Av 1.2/B
1.3/B 1.2/N 1.3/N 1.2/Z 1.3/Z 1.2/l 1.3/l 1.2/x 1.3/x | No description
available  
1.2/9 1.3/9 1.2/A 1.3/A 1.2/AK 1.3/AK 1.2/AW 1.3/AW 1.2/Ai 1.3/Ai 1.2/Au
1.3/Au 1.2/M 1.3/M 1.2/Y 1.3/Y 1.2/k 1.3/k 1.2/w 1.3/w | No description
available  
  

> hide atoms

> show cartoons

> select add #1

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 10 models
selected  

> save /home/pauline/Desktop/test.pdb relModel #1

> hide #!1 models

> select subtract #1

Nothing selected  

> select add #1.1

67640 atoms, 69210 bonds, 130 pseudobonds, 9030 residues, 3 models selected  

> select add #1.2

135280 atoms, 138420 bonds, 260 pseudobonds, 18060 residues, 6 models selected  

> select add #1.3

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 9 models selected  

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> select subtract #1.1

135280 atoms, 138420 bonds, 260 pseudobonds, 18060 residues, 6 models selected  

> select add #1.1

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 9 models selected  

> select subtract #1.2

135280 atoms, 138420 bonds, 260 pseudobonds, 18060 residues, 6 models selected  

> select subtract #1.3

67640 atoms, 69210 bonds, 130 pseudobonds, 9030 residues, 3 models selected  

> select add #1.3

135280 atoms, 138420 bonds, 260 pseudobonds, 18060 residues, 6 models selected  

> select subtract #1.1

67640 atoms, 69210 bonds, 130 pseudobonds, 9030 residues, 3 models selected  

> select subtract #1.3

Nothing selected  

> hide #!1.1 models

> hide #!1 models

> show #!1 models

> show #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.3 models

> show #!1.2 models

> ui tool show "Map Coordinates"

No model chosen to save relative to  

> save /home/pauline/Desktop/test.cif displayedOnly true bestGuess true
> relModel #1

> select add #1

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 10 models
selected  

> select subtract #1

Nothing selected  

> select add #1

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 10 models
selected  

> save /home/pauline/Desktop/test.cif selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> select subtract #1

Nothing selected  

> select add #1

202920 atoms, 207630 bonds, 390 pseudobonds, 27090 residues, 10 models
selected  

> hide (#!1.1-3 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!1.1-3 & sel-residues)

> show (#!1.1-3 & sel-residues & backbone) target ab

> hide sel cartoons

> hide sel surfaces

> style (#!1.1-3 & sel) stick

Changed 202920 atom styles  

> select subtract #1

Nothing selected  

> close session

> open /home/pauline/Desktop/flipvol_maps/refined_7lrf_x2.pdb format pdb

Chain information for refined_7lrf_x2.pdb  
---  
Chain | Description  
1.1/A 1.1/B | No description available  
1.2/A | No description available  
1.2/B | No description available  
  

> close session

> open /home/pauline/Desktop/flipvol_maps/fitted_7lrf_monomer_trim.pdb format
> pdb

Chain information for fitted_7lrf_monomer_trim.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close session

> open /home/pauline/Desktop/flipvol_maps/fitted_7lrf_monomer_trim.pdb format
> pdb

Chain information for fitted_7lrf_monomer_trim.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /home/pauline/Desktop/flipvol_maps/cryosparc_P31_J316_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P31_J316_010_volume_map_sharp.mrc as #2, grid size
900,900,900, pixel 0.485, shown at step 1, values float32  

> volume #2 region 0,0,0,899,899,899 step 4

> isolde start

> set selectionWidth 4


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/pauline/Desktop/phenix/refined_cryosparc_maps/LocalResolution_5/cryosparc_P31_J316_010_volume_map_half_A_and_cryosparc_P31_J316_010_volume_map_half_B_local_resolution.ccp4

Opened
cryosparc_P31_J316_010_volume_map_half_A_and_cryosparc_P31_J316_010_volume_map_half_B_local_resolution.ccp4
as #1, grid size 900,900,900, pixel 0.485, shown at step 1, values float32  




OpenGL version: 3.3.0 NVIDIA 470.199.02
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_CA.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Precision 7820 Tower
OS: Gentoo 2.14 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           157Gi        71Gi        51Gi        26Mi        33Gi        84Gi
	Swap:          159Gi        30Gi       129Gi

Graphics:
	0000:5b:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106 [GeForce GTX 1060 6GB] [10de:1c03] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] GP106 [GeForce GTX 1060 6GB] [1462:3283]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tristan Croll]

Hmm... I think I'm going to just have to get rid of this approach of loading the force field in a separate thread. In theory it should work fine; in practice it seems to be doing something that's not thread-safe. In honesty I mainly added it at the time when I was pre-loading all the ~15k ligand definitions into the force field making it take a rather long time to instantiate; now I only load those as-needed so loading the core force field is pretty quick.

[Tristan Croll]

Unless there's something deeper going on (who knows... I've never been able to replicate this crash myself), this *should* be fixed. I've moved loading of the force field back to the main thread. The good news is that due to some combination of the march of CPU speed and the more-streamlined main force field, the difference in startup time is practically unnoticeable.