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Opened 2 years ago
Closed 7 months ago
#10135 closed defect (can't reproduce)
Crash saving mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-46-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007f54d11f3740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/weakref.py", line 577 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 1604 in remove_deleted_pointers
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 123 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 798 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 112 in save
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 90 in provider_save
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 51 in display
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> lighting soft
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 87528 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> transparency 50
> combine #2#3#4#5
Remapping chain ID 'A' in temp2.pdb #3 to 'q'
Remapping chain ID 'B' in temp2.pdb #3 to 'r'
Remapping chain ID 'C' in temp2.pdb #3 to 's'
Remapping chain ID 'D' in temp2.pdb #3 to 't'
Remapping chain ID 'E' in temp2.pdb #3 to 'u'
Remapping chain ID 'F' in temp2.pdb #3 to 'v'
Remapping chain ID 'G' in temp2.pdb #3 to 'w'
Remapping chain ID 'H' in temp2.pdb #3 to 'x'
Remapping chain ID 'I' in temp2.pdb #3 to 'y'
Remapping chain ID 'J' in temp2.pdb #3 to 'z'
Remapping chain ID 'K' in temp2.pdb #3 to '1'
Remapping chain ID 'L' in temp2.pdb #3 to '2'
Remapping chain ID 'M' in temp2.pdb #3 to '3'
Remapping chain ID 'N' in temp2.pdb #3 to '4'
Remapping chain ID 'O' in temp2.pdb #3 to '5'
Remapping chain ID 'P' in temp2.pdb #3 to '6'
Remapping chain ID 'Q' in temp2.pdb #3 to '7'
Remapping chain ID 'R' in temp2.pdb #3 to '8'
Remapping chain ID 'S' in temp2.pdb #3 to '9'
Remapping chain ID 'T' in temp2.pdb #3 to '0'
Remapping chain ID 'U' in temp2.pdb #3 to 'AA'
Remapping chain ID 'V' in temp2.pdb #3 to 'AB'
Remapping chain ID 'W' in temp2.pdb #3 to 'AC'
Remapping chain ID 'X' in temp2.pdb #3 to 'AD'
Remapping chain ID 'Y' in temp2.pdb #3 to 'AE'
Remapping chain ID 'Z' in temp2.pdb #3 to 'AF'
Remapping chain ID 'a' in temp2.pdb #3 to 'AG'
Remapping chain ID 'b' in temp2.pdb #3 to 'AH'
Remapping chain ID 'c' in temp2.pdb #3 to 'AI'
Remapping chain ID 'd' in temp2.pdb #3 to 'AJ'
Remapping chain ID 'e' in temp2.pdb #3 to 'AK'
Remapping chain ID 'f' in temp2.pdb #3 to 'AL'
Remapping chain ID 'g' in temp2.pdb #3 to 'AM'
Remapping chain ID 'h' in temp2.pdb #3 to 'AN'
Remapping chain ID 'i' in temp2.pdb #3 to 'AO'
Remapping chain ID 'j' in temp2.pdb #3 to 'AP'
Remapping chain ID 'k' in temp2.pdb #3 to 'AQ'
Remapping chain ID 'l' in temp2.pdb #3 to 'AR'
Remapping chain ID 'm' in temp2.pdb #3 to 'AS'
Remapping chain ID 'n' in temp2.pdb #3 to 'AT'
Remapping chain ID 'o' in temp2.pdb #3 to 'AU'
Remapping chain ID 'p' in temp2.pdb #3 to 'AV'
Remapping chain ID 'A' in temp3.pdb #4 to 'AW'
Remapping chain ID 'B' in temp3.pdb #4 to 'AX'
Remapping chain ID 'C' in temp3.pdb #4 to 'AY'
Remapping chain ID 'D' in temp3.pdb #4 to 'AZ'
Remapping chain ID 'E' in temp3.pdb #4 to 'Aa'
Remapping chain ID 'F' in temp3.pdb #4 to 'Ab'
Remapping chain ID 'G' in temp3.pdb #4 to 'Ac'
Remapping chain ID 'H' in temp3.pdb #4 to 'Ad'
Remapping chain ID 'I' in temp3.pdb #4 to 'Ae'
Remapping chain ID 'J' in temp3.pdb #4 to 'Af'
Remapping chain ID 'K' in temp3.pdb #4 to 'Ag'
Remapping chain ID 'L' in temp3.pdb #4 to 'Ah'
Remapping chain ID 'M' in temp3.pdb #4 to 'Ai'
Remapping chain ID 'N' in temp3.pdb #4 to 'Aj'
Remapping chain ID 'O' in temp3.pdb #4 to 'Ak'
Remapping chain ID 'P' in temp3.pdb #4 to 'Al'
Remapping chain ID 'Q' in temp3.pdb #4 to 'Am'
Remapping chain ID 'R' in temp3.pdb #4 to 'An'
Remapping chain ID 'S' in temp3.pdb #4 to 'Ao'
Remapping chain ID 'T' in temp3.pdb #4 to 'Ap'
Remapping chain ID 'U' in temp3.pdb #4 to 'Aq'
Remapping chain ID 'V' in temp3.pdb #4 to 'Ar'
Remapping chain ID 'W' in temp3.pdb #4 to 'As'
Remapping chain ID 'X' in temp3.pdb #4 to 'At'
Remapping chain ID 'Y' in temp3.pdb #4 to 'Au'
Remapping chain ID 'Z' in temp3.pdb #4 to 'Av'
Remapping chain ID 'a' in temp3.pdb #4 to 'Aw'
Remapping chain ID 'b' in temp3.pdb #4 to 'Ax'
Remapping chain ID 'c' in temp3.pdb #4 to 'Ay'
Remapping chain ID 'd' in temp3.pdb #4 to 'Az'
Remapping chain ID 'e' in temp3.pdb #4 to 'A1'
Remapping chain ID 'f' in temp3.pdb #4 to 'A2'
Remapping chain ID 'g' in temp3.pdb #4 to 'A3'
Remapping chain ID 'h' in temp3.pdb #4 to 'A4'
Remapping chain ID 'i' in temp3.pdb #4 to 'A5'
Remapping chain ID 'j' in temp3.pdb #4 to 'A6'
Remapping chain ID 'k' in temp3.pdb #4 to 'A7'
Remapping chain ID 'l' in temp3.pdb #4 to 'A8'
Remapping chain ID 'm' in temp3.pdb #4 to 'A9'
Remapping chain ID 'n' in temp3.pdb #4 to 'A0'
Remapping chain ID 'o' in temp3.pdb #4 to 'BA'
Remapping chain ID 'p' in temp3.pdb #4 to 'BB'
Remapping chain ID 'A' in temp4.pdb #5 to 'BC'
Remapping chain ID 'B' in temp4.pdb #5 to 'BD'
Remapping chain ID 'C' in temp4.pdb #5 to 'BE'
Remapping chain ID 'D' in temp4.pdb #5 to 'BF'
Remapping chain ID 'E' in temp4.pdb #5 to 'BG'
Remapping chain ID 'F' in temp4.pdb #5 to 'BH'
Remapping chain ID 'G' in temp4.pdb #5 to 'BI'
Remapping chain ID 'H' in temp4.pdb #5 to 'BJ'
Remapping chain ID 'I' in temp4.pdb #5 to 'BK'
Remapping chain ID 'J' in temp4.pdb #5 to 'BL'
Remapping chain ID 'K' in temp4.pdb #5 to 'BM'
Remapping chain ID 'L' in temp4.pdb #5 to 'BN'
Remapping chain ID 'M' in temp4.pdb #5 to 'BO'
Remapping chain ID 'N' in temp4.pdb #5 to 'BP'
Remapping chain ID 'O' in temp4.pdb #5 to 'BQ'
Remapping chain ID 'P' in temp4.pdb #5 to 'BR'
Remapping chain ID 'Q' in temp4.pdb #5 to 'BS'
Remapping chain ID 'R' in temp4.pdb #5 to 'BT'
Remapping chain ID 'S' in temp4.pdb #5 to 'BU'
Remapping chain ID 'T' in temp4.pdb #5 to 'BV'
Remapping chain ID 'U' in temp4.pdb #5 to 'BW'
Remapping chain ID 'V' in temp4.pdb #5 to 'BX'
Remapping chain ID 'W' in temp4.pdb #5 to 'BY'
Remapping chain ID 'X' in temp4.pdb #5 to 'BZ'
Remapping chain ID 'Y' in temp4.pdb #5 to 'Ba'
Remapping chain ID 'Z' in temp4.pdb #5 to 'Bb'
Remapping chain ID 'a' in temp4.pdb #5 to 'Bc'
Remapping chain ID 'b' in temp4.pdb #5 to 'Bd'
Remapping chain ID 'c' in temp4.pdb #5 to 'Be'
Remapping chain ID 'd' in temp4.pdb #5 to 'Bf'
Remapping chain ID 'e' in temp4.pdb #5 to 'Bg'
Remapping chain ID 'f' in temp4.pdb #5 to 'Bh'
Remapping chain ID 'g' in temp4.pdb #5 to 'Bi'
Remapping chain ID 'h' in temp4.pdb #5 to 'Bj'
Remapping chain ID 'i' in temp4.pdb #5 to 'Bk'
Remapping chain ID 'j' in temp4.pdb #5 to 'Bl'
Remapping chain ID 'k' in temp4.pdb #5 to 'Bm'
Remapping chain ID 'l' in temp4.pdb #5 to 'Bn'
Remapping chain ID 'm' in temp4.pdb #5 to 'Bo'
Remapping chain ID 'n' in temp4.pdb #5 to 'Bp'
Remapping chain ID 'o' in temp4.pdb #5 to 'Bq'
Remapping chain ID 'p' in temp4.pdb #5 to 'Br'
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #6 models
> show #6 models
> open /data2/zhuyun/HFBI/Result/HFBI_fit_6mer_flipmap.pdb
Chain information for HFBI_fit_6mer_flipmap.pdb #7
---
Chain | Description
A B C D E F | No description available
> hide #7 models
> show #7 models
> select add #7
3126 atoms, 3174 bonds, 450 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,68.4,0,1,0,66.117,0,0,1,1.692
> view matrix models
> #7,0.99463,0.078982,0.066835,63.454,-0.075348,0.99563,-0.055252,70.947,-0.070907,0.049919,0.99623,2.6328
> view matrix models
> #7,0.99463,0.078982,0.066835,62.61,-0.075348,0.99563,-0.055252,73.759,-0.070907,0.049919,0.99623,2.7703
> view matrix models
> #7,0.99362,0.062945,0.093599,61.705,-0.067793,0.99647,0.049553,67.95,-0.090149,-0.055582,0.99438,7.6518
> view matrix models
> #7,0.99362,0.062945,0.093599,63.218,-0.067793,0.99647,0.049553,71.224,-0.090149,-0.055582,0.99438,7.7683
> view matrix models
> #7,0.99362,0.062945,0.093599,63.216,-0.067793,0.99647,0.049553,66.44,-0.090149,-0.055582,0.99438,7.5594
> view matrix models
> #7,0.99362,0.062945,0.093599,64.521,-0.067793,0.99647,0.049553,63.495,-0.090149,-0.055582,0.99438,73.77
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 3126 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Fit in Map"
> fitmap #7 inMap #1
Fit molecule HFBI_fit_6mer_flipmap.pdb (#7) to map map_42mer_flip_EMR.mrc (#1)
using 3126 atoms
average map value = 4.17, steps = 76
shifted from previous position = 5.86
rotated from previous position = 7.4 degrees
atoms outside contour = 2238, contour level = 6.4489
Position of HFBI_fit_6mer_flipmap.pdb (#7) relative to map_42mer_flip_EMR.mrc
(#1) coordinates:
Matrix rotation and translation
0.99997211 -0.00745919 -0.00036967 65.88559270
0.00745913 0.99997216 -0.00017620 65.35459059
0.00037097 0.00017344 0.99999992 65.30925600
Axis 0.02340146 -0.04957151 0.99849639
Axis point -9151.44236508 8667.76460411 0.00000000
Rotation angle (degrees) 0.42802587
Shift along axis 63.51314996
> close #6
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> combine #2#3#4#5#7
Remapping chain ID 'A' in temp2.pdb #3 to 'q'
Remapping chain ID 'B' in temp2.pdb #3 to 'r'
Remapping chain ID 'C' in temp2.pdb #3 to 's'
Remapping chain ID 'D' in temp2.pdb #3 to 't'
Remapping chain ID 'E' in temp2.pdb #3 to 'u'
Remapping chain ID 'F' in temp2.pdb #3 to 'v'
Remapping chain ID 'G' in temp2.pdb #3 to 'w'
Remapping chain ID 'H' in temp2.pdb #3 to 'x'
Remapping chain ID 'I' in temp2.pdb #3 to 'y'
Remapping chain ID 'J' in temp2.pdb #3 to 'z'
Remapping chain ID 'K' in temp2.pdb #3 to '1'
Remapping chain ID 'L' in temp2.pdb #3 to '2'
Remapping chain ID 'M' in temp2.pdb #3 to '3'
Remapping chain ID 'N' in temp2.pdb #3 to '4'
Remapping chain ID 'O' in temp2.pdb #3 to '5'
Remapping chain ID 'P' in temp2.pdb #3 to '6'
Remapping chain ID 'Q' in temp2.pdb #3 to '7'
Remapping chain ID 'R' in temp2.pdb #3 to '8'
Remapping chain ID 'S' in temp2.pdb #3 to '9'
Remapping chain ID 'T' in temp2.pdb #3 to '0'
Remapping chain ID 'U' in temp2.pdb #3 to 'AA'
Remapping chain ID 'V' in temp2.pdb #3 to 'AB'
Remapping chain ID 'W' in temp2.pdb #3 to 'AC'
Remapping chain ID 'X' in temp2.pdb #3 to 'AD'
Remapping chain ID 'Y' in temp2.pdb #3 to 'AE'
Remapping chain ID 'Z' in temp2.pdb #3 to 'AF'
Remapping chain ID 'a' in temp2.pdb #3 to 'AG'
Remapping chain ID 'b' in temp2.pdb #3 to 'AH'
Remapping chain ID 'c' in temp2.pdb #3 to 'AI'
Remapping chain ID 'd' in temp2.pdb #3 to 'AJ'
Remapping chain ID 'e' in temp2.pdb #3 to 'AK'
Remapping chain ID 'f' in temp2.pdb #3 to 'AL'
Remapping chain ID 'g' in temp2.pdb #3 to 'AM'
Remapping chain ID 'h' in temp2.pdb #3 to 'AN'
Remapping chain ID 'i' in temp2.pdb #3 to 'AO'
Remapping chain ID 'j' in temp2.pdb #3 to 'AP'
Remapping chain ID 'k' in temp2.pdb #3 to 'AQ'
Remapping chain ID 'l' in temp2.pdb #3 to 'AR'
Remapping chain ID 'm' in temp2.pdb #3 to 'AS'
Remapping chain ID 'n' in temp2.pdb #3 to 'AT'
Remapping chain ID 'o' in temp2.pdb #3 to 'AU'
Remapping chain ID 'p' in temp2.pdb #3 to 'AV'
Remapping chain ID 'A' in temp3.pdb #4 to 'AW'
Remapping chain ID 'B' in temp3.pdb #4 to 'AX'
Remapping chain ID 'C' in temp3.pdb #4 to 'AY'
Remapping chain ID 'D' in temp3.pdb #4 to 'AZ'
Remapping chain ID 'E' in temp3.pdb #4 to 'Aa'
Remapping chain ID 'F' in temp3.pdb #4 to 'Ab'
Remapping chain ID 'G' in temp3.pdb #4 to 'Ac'
Remapping chain ID 'H' in temp3.pdb #4 to 'Ad'
Remapping chain ID 'I' in temp3.pdb #4 to 'Ae'
Remapping chain ID 'J' in temp3.pdb #4 to 'Af'
Remapping chain ID 'K' in temp3.pdb #4 to 'Ag'
Remapping chain ID 'L' in temp3.pdb #4 to 'Ah'
Remapping chain ID 'M' in temp3.pdb #4 to 'Ai'
Remapping chain ID 'N' in temp3.pdb #4 to 'Aj'
Remapping chain ID 'O' in temp3.pdb #4 to 'Ak'
Remapping chain ID 'P' in temp3.pdb #4 to 'Al'
Remapping chain ID 'Q' in temp3.pdb #4 to 'Am'
Remapping chain ID 'R' in temp3.pdb #4 to 'An'
Remapping chain ID 'S' in temp3.pdb #4 to 'Ao'
Remapping chain ID 'T' in temp3.pdb #4 to 'Ap'
Remapping chain ID 'U' in temp3.pdb #4 to 'Aq'
Remapping chain ID 'V' in temp3.pdb #4 to 'Ar'
Remapping chain ID 'W' in temp3.pdb #4 to 'As'
Remapping chain ID 'X' in temp3.pdb #4 to 'At'
Remapping chain ID 'Y' in temp3.pdb #4 to 'Au'
Remapping chain ID 'Z' in temp3.pdb #4 to 'Av'
Remapping chain ID 'a' in temp3.pdb #4 to 'Aw'
Remapping chain ID 'b' in temp3.pdb #4 to 'Ax'
Remapping chain ID 'c' in temp3.pdb #4 to 'Ay'
Remapping chain ID 'd' in temp3.pdb #4 to 'Az'
Remapping chain ID 'e' in temp3.pdb #4 to 'A1'
Remapping chain ID 'f' in temp3.pdb #4 to 'A2'
Remapping chain ID 'g' in temp3.pdb #4 to 'A3'
Remapping chain ID 'h' in temp3.pdb #4 to 'A4'
Remapping chain ID 'i' in temp3.pdb #4 to 'A5'
Remapping chain ID 'j' in temp3.pdb #4 to 'A6'
Remapping chain ID 'k' in temp3.pdb #4 to 'A7'
Remapping chain ID 'l' in temp3.pdb #4 to 'A8'
Remapping chain ID 'm' in temp3.pdb #4 to 'A9'
Remapping chain ID 'n' in temp3.pdb #4 to 'A0'
Remapping chain ID 'o' in temp3.pdb #4 to 'BA'
Remapping chain ID 'p' in temp3.pdb #4 to 'BB'
Remapping chain ID 'A' in temp4.pdb #5 to 'BC'
Remapping chain ID 'B' in temp4.pdb #5 to 'BD'
Remapping chain ID 'C' in temp4.pdb #5 to 'BE'
Remapping chain ID 'D' in temp4.pdb #5 to 'BF'
Remapping chain ID 'E' in temp4.pdb #5 to 'BG'
Remapping chain ID 'F' in temp4.pdb #5 to 'BH'
Remapping chain ID 'G' in temp4.pdb #5 to 'BI'
Remapping chain ID 'H' in temp4.pdb #5 to 'BJ'
Remapping chain ID 'I' in temp4.pdb #5 to 'BK'
Remapping chain ID 'J' in temp4.pdb #5 to 'BL'
Remapping chain ID 'K' in temp4.pdb #5 to 'BM'
Remapping chain ID 'L' in temp4.pdb #5 to 'BN'
Remapping chain ID 'M' in temp4.pdb #5 to 'BO'
Remapping chain ID 'N' in temp4.pdb #5 to 'BP'
Remapping chain ID 'O' in temp4.pdb #5 to 'BQ'
Remapping chain ID 'P' in temp4.pdb #5 to 'BR'
Remapping chain ID 'Q' in temp4.pdb #5 to 'BS'
Remapping chain ID 'R' in temp4.pdb #5 to 'BT'
Remapping chain ID 'S' in temp4.pdb #5 to 'BU'
Remapping chain ID 'T' in temp4.pdb #5 to 'BV'
Remapping chain ID 'U' in temp4.pdb #5 to 'BW'
Remapping chain ID 'V' in temp4.pdb #5 to 'BX'
Remapping chain ID 'W' in temp4.pdb #5 to 'BY'
Remapping chain ID 'X' in temp4.pdb #5 to 'BZ'
Remapping chain ID 'Y' in temp4.pdb #5 to 'Ba'
Remapping chain ID 'Z' in temp4.pdb #5 to 'Bb'
Remapping chain ID 'a' in temp4.pdb #5 to 'Bc'
Remapping chain ID 'b' in temp4.pdb #5 to 'Bd'
Remapping chain ID 'c' in temp4.pdb #5 to 'Be'
Remapping chain ID 'd' in temp4.pdb #5 to 'Bf'
Remapping chain ID 'e' in temp4.pdb #5 to 'Bg'
Remapping chain ID 'f' in temp4.pdb #5 to 'Bh'
Remapping chain ID 'g' in temp4.pdb #5 to 'Bi'
Remapping chain ID 'h' in temp4.pdb #5 to 'Bj'
Remapping chain ID 'i' in temp4.pdb #5 to 'Bk'
Remapping chain ID 'j' in temp4.pdb #5 to 'Bl'
Remapping chain ID 'k' in temp4.pdb #5 to 'Bm'
Remapping chain ID 'l' in temp4.pdb #5 to 'Bn'
Remapping chain ID 'm' in temp4.pdb #5 to 'Bo'
Remapping chain ID 'n' in temp4.pdb #5 to 'Bp'
Remapping chain ID 'o' in temp4.pdb #5 to 'Bq'
Remapping chain ID 'p' in temp4.pdb #5 to 'Br'
Remapping chain ID 'A' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bs'
Remapping chain ID 'B' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bt'
Remapping chain ID 'C' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bu'
Remapping chain ID 'D' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bv'
Remapping chain ID 'E' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bw'
Remapping chain ID 'F' in HFBI_fit_6mer_flipmap.pdb #7 to 'Bx'
> hide #7 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> select subtract #7
Nothing selected
No model chosen to save relative to
> save /data2/zhuyun/HFBI/Result/HFBI_fit_169mer.cif models #6 relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close #2-7
> open /data2/zhuyun/HFBI/Result/HFBI_fit_169mer.cif
Summary of feedback from opening /data2/zhuyun/HFBI/Result/HFBI_fit_169mer.cif
---
warnings | Unknown polymer entity '1' near line 458
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for HFBI_fit_169mer.cif #2
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI
AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai
Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B BA BB BC BD BE BF BG BH
BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh
Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx C D E F G H I J K L M N O P Q
R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No
description available
> select add #2
90654 atoms, 92046 bonds, 13050 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> view matrix models #2,1,0,0,29.736,0,1,0,143.15,0,0,1,-0.17556
> view matrix models #2,1,0,0,164.91,0,1,0,93.316,0,0,1,-2.1449
> fitmap #2 inMap #1
Fit molecule HFBI_fit_169mer.cif (#2) to map map_42mer_flip_EMR.mrc (#1) using
90654 atoms
average map value = 3.217, steps = 2000
shifted from previous position = 3.58
rotated from previous position = 0.683 degrees
atoms outside contour = 88183, contour level = 6.4489
Position of HFBI_fit_169mer.cif (#2) relative to map_42mer_flip_EMR.mrc (#1)
coordinates:
Matrix rotation and translation
0.99994362 0.00355198 -0.01000679 164.76508081
-0.00360596 0.99997902 -0.00538201 95.74107094
0.00998747 0.00541779 0.99993545 -0.60357859
Axis 0.45329220 -0.83920493 -0.30043512
Axis point 333.24188171 0.00000000 16711.60222250
Rotation angle (degrees) 0.68255912
Shift along axis -5.47831738
> fitmap #2 inMap #1
Fit molecule HFBI_fit_169mer.cif (#2) to map map_42mer_flip_EMR.mrc (#1) using
90654 atoms
average map value = 3.26, steps = 2000
shifted from previous position = 0.431
rotated from previous position = 0.152 degrees
atoms outside contour = 88159, contour level = 6.4489
Position of HFBI_fit_169mer.cif (#2) relative to map_42mer_flip_EMR.mrc (#1)
coordinates:
Matrix rotation and translation
0.99995514 0.00509835 -0.00798299 164.79856228
-0.00513559 0.99997600 -0.00465052 95.94595730
0.00795909 0.00469130 0.99995732 -0.45797714
Axis 0.44227220 -0.75474973 -0.48450814
Axis point 125.87093191 -0.00000000 20604.64249341
Rotation angle (degrees) 0.60512154
Shift along axis 0.69253128
> fitmap #2 inMap #1
Fit molecule HFBI_fit_169mer.cif (#2) to map map_42mer_flip_EMR.mrc (#1) using
90654 atoms
average map value = 3.272, steps = 2000
shifted from previous position = 0.386
rotated from previous position = 0.253 degrees
atoms outside contour = 88139, contour level = 6.4489
Position of HFBI_fit_169mer.cif (#2) relative to map_42mer_flip_EMR.mrc (#1)
coordinates:
Matrix rotation and translation
0.99995666 0.00092501 -0.00926362 165.21933662
-0.00097439 0.99998534 -0.00532698 95.84332507
0.00925856 0.00533577 0.99994290 -0.42263196
Axis 0.49695193 -0.86325097 -0.08852423
Axis point 161.50252574 0.00000000 17866.36508285
Rotation angle (degrees) 0.61468964
Shift along axis -0.59336305
> save /data2/zhuyun/HFBI/Result/temp1.cif relModel #2
Not saving entity_poly_seq for non-authoritative sequences
===== 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 map_42mer_flip.mrc
Opened map_42mer_flip.mrc as #1, grid size 256,256,256, pixel 1.64, shown at
level 0.00413, step 1, values float32
> open HFBI_fit_169mer.cif
Summary of feedback from opening HFBI_fit_169mer.cif
---
warnings | Unknown polymer entity '1' near line 458
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for HFBI_fit_169mer.cif #2
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI
AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai
Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B BA BB BC BD BE BF BG BH
BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh
Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx C D E F G H I J K L M N O P Q
R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No
description available
> open HFBI_fit_169mer.cif
Summary of feedback from opening HFBI_fit_169mer.cif
---
warnings | Unknown polymer entity '1' near line 458
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for HFBI_fit_169mer.cif #3
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI
AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai
Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax Ay Az B BA BB BC BD BE BF BG BH
BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh
Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx C D E F G H I J K L M N O P Q
R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No
description available
OpenGL version: 3.3.0 NVIDIA 525.89.02
OpenGL renderer: Quadro RTX 6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: X11DPi-N(T)
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
Cache Size: 14080 KB
Memory:
total used free shared buff/cache available
Mem: 141Gi 27Gi 7.0Gi 1.7Gi 106Gi 110Gi
Swap: 2.0Gi 2.0Gi 0.0Ki
Graphics:
03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: Aspeed Video 2500
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
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-ArtiaX: 0.3
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
geomdl: 5.3.1
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
pandas: 2.0.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
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
starfile: 0.4.12
superqt: 0.4.1
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
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving mmCIF |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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