Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8598 closed defect (can't reproduce)

Crash in calculate_surface_geometry

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.19.1-051901-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x00007f4c0e852b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molsurf.py", line 248 in calculate_surface_geometry
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molsurf.py", line 211 in _recompute_shape
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molsurf.py", line 178 in _atoms_changed
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/changes.py", line 43 in check_for_changes
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 58 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py", line 43 in draw_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py", line 32 in wait
  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/core/scripting.py", line 173 in _run_commands
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 160 in open_command_script
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 428 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 440 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 193 in provider_open
  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/open_command/cmd.py", line 118 in cmd_open
  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/core/__main__.py", line 863 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 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:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> lose

Unknown command: lose  

> open morph_stage1_2.pdb

morph_stage1_2.pdb title:  
50S ribosomal subunit assembly intermediate state 1 [more info...]  
  
Chain information for morph_stage1_2.pdb #1  
---  
Chain | Description | UniProt  
0 | large ribosomal subunit protein BL32 | RL32_ECOLI  
2 | large ribosomal subunit protein BL34 | RL34_ECOLI  
A | 23S ribosomal RNA |  
D | large ribosomal subunit protein UL3 | RL3_ECOLI  
E | large ribosomal subunit protein UL4 | RL4_ECOLI  
J | large ribosomal subunit protein UL13 | RL13_ECOLI  
K | large ribosomal subunit protein UL14 | RL14_ECOLI  
L | large ribosomal subunit protein UL15 | RL15_ECOLI  
N | large ribosomal subunit protein BL17 | RL17_ECOLI  
P | large ribosomal subunit protein BL19 | RL19_ECOLI  
Q | large ribosomal subunit protein BL20 | RL20_ECOLI  
R | large ribosomal subunit protein BL21 | RL21_ECOLI  
S | large ribosomal subunit protein UL22 | RL22_ECOLI  
T | large ribosomal subunit protein UL23 | RL23_ECOLI  
U | large ribosomal subunit protein UL24 | RL24_ECOLI  
Y | large ribosomal subunit protein UL29 | RL29_ECOLI  
Z | large ribosomal subunit protein UL30 | RL30_ECOLI  
  

> open morph_stage1_2.dcd structureModel #1

Replaced existing frames of morph_stage1_2.pdb #1 with 301 new frames  

> open morph_stage2_3.pdb

morph_stage2_3.pdb title:  
50S ribosomal subunit assembly intermediate state 2 [more info...]  
  
Chain information for morph_stage2_3.pdb #2  
---  
Chain | Description | UniProt  
0 | large ribosomal subunit protein BL32 | RL32_ECOLI  
2 | large ribosomal subunit protein BL34 | RL34_ECOLI  
A | 23S ribosomal RNA |  
C | large ribosomal subunit protein UL2 | RL2_ECOLI  
D | large ribosomal subunit protein UL3 | RL3_ECOLI  
E | large ribosomal subunit protein UL4 | RL4_ECOLI  
G | large ribosomal subunit protein UL6 | RL6_ECOLI  
J | large ribosomal subunit protein UL13 | RL13_ECOLI  
K | large ribosomal subunit protein UL14 | RL14_ECOLI  
L | large ribosomal subunit protein UL15 | RL15_ECOLI  
N | large ribosomal subunit protein BL17 | RL17_ECOLI  
P | large ribosomal subunit protein BL19 | RL19_ECOLI  
Q | large ribosomal subunit protein BL20 | RL20_ECOLI  
R | large ribosomal subunit protein BL21 | RL21_ECOLI  
S | large ribosomal subunit protein UL22 | RL22_ECOLI  
T | large ribosomal subunit protein UL23 | RL23_ECOLI  
U | large ribosomal subunit protein UL24 | RL24_ECOLI  
Y | large ribosomal subunit protein UL29 | RL29_ECOLI  
Z | large ribosomal subunit protein UL30 | RL30_ECOLI  
  

> open morph_stage2_3.dcd structureModel #2

Replaced existing frames of morph_stage2_3.pdb #2 with 301 new frames  

> open morph_stage3_4.pdb

morph_stage3_4.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for morph_stage3_4.pdb #3  
---  
Chain | Description | UniProt  
0 | large ribosomal subunit protein BL32 | RL32_ECOLI  
2 | large ribosomal subunit protein BL34 | RL34_ECOLI  
A | 23S ribosomal RNA |  
B | 5S ribosomal RNA |  
C | large ribosomal subunit protein UL2 | RL2_ECOLI  
D | large ribosomal subunit protein UL3 | RL3_ECOLI  
E | large ribosomal subunit protein UL4 | RL4_ECOLI  
F | large ribosomal subunit protein UL5 | RL5_ECOLI  
G | large ribosomal subunit protein UL6 | RL6_ECOLI  
H | large ribosomal subunit protein BL9 | RL9_ECOLI  
J | large ribosomal subunit protein UL13 | RL13_ECOLI  
K | large ribosomal subunit protein UL14 | RL14_ECOLI  
L | large ribosomal subunit protein UL15 | RL15_ECOLI  
N | large ribosomal subunit protein BL17 | RL17_ECOLI  
O | large ribosomal subunit protein UL18 | RL18_ECOLI  
P | large ribosomal subunit protein BL19 | RL19_ECOLI  
Q | large ribosomal subunit protein BL20 | RL20_ECOLI  
R | large ribosomal subunit protein BL21 | RL21_ECOLI  
S | large ribosomal subunit protein UL22 | RL22_ECOLI  
T | large ribosomal subunit protein UL23 | RL23_ECOLI  
U | large ribosomal subunit protein UL24 | RL24_ECOLI  
V | large ribosomal subunit protein BL25 | RL25_ECOLI  
W | large ribosomal subunit protein BL27 | RL27_ECOLI  
X | large ribosomal subunit protein BL28 | RL28_ECOLI  
Y | large ribosomal subunit protein UL29 | RL29_ECOLI  
Z | large ribosomal subunit protein UL30 | RL30_ECOLI  
  

> open morph_stage3_4.dcd structureModel #3

Replaced existing frames of morph_stage3_4.pdb #3 with 301 new frames  

> open morph_stage4_5.pdb

morph_stage4_5.pdb title:  
50S ribosomal subunit assembly intermediate state 4 [more info...]  
  
Chain information for morph_stage4_5.pdb #4  
---  
Chain | Description | UniProt  
0 | large ribosomal subunit protein BL32 | RL32_ECOLI  
1 | large ribosomal subunit protein BL33 | RL33_ECOLI  
2 | large ribosomal subunit protein BL34 | RL34_ECOLI  
3 | 50S ribosomal protein L35 | RL35_ECOLI  
A | 23S ribosomal RNA |  
B | 5S ribosomal RNA |  
C | large ribosomal subunit protein UL2 | RL2_ECOLI  
D | large ribosomal subunit protein UL3 | RL3_ECOLI  
E | large ribosomal subunit protein UL4 | RL4_ECOLI  
F | large ribosomal subunit protein UL5 | RL5_ECOLI  
G | large ribosomal subunit protein UL6 | RL6_ECOLI  
H | large ribosomal subunit protein BL9 | RL9_ECOLI  
J | large ribosomal subunit protein UL13 | RL13_ECOLI  
K | large ribosomal subunit protein UL14 | RL14_ECOLI  
L | large ribosomal subunit protein UL15 | RL15_ECOLI  
N | large ribosomal subunit protein BL17 | RL17_ECOLI  
O | large ribosomal subunit protein UL18 | RL18_ECOLI  
P | large ribosomal subunit protein BL19 | RL19_ECOLI  
Q | large ribosomal subunit protein BL20 | RL20_ECOLI  
R | large ribosomal subunit protein BL21 | RL21_ECOLI  
S | large ribosomal subunit protein UL22 | RL22_ECOLI  
T | large ribosomal subunit protein UL23 | RL23_ECOLI  
U | large ribosomal subunit protein UL24 | RL24_ECOLI  
V | large ribosomal subunit protein BL25 | RL25_ECOLI  
W | large ribosomal subunit protein BL27 | RL27_ECOLI  
X | large ribosomal subunit protein BL28 | RL28_ECOLI  
Y | large ribosomal subunit protein UL29 | RL29_ECOLI  
Z | large ribosomal subunit protein UL30 | RL30_ECOLI  
  

> open morph_stage4_5.dcd structureModel #4

Replaced existing frames of morph_stage4_5.pdb #4 with 301 new frames  

> open morph_stage5_6.pdb

morph_stage5_6.pdb title:  
50S ribosomal subunit assembly intermediate state 5 [more info...]  
  
Chain information for morph_stage5_6.pdb #5  
---  
Chain | Description | UniProt  
0 | large ribosomal subunit protein BL32 | RL32_ECOLI  
1 | large ribosomal subunit protein BL33 | RL33_ECOLI  
2 | large ribosomal subunit protein BL34 | RL34_ECOLI  
3 | 50S ribosomal protein L35 | RL35_ECOLI  
A | 23S ribosomal RNA |  
B | 5S ribosomal RNA |  
C | large ribosomal subunit protein UL2 | RL2_ECOLI  
D | large ribosomal subunit protein UL3 | RL3_ECOLI  
E | large ribosomal subunit protein UL4 | RL4_ECOLI  
F | large ribosomal subunit protein UL5 | RL5_ECOLI  
G | large ribosomal subunit protein UL6 | RL6_ECOLI  
H | large ribosomal subunit protein BL9 | RL9_ECOLI  
J | large ribosomal subunit protein UL13 | RL13_ECOLI  
K | large ribosomal subunit protein UL14 | RL14_ECOLI  
L | large ribosomal subunit protein UL15 | RL15_ECOLI  
M | large ribosomal subunit protein UL16 | RL16_ECOLI  
N | large ribosomal subunit protein BL17 | RL17_ECOLI  
O | large ribosomal subunit protein UL18 | RL18_ECOLI  
P | large ribosomal subunit protein BL19 | RL19_ECOLI  
Q | large ribosomal subunit protein BL20 | RL20_ECOLI  
R | large ribosomal subunit protein BL21 | RL21_ECOLI  
S | large ribosomal subunit protein UL22 | RL22_ECOLI  
T | large ribosomal subunit protein UL23 | RL23_ECOLI  
U | large ribosomal subunit protein UL24 | RL24_ECOLI  
V | large ribosomal subunit protein BL25 | RL25_ECOLI  
W | large ribosomal subunit protein BL27 | RL27_ECOLI  
X | large ribosomal subunit protein BL28 | RL28_ECOLI  
Y | large ribosomal subunit protein UL29 | RL29_ECOLI  
Z | large ribosomal subunit protein UL30 | RL30_ECOLI  
  

> open morph_stage5_6.dcd structureModel #5

Replaced existing frames of morph_stage5_6.pdb #5 with 301 new frames  

> open stage2_aligned_c.pdb

Summary of feedback from opening stage2_aligned_c.pdb  
---  
warnings | CONECT record for nonexistent atom: 18615  
Start residue of secondary structure not found: HELIX 4 4 THR D 61 GLY D 72 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL D 98 ALA D 102 1
5  
Start residue of secondary structure not found: HELIX 6 6 SER E 15 GLY E 20 1
6  
Start residue of secondary structure not found: HELIX 7 7 GLU E 25 ALA E 37 1
13  
Start residue of secondary structure not found: HELIX 8 8 ASN E 97 SER E 110 1
14  
127 messages similar to the above omitted  
  
stage2_aligned_c.pdb title:  
50S ribosomal subunit assembly intermediate state 2 [more info...]  
  
Chain information for stage2_aligned_c.pdb #6  
---  
Chain | Description | UniProt  
C | large ribosomal subunit protein UL2 | RL2_ECOLI  
  

> open stage2_aligned_g.pdb

Summary of feedback from opening stage2_aligned_g.pdb  
---  
warnings | CONECT record for nonexistent atom: 18615  
Start residue of secondary structure not found: HELIX 1 1 PHE C 29 LEU C 33 1
5  
Start residue of secondary structure not found: HELIX 2 2 ALA C 197 ARG C 202
1 6  
Start residue of secondary structure not found: HELIX 3 3 ALA C 207 ARG C 211
1 5  
Start residue of secondary structure not found: HELIX 4 4 THR D 61 GLY D 72 1
12  
Start residue of secondary structure not found: HELIX 5 5 VAL D 98 ALA D 102 1
5  
131 messages similar to the above omitted  
  
stage2_aligned_g.pdb title:  
50S ribosomal subunit assembly intermediate state 2 [more info...]  
  
Chain information for stage2_aligned_g.pdb #7  
---  
Chain | Description | UniProt  
G | large ribosomal subunit protein UL6 | RL6_ECOLI  
  

> open stage3_aligned_b.pdb

Summary of feedback from opening stage3_aligned_b.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
202 messages similar to the above omitted  
  
stage3_aligned_b.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_b.pdb #8  
---  
Chain | Description  
B | 5S ribosomal RNA  
  

> open stage3_aligned_f.pdb

Summary of feedback from opening stage3_aligned_f.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
189 messages similar to the above omitted  
  
stage3_aligned_f.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_f.pdb #9  
---  
Chain | Description | UniProt  
F | large ribosomal subunit protein UL5 | RL5_ECOLI  
  

> open stage3_aligned_h.pdb

Summary of feedback from opening stage3_aligned_h.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
198 messages similar to the above omitted  
  
stage3_aligned_h.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_h.pdb #10  
---  
Chain | Description | UniProt  
H | large ribosomal subunit protein BL9 | RL9_ECOLI  
  

> open stage3_aligned_o.pdb

Summary of feedback from opening stage3_aligned_o.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
194 messages similar to the above omitted  
  
stage3_aligned_o.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_o.pdb #11  
---  
Chain | Description | UniProt  
O | large ribosomal subunit protein UL18 | RL18_ECOLI  
  

> open stage3_aligned_v.pdb

Summary of feedback from opening stage3_aligned_v.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
Start residue of secondary structure not found: HELIX 6 6 LYS C 206 TRP C 212
1 7  
Start residue of secondary structure not found: HELIX 7 7 THR D 61 GLY D 72 1
12  
193 messages similar to the above omitted  
  
stage3_aligned_v.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_v.pdb #12  
---  
Chain | Description | UniProt  
V | large ribosomal subunit protein BL25 | RL25_ECOLI  
  

> open stage3_aligned_w.pdb

Summary of feedback from opening stage3_aligned_w.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
195 messages similar to the above omitted  
  
stage3_aligned_w.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_w.pdb #13  
---  
Chain | Description | UniProt  
W | large ribosomal subunit protein BL27 | RL27_ECOLI  
  

> open stage3_aligned_x.pdb

Summary of feedback from opening stage3_aligned_x.pdb  
---  
warnings | CONECT record for nonexistent atom: 23151  
Start residue of secondary structure not found: HELIX 1 1 GLY V 13 ALA V 22 1
10  
Start residue of secondary structure not found: HELIX 2 2 HIS V 44 GLN V 51 1
8  
Start residue of secondary structure not found: HELIX 3 3 PHE C 29 PRO C 31 1
3  
Start residue of secondary structure not found: HELIX 4 4 ARG C 132 ILE C 134
1 3  
Start residue of secondary structure not found: HELIX 5 5 ASN C 196 ARG C 202
1 7  
196 messages similar to the above omitted  
  
stage3_aligned_x.pdb title:  
50S ribosomal subunit assembly intermediate state 3 [more info...]  
  
Chain information for stage3_aligned_x.pdb #14  
---  
Chain | Description | UniProt  
X | large ribosomal subunit protein BL28 | RL28_ECOLI  
  

> open stage4_aligned_1.pdb

Summary of feedback from opening stage4_aligned_1.pdb  
---  
warnings | CONECT record for nonexistent atom: 41779  
Start residue of secondary structure not found: HELIX 1 1 ALA C 197 ARG C 202
1 6  
Start residue of secondary structure not found: HELIX 2 2 THR C 262 LYS C 264
1 3  
Start residue of secondary structure not found: HELIX 3 3 THR D 61 GLY D 72 1
12  
Start residue of secondary structure not found: HELIX 4 4 SER D 97 ASP D 103 1
7  
Start residue of secondary structure not found: HELIX 5 5 GLY D 120 ASN D 126
1 7  
212 messages similar to the above omitted  
  
stage4_aligned_1.pdb title:  
50S ribosomal subunit assembly intermediate state 4 [more info...]  
  
Chain information for stage4_aligned_1.pdb #15  
---  
Chain | Description | UniProt  
1 | large ribosomal subunit protein BL33 | RL33_ECOLI  
  

> open stage4_aligned_3.pdb

Summary of feedback from opening stage4_aligned_3.pdb  
---  
warnings | CONECT record for nonexistent atom: 41779  
Start residue of secondary structure not found: HELIX 1 1 ALA C 197 ARG C 202
1 6  
Start residue of secondary structure not found: HELIX 2 2 THR C 262 LYS C 264
1 3  
Start residue of secondary structure not found: HELIX 3 3 THR D 61 GLY D 72 1
12  
Start residue of secondary structure not found: HELIX 4 4 SER D 97 ASP D 103 1
7  
Start residue of secondary structure not found: HELIX 5 5 GLY D 120 ASN D 126
1 7  
209 messages similar to the above omitted  
  
stage4_aligned_3.pdb title:  
50S ribosomal subunit assembly intermediate state 4 [more info...]  
  
Chain information for stage4_aligned_3.pdb #16  
---  
Chain | Description | UniProt  
3 | 50S ribosomal protein L35 | RL35_ECOLI  
  

> view matrix camera
> 0.385,-0.917,-0.0930,81.811,-0.102,0.0577,-0.993,-611.08,0.916,0.392,-0.071,123.48

> view name p_all_bound

> view p_all_bound

> move -40,0,60 models #6

> move 0,40,30 models #7

> move 0,50,60 models #8

> move 70,60,30 models #9

> move 30,70,60 models #10

> move 0,70,-60 models #11

> move 0,30,60 models #12

> move 0,50,60 models #13

> move -60,0,50 models #14

> move -20,50,60 models #15

> move 0,80,60 models #16

> turn x -60 center #6 models #6

> turn y 10 center #7 models #7

> turn z 30 center #7 models #7

> turn x 60 center #8 models #8

> turn y 60 center #9 models #9

> turn x 0 center #10 models #10

> turn x -60 center #11 models #11

> turn y -60 center #12 models #12

> turn z -60 center #13 models #13

> turn x 60 center #14 models #14

> turn x 60 center #15 models #15

> turn x 60 center #16 models #16

> view name p_zoomed_out

> view p_all_bound

> fly p_zoomed_out p_all_bound

> hide all atoms




OpenGL version: 3.3.0 NVIDIA 520.61.05
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z370P D3
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 6 Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz
Cache Size: 9216 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       3.4Gi       9.9Gi        97Mi        18Gi        27Gi
	Swap:          127Gi       864Mi       127Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti Rev. A] [10de:1e07] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] TU102 [GeForce RTX 2080 Ti Rev. A] [1462:3713]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in calculate_surface_geometry

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed

Crashed in sharp edge code during a molecular surface recalculation. Would need a reproducible case to debug this.

comment:3 by Tom Goddard, 3 years ago

I don't see any command that computed a surface in the log. They were opening a command script according to the traceback. Looks like the log for the crash was not reported. There are no surface commands in the log of this session that was after the crash.

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