Crash in calculate_surface_geometry

[chimerax-bug-report@…]

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