Opened 3 years ago

Closed 3 years ago

#8605 closed defect (can't reproduce)

Various surface errors

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: Aborted

Current thread 0x00007f6accc09b80 (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/cmd_line/tool.py", line 319 in execute
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 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 before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close

> 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

> hide all atoms

> set bgColor white

> surface protein color 0,34,50,100

> surface nucleic color 50,45,5,30

> cartoon style nucleic xsection oval width 1.6 thickness 1.6

> cartoon nucleic & ~backbone

> nucleotides ladder hideAtoms true

> style nucleic stick

Changed 269906 atom styles  

> show atoms

> hide protein

> movie record supersample 3 size 5000,5000

> hide all models

> view p_zoomed_out

> log save _1.log

> 2dlabels text stage1->2 color light sea green size 26 xpos .3 ypos .92

> show #1 models

> coordset #1 1,300,2

> show #6 #7 models

> fly 151 p_zoomed_out p_all_bound

> wait 151

> hide #1 #6 #7 models

> hide #17.1 models

> log save _2.log

> 2dlabels text stage2->3 color light sea green size 26 xpos .3 ypos .92

> show #2 models

> coordset #2 1,300,2

> perframe "color /C,G $1,34,50,100" ranges 100,0 frames 20

> show #8 #9 #10 #11 #12 #13 #14 models

> fly 151 p_zoomed_out p_all_bound

> wait 151

> hide #2 models

> hide #8 #9 #10 #11 #12 #13 #14 models

> hide #17.2 models

> log save _3.log

> 2dlabels text stage3->4 color light sea green size 26 xpos .3 ypos .92

> show #3 models

> hide #3/B:1@OP2 #3/B:1@OP1 atoms

> hide #3/B:1@OP2 #3/B:1@OP1 surfaces

> hide #3/B:1@OP2 #3/B:1@OP1 atoms

> hide #3/B:1@OP2 #3/B:1@OP1 surfaces

> coordset #3 1,300,2

> perframe "color /F,H,O,V,W,X $1,34,50,100" ranges 100,0 frames 20

> perframe "color /B 50,45,$1,30 surfaces" ranges 100,5 frames 20

> show #15 #16 models

> fly 151 p_zoomed_out p_all_bound

> wait 151

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 255, in calculate_surface_geometry  
self.update_selection()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 574, in update_selection  
tmask = self._atom_triangle_mask(asel)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
IndexError: index 5332525 is out of bounds for axis 0 with size 5055451  
  
Error processing trigger "changes":  
IndexError: index 5332525 is out of bounds for axis 0 with size 5055451  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 255, in calculate_surface_geometry  
self.update_selection()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 574, in update_selection  
tmask = self._atom_triangle_mask(asel)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
IndexError: index 5818142 is out of bounds for axis 0 with size 5042421  
  
Error processing trigger "changes":  
IndexError: index 5818142 is out of bounds for axis 0 with size 5042421  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 255, in calculate_surface_geometry  
self.update_selection()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 574, in update_selection  
tmask = self._atom_triangle_mask(asel)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 359, in _atom_triangle_mask  
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)  
IndexError: index 5538745 is out of bounds for axis 0 with size 4992439  
  
Error processing trigger "changes":  
IndexError: index 5538745 is out of bounds for axis 0 with size 4992439  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 359, in _atom_triangle_mask  
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 255, in calculate_surface_geometry  
self.update_selection()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 574, in update_selection  
tmask = self._atom_triangle_mask(asel)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
IndexError: index 5703915 is out of bounds for axis 0 with size 4986987  
  
Error processing trigger "changes":  
IndexError: index 5703915 is out of bounds for axis 0 with size 4986987  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 360, in _atom_triangle_mask  
logical_and(shown_triangles, shown_vertices[t[:,2]], shown_triangles)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 235, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/gridsurf.py", line 99, in ses_surface_geometry  
va,na,ta = reduce_geometry(ses_va, ses_na, ses_ta, keepv, keept)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
IndexError: index 3987956 is out of bounds for axis 0 with size 3653778  
  
Error processing trigger "changes":  
IndexError: index 3987956 is out of bounds for axis 0 with size 3653778  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 235, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/gridsurf.py", line 99, in ses_surface_geometry  
va,na,ta = reduce_geometry(ses_va, ses_na, ses_ta, keepv, keept)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
IndexError: index 3992257 is out of bounds for axis 0 with size 3651298  
  
Error processing trigger "changes":  
IndexError: index 3992257 is out of bounds for axis 0 with size 3651298  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 243, in calculate_surface_geometry  
v2a = self.vertex_to_atom_map(va)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 301, in vertex_to_atom_map  
raise RuntimeError('Surface further from atoms than expected (%g) for %d of %d
atoms'  
RuntimeError: Surface further from atoms than expected (4.4) for 1 of 1975188
atoms  
  
Error processing trigger "changes":  
RuntimeError: Surface further from atoms than expected (4.4) for 1 of 1975188
atoms  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 301, in vertex_to_atom_map  
raise RuntimeError('Surface further from atoms than expected (%g) for %d of %d
atoms'  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 178, in _atoms_changed  
self._recompute_shape()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 211, in _recompute_shape  
self.calculate_surface_geometry()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 235, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/gridsurf.py", line 99, in ses_surface_geometry  
va,na,ta = reduce_geometry(ses_va, ses_na, ses_ta, keepv, keept)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
IndexError: index 4221118 is out of bounds for axis 0 with size 3646462  
  
Error processing trigger "changes":  
IndexError: index 4221118 is out of bounds for axis 0 with size 3646462  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/split.py", line 73, in reduce_geometry  
rta = vmap.take(rta.ravel()).reshape((len(ti),3))  
  
See log for complete Python traceback.  
  

> hide #3 models

> hide #15 #16 models

> hide #17.3 models

> log save _4.log

> 2dlabels text stage4->5 color light sea green size 26 xpos .3 ypos .92

> show #4 models

> coordset #4 1,300,2

> perframe "color /1,3 $1,34,50,100" ranges 100,0 frames 10

> wait 151


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

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  




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       8.0Gi       2.3Gi        66Mi        21Gi        22Gi
	Swap:          127Gi       1.0Gi       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
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
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    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
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    wheel: 0.37.1
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    zipp: 3.11.0

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Various surface errors

comment:2 by Tom Goddard, 3 years ago

Same reporter and reporting similar surface recalculation errors as #8549

comment:3 by Tom Goddard, 3 years ago

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

The first four tracebacks indicate that surface.triangles contains vertex indices that are greater than the number of vertices in the vertex_to_atom mapping. But the vertex to atom map did a check that it has the same number of vertices as self.vertices. So it appears that self.triangles has vertex indices that are greater than the number of vertices in self.vertices. I'm baffled. The log shows a movie recording script with surfaces on models #2 and #3 and those are playing coordsets, so the surface would be recomputing. The subsequent errors in reduce_geometry() are also because the triangle array contains vertex indices greater than the number of vertices. And then there is one error saying the surface is too far away from the atoms: "Surface further from atoms than expected (4.4) for 1 of 1975188".

It seems like the basic problem is the triangle array has out of bounds vertex indices. Maybe a bug in the sharp edges calculation caused that. Hard to tell without a test case that demonstrates the error.

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