Opened 4 years ago

Closed 4 years ago

#6375 closed defect (fixed)

Segger make_surfaces recursion

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-104-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f1a55323700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a227fc700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a22ffd700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a237fe700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a23fff700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a40bcf700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a413d0700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f1a41bd1700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f1ad0706740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1866 in make_surfaces
  ...
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/keinoh/MD/MetaI/AE1/2-CRYO/AE1_NIF.mrc

Opened AE1_NIF.mrc as #1, grid size 336,336,336, pixel 1.08, shown at level
0.0363, step 2, values float32  

> volume style mesh

> volume #1 level 0.1954

> select #1

2 models selected  
No visible atoms or bonds selected  

> surface style mesh

> close #1

> open /home/keinoh/MD/MetaI/AE1/0-PREP/AE1_pdb_fit.mrc

Opened AE1_pdb_fit.mrc as #1, grid size 336,335,336, pixel 1.08,1.08,1.08,
shown at level 0.0363, step 2, values float32  

> volume #1 level 0.08788

> volume style mesh

> surface dust #1 size 10.8

> open /home/keinoh/MD/MetaI/AE1/2-CRYO/eq_centered.pdb

Summary of feedback from opening
/home/keinoh/MD/MetaI/AE1/2-CRYO/eq_centered.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
eq_centered.pdb title:  
Title t= 0.00000 step= 0 [more info...]  
  
Chain information for eq_centered.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in eq_centered.pdb #2  
---  
HSD — (HSD)  
NIF — (NIF)  
  

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  

> fitmap #2 inMap #1

Fit molecule eq_centered.pdb (#2) to map AE1_pdb_fit.mrc (#1) using 8390 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 8390, contour level = 0.087875  
  
Position of eq_centered.pdb (#2) relative to AE1_pdb_fit.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> ui tool show "Fit in Map"

Fit molecule eq_centered.pdb (#2) to map AE1_pdb_fit.mrc (#1) using 8390 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 8390, contour level = 0.087875  
  
Position of eq_centered.pdb (#2) relative to AE1_pdb_fit.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> open /home/keinoh/MD/MetaI/AE1/0-PREP/eq_centered_fit_in_map.pdb

Summary of feedback from opening
/home/keinoh/MD/MetaI/AE1/0-PREP/eq_centered_fit_in_map.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
eq_centered_fit_in_map.pdb title:  
Title t= 0.00000 step= 0 [more info...]  
  
Chain information for eq_centered_fit_in_map.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in eq_centered_fit_in_map.pdb #3  
---  
HSD — (HSD)  
NIF — (NIF)  
  

> ui tool show Matchmaker

> matchmaker #2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker eq_centered_fit_in_map.pdb, chain A (#3) with eq_centered.pdb,
chain A (#2), sequence alignment score = 2542.3  
RMSD between 516 pruned atom pairs is 0.469 angstroms; (across all 516 pairs:
0.469)  
  

> ~select #2

Nothing selected  

> select #3

8390 atoms, 8495 bonds, 517 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Surface Zone"

> lighting default

> surface zone #1 nearAtoms #2 distance 5

> surface dust #1 size 10.8

> surface zone #1 nearAtoms #2 distance 5

Average map value = 0.1551 for 8390 atoms, 4552 outside contour  
Fit molecule eq_centered.pdb (#2) to map AE1_pdb_fit.mrc (#1) using 8390 atoms  
average map value = 0.1552, steps = 40  
shifted from previous position = 0.0298  
rotated from previous position = 0.0343 degrees  
atoms outside contour = 4553, contour level = 0.087875  
  
Position of eq_centered.pdb (#2) relative to AE1_pdb_fit.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.22488085 -0.96636115 0.12479873 198.00414804  
-0.92089697 0.25263768 0.29685515 205.70983850  
-0.31839815 -0.04816973 -0.94673243 245.54891720  
Axis -0.61228869 0.78650685 0.08068174  
Axis point 201.07390107 0.00000000 90.74528025  
Rotation angle (degrees) 163.63531188  
Shift along axis 60.36781069  
  

> volume #1 level 0.04058

> surface zone #1 nearAtoms #2 distance 5

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  

> save /home/keinoh/MD/MetaI/AE1/Cryo-Maps/eq_mapfit.pdb selectedOnly true
> relModel #1

> ~select #2

Nothing selected  

> select #1

2 models selected  

> save /home/keinoh/MD/MetaI/AE1/Cryo-Maps/AE1_mapfit.mrc models #1

> open /home/keinoh/MD/MetaI/AE1/Cryo-Maps/AE1_mapfit.mrc

Opened AE1_mapfit.mrc as #3, grid size 336,335,336, pixel 1.08,1.08,1.08,
shown at level 0.0363, step 2, values float32  

> ~select #1

Nothing selected  

> hide #!1 models

> hide #2 models

> volume #!3 style mesh

> volume #3 level 0.1094

> volume #3 level 0.2298

> volume #3 level 0.1137

> hide #!3 models

> show #!3 models

> select #3

2 models selected  

> close #3

> show #!1 models

> show #2 models

> surface zone #1 nearAtoms #2 distance 4.99

> surface zone #1 nearAtoms #2 distance 5

> hide #1.1 models

> show #1.1 models

> view #1 clip false

No atomic structure models chosen  

> ui tool show "Map Eraser"

> volume erase #1 center 156.17,194.66,177.27 radius 44.429 outside true

Opened AE1_pdb_fit.mrc copy as #4, grid size 336,335,336, pixel
1.08,1.08,1.08, shown at step 1, values float32  

> surface zone #1 nearAtoms #2 distance 5

> hide #1.1 models

> surface unzone #1

> select #4

2 models selected  

> ~select #4

Nothing selected  

> volume #4 level 0.06319

> surface zone #1 nearAtoms #2 distance 5

> surface zone #1 nearAtoms #2 distance 2.55

> surface unzone #1

> hide #2 models

> select #4

2 models selected  

> close #4

> show #!1 models

> show #2 models

> show #1.1 models

> volume #1 level 0.07498

> surface dust #1 size 10.8

> lighting default

> surface zone #1 nearAtoms #2 distance 5

> select #1

2 models selected  

> log metadata #2

Metadata for eq_centered.pdb #2  
---  
Title | Title t= 0.00000 step= 0  
Non-standard residues | HSD — (HSD)  
NIF — (NIF)  
  
> log chains #2

Chain information for eq_centered.pdb #2  
---  
Chain | Description  
A | No description available  
  

> log metadata #2

Metadata for eq_centered.pdb #2  
---  
Title | Title t= 0.00000 step= 0  
Non-standard residues | HSD — (HSD)  
NIF — (NIF)  
  
> log chains #2

Chain information for eq_centered.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Segment Map"

No segmentation chosen  
No segmentation selected  

> ~select #1

Nothing selected  
No segmentation chosen  
No segmentation selected  

> select #1

2 models selected  
No segmentation chosen  
No segmentation selected  
No segmentation chosen  

> hide #2 models

> help help:user/tools/surfacezone.html

No segmentation chosen  

> hide #!1 models

No segmentation chosen  

> show #!1 models

Fit molecule eq_centered.pdb (#2) to map AE1_pdb_fit.mrc (#1) using 8390 atoms  
average map value = 0.1552, steps = 44  
shifted from previous position = 0.0106  
rotated from previous position = 0.0032 degrees  
atoms outside contour = 4280, contour level = 0.074976  
  
Position of eq_centered.pdb (#2) relative to AE1_pdb_fit.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.22485001 -0.96636235 0.12484503 198.00642815  
-0.92090212 0.25262296 0.29685170 205.70624239  
-0.31840502 -0.04822295 -0.94672741 245.54372026  
Axis -0.61229878 0.78650076 0.08066441  
Axis point 201.07839055 0.00000000 90.74244059  
Rotation angle (degrees) 163.63316289  
Shift along axis 60.35566177  
  
No segmentation chosen  

> ~select #1

Nothing selected  
No segmentation chosen  

> select #1

2 models selected  
No segmentation chosen  
No segmentation selected  

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> show #2 models

> ui tool show "Surface Zone"

> surface zone #1 nearAtoms #2 distance 1.08

> surface zone #1 nearAtoms #2 distance 5

> surface unzone #1

> ~select #1

Nothing selected  

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  
No segmentation chosen  

> select #1

2 models selected  

> surface zone #1 nearAtoms #2 distance 5

No segmentation chosen  
No segmentation selected...  

> surface unzone #1

> surface zone #1 nearAtoms #2 distance 5

> volume zone #1 nearAtoms #2 range 6.46

Segmenting AE1_pdb_fit.mrc, density threshold 0.074976  
Only showing 60 of 607 regions.  
Showing 60 of 607 region surfaces  
6411 watershed regions, grouped to 607 regions  
Showing AE1_pdb_fit.seg - 607 regions, 60 surfaces  

> hide #!1 models

> ~select #1

Nothing selected  

> hide #1.1 models

> hide #2 models

> hide #!3 models

> show #!3 models

Only showing 60 of 607 regions.  
Showing 60 of 607 region surfaces  

> show #2 models

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  
Only showing 60 of 607 regions.  
Showing 60 of 607 region surfaces  
Ungrouped to 749 regions, but did not show all surfaces, see Options  

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> show #!1 models

> select #1

2 models selected  

> ~select #1

Nothing selected  

> hide #2 models

> close #3

> select #1

2 models selected  

> show target m

No segmentation chosen  
No segmentation selected  
No segmentation chosen  

> ui tool show "Fit in Map"

Fit molecule eq_centered.pdb (#2) to map AE1_pdb_fit.mrc (#1) using 8390 atoms  
average map value = 0.1552, steps = 40  
shifted from previous position = 0.0256  
rotated from previous position = 0.0243 degrees  
atoms outside contour = 4276, contour level = 0.074976  
  
Position of eq_centered.pdb (#2) relative to AE1_pdb_fit.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.22484710 -0.96631687 0.12520177 197.97243164  
-0.92094777 0.25272290 0.29662491 205.72444603  
-0.31827501 -0.04860904 -0.94675138 245.57539171  
Axis -0.61228972 0.78652831 0.08046437  
Axis point 201.07867448 0.00000000 90.77734131  
Rotation angle (degrees) 163.62514538  
Shift along axis 60.35168537  
  

> ~select #1

Nothing selected  

> ui tool show "Segment Map"

Segmenting AE1_pdb_fit.mrc, density threshold 0.074976  
Only showing 60 of 607 regions.  
Showing 60 of 607 region surfaces  
6411 watershed regions, grouped to 607 regions  
Showing AE1_pdb_fit.seg - 607 regions, 60 surfaces  

> hide #!1 models

> hide #1.1 models

> hide #2 models

> hide #!3 models

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  

> show #2 models

> hide #2 models

> ~select #2

Nothing selected  

> show #!3 models

> show #2 models

> select #2

8390 atoms, 8495 bonds, 517 residues, 1 model selected  
Overlapping 8390 atoms with 607 regions  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: Quadro K600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T3610
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 4 Intel(R) Xeon(R) CPU E5-1607 v2 @ 3.00GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        3.6G        6.4G        222M        5.7G         11G
	Swap:          2.0G          0B        2.0G

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK107GL [Quadro K600] [10de:0ffa] (rev a1)	
	Subsystem: NVIDIA Corporation GK107GL [Quadro K600] [10de:094b]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger make_surfaces recursion

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The Segger menu entry Regions / Regions Overlapping Current Selection caused an infinite recursion when not all the region surfaces have been computed. This was broken in porting the Chimera Segger code by changes to handle the missing Task class in ChimeraX.

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