Crash opening MTZ file: clipper/maps/xmapset.py", line 450 in _launch_live_xmap_mgr

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-84-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fb333fff640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb350ff9640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3517fa640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/selectors.py", line 416 in select
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb351ffb640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3527fc640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb352ffd640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3537fe640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb353fff640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb374ff9640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3757fa640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb375ffb640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3767fc640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb376ffd640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3777fe640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb377fff640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb398ff9640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb3997fa640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb399ffb640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb39a7fc640 (most recent call first):
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 910 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007fb424a45740 (most recent call first):
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/maps/xmapset.py", line 450 in _launch_live_xmap_mgr
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/maps/xmapset.py", line 257 in init_maps
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/maps/xmapset.py", line 185 in __init__
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/maps/map_mgr.py", line 324 in add_xmapset_from_file
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/cmd.py", line 32 in open_structure_factors
  File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-packages/chimerax/clipper/__init__.py", line 244 in open
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 464 in collated_open
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/runpy.py", line 87 in _run_code
  File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-manylinux_2_28_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.3  
[notice] To update, run: pip3.9 install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/exports/people/csgid/ssq2911/Downloads/ChimeraX_ISOLDE-1.6.0-cp39-cp39-manylinux_2_28_x86_64.whl  
Requirement already satisfied: ChimeraX-Core=1.6rc202304252053 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.6.0) (1.6.1)  
Collecting ChimeraX-Clipper~=0.21.0  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.21.0/ChimeraX_Clipper-0.21.0-cp39-cp39-manylinux_2_28_x86_64.whl
(27.4 MB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.4/27.4 MB 8.2 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-Atomic~=1.36 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.6.0) (1.43.10)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.6.0) (1.1)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.6.0) (10.0.6)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.12)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0.3)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.7.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.0.2)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.2.3)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.10.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.28.4)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.0.1)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
ISOLDE==1.6.0) (1.0.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.10.3)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.1.4)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.2)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0.1)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.0.1)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (1.4)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/exports/software/Linux/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.6.0) (2.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Successfully installed ChimeraX-Clipper-0.21.0 ChimeraX-ISOLDE-1.6.0  
\---  

Successfully installed ChimeraX-Clipper-0.21.0 ChimeraX-ISOLDE-1.6.0  
Installed ChimeraX-Clipper (0.21.0)  
Installed ChimeraX-ISOLDE (1.6.0)  

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1269, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 158, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, tool_name, create=True)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/tool.py", line 29, in __init__  
isolde = Isolde(session)  
File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 310, in __init__  
session._isolde_tb.isolde_started()  
File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 160, in isolde_started  
self.set_enabled('Start ISOLDE', False)  
File "/exports/people/csgid/ssq2911/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 127, in set_enabled  
self.session.toolbar.set_enabled(enabled, tab, section, display_name)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/toolbar/manager.py", line 164, in set_enabled  
tb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 246, in set_enabled  
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/tabbedtoolbar.py", line 496, in set_enabled  
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")  
ValueError: Didn't find section 'Main' in tab 'ISOLDE'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1656, in   
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Didn't find section 'Main' in tab 'ISOLDE'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Didn't find section 'Main' in tab 'ISOLDE'  
  
File "/opt/chimerax/x64/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> open /exports/people/csgid/ssq2911/Documents/PilU-
> EM/Model_fitting_refinement/J422/map_to_structure_factors.mtz


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.104.12
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:0
Manufacturer: Supermicro
Model: Super Server
OS: Linux Mint 21.2 Victoria
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Xeon(R) CPU E5-2637 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       3.0Gi        47Gi        71Mi        11Gi        59Gi
	Swap:           32Gi          0B        32Gi

Graphics:
	04:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K2200] [10de:13ba] (rev a2)	
	Subsystem: NVIDIA Corporation GM107GL [Quadro K2200] [10de:1097]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0