Opened 5 months ago

Closed 4 months ago

#18096 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.14.0-570.23.1.el9_6.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f8a13fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 324 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 622 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1392 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89d27fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89d2ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89d37fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/selectors.py", line 415 in select
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89d3fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f0ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f17fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f1ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f27fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f2ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f37fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f89f3fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8a10ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8a117fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8a11ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8a127fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f8ab67feb80 (most recent call first):
  Garbage-collecting
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 88 in cmd_coulombic
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 55)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /old-
> home/euribe/EM/ssip-1/3-fold_pseudo3-fold/20250624_peripentonals.pdb

Chain information for 20250624_peripentonals.pdb #1  
---  
Chain | Description  
A B C D E F J K L V W X | No description available  
  

> open /old-
> home/euribe/EM/ssip-1/3-fold_pseudo3-fold/20250624_peripentonals.pdb /old-
> home/euribe/EM/ssip-1/3-fold_pseudo3-fold/20250624_capsomers2-4-5.pdb

Chain information for 20250624_peripentonals.pdb #2  
---  
Chain | Description  
A B C D E F J K L V W X | No description available  
  
Chain information for 20250624_capsomers2-4-5.pdb #3  
---  
Chain | Description  
J K L | No description available  
M N O S T U | No description available  
j k l m n o s t u | No description available  
  

> open /old-
> home/euribe/EM/ssip-1/3-fold_pseudo3-fold/20250624_pseudo3-fold.pdb

Chain information for 20250624_pseudo3-fold.pdb #4  
---  
Chain | Description  
J K L P | No description available  
Q | No description available  
R S T U | No description available  
j k l p q s t u | No description available  
r | No description available  
  

> close #1

> coulombic #1

> coulombic #2

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
20250624_peripentonals.pdb #2/A TYR 14  
20250624_peripentonals.pdb #2/A TYR 33  
20250624_peripentonals.pdb #2/A ARG 39  
20250624_peripentonals.pdb #2/A ARG 44  
20250624_peripentonals.pdb #2/A ARG 56  
20250624_peripentonals.pdb #2/A ARG 79  
20250624_peripentonals.pdb #2/A TYR 84  
20250624_peripentonals.pdb #2/A ARG 127  
20250624_peripentonals.pdb #2/A ARG 132  
20250624_peripentonals.pdb #2/A ARG 137  
20250624_peripentonals.pdb #2/A TYR 145  
20250624_peripentonals.pdb #2/A TRP 168  
20250624_peripentonals.pdb #2/A ARG 172  
20250624_peripentonals.pdb #2/A ARG 185  
20250624_peripentonals.pdb #2/A ARG 190  
20250624_peripentonals.pdb #2/A ARG 200  
20250624_peripentonals.pdb #2/A ARG 208  
20250624_peripentonals.pdb #2/A TYR 221  
20250624_peripentonals.pdb #2/A TYR 255  
20250624_peripentonals.pdb #2/B TYR 14  
20250624_peripentonals.pdb #2/B TYR 33  
20250624_peripentonals.pdb #2/B ARG 39  
20250624_peripentonals.pdb #2/B ARG 44  
20250624_peripentonals.pdb #2/B ARG 56  
20250624_peripentonals.pdb #2/B ARG 79  
20250624_peripentonals.pdb #2/B TYR 84  
20250624_peripentonals.pdb #2/B ARG 127  
20250624_peripentonals.pdb #2/B ARG 132  
20250624_peripentonals.pdb #2/B ARG 137  
20250624_peripentonals.pdb #2/B TYR 145  
20250624_peripentonals.pdb #2/B TRP 168  
20250624_peripentonals.pdb #2/B ARG 172  
20250624_peripentonals.pdb #2/B ARG 185  
20250624_peripentonals.pdb #2/B ARG 190  
20250624_peripentonals.pdb #2/B ARG 200  
20250624_peripentonals.pdb #2/B ARG 208  
20250624_peripentonals.pdb #2/B TYR 221  
20250624_peripentonals.pdb #2/B TYR 255  
20250624_peripentonals.pdb #2/C TYR 14  
20250624_peripentonals.pdb #2/C TYR 33  
20250624_peripentonals.pdb #2/C ARG 39  
20250624_peripentonals.pdb #2/C ARG 44  
20250624_peripentonals.pdb #2/C ARG 56  
20250624_peripentonals.pdb #2/C ARG 79  
20250624_peripentonals.pdb #2/C TYR 84  
20250624_peripentonals.pdb #2/C ARG 127  
20250624_peripentonals.pdb #2/C ARG 132  
20250624_peripentonals.pdb #2/C ARG 137  
20250624_peripentonals.pdb #2/C TYR 145  
20250624_peripentonals.pdb #2/C TRP 168  
20250624_peripentonals.pdb #2/C ARG 172  
20250624_peripentonals.pdb #2/C ARG 185  
20250624_peripentonals.pdb #2/C ARG 190  
20250624_peripentonals.pdb #2/C ARG 200  
20250624_peripentonals.pdb #2/C ARG 208  
20250624_peripentonals.pdb #2/C TYR 221  
20250624_peripentonals.pdb #2/C TYR 255  
20250624_peripentonals.pdb #2/D TYR 14  
20250624_peripentonals.pdb #2/D TYR 33  
20250624_peripentonals.pdb #2/D ARG 39  
20250624_peripentonals.pdb #2/D ARG 44  
20250624_peripentonals.pdb #2/D ARG 56  
20250624_peripentonals.pdb #2/D ARG 79  
20250624_peripentonals.pdb #2/D TYR 84  
20250624_peripentonals.pdb #2/D ARG 127  
20250624_peripentonals.pdb #2/D ARG 132  
20250624_peripentonals.pdb #2/D ARG 137  
20250624_peripentonals.pdb #2/D TYR 145  
20250624_peripentonals.pdb #2/D TRP 168  
20250624_peripentonals.pdb #2/D ARG 172  
20250624_peripentonals.pdb #2/D ARG 185  
20250624_peripentonals.pdb #2/D ARG 190  
20250624_peripentonals.pdb #2/D ARG 200  
20250624_peripentonals.pdb #2/D ARG 208  
20250624_peripentonals.pdb #2/D TYR 221  
20250624_peripentonals.pdb #2/D TYR 255  
20250624_peripentonals.pdb #2/E TYR 14  
20250624_peripentonals.pdb #2/E TYR 33  
20250624_peripentonals.pdb #2/E ARG 39  
20250624_peripentonals.pdb #2/E ARG 44  
20250624_peripentonals.pdb #2/E ARG 56  
20250624_peripentonals.pdb #2/E ARG 79  
20250624_peripentonals.pdb #2/E TYR 84  
20250624_peripentonals.pdb #2/E ARG 127  
20250624_peripentonals.pdb #2/E ARG 132  
20250624_peripentonals.pdb #2/E ARG 137  
20250624_peripentonals.pdb #2/E TYR 145  
20250624_peripentonals.pdb #2/E TRP 168  
20250624_peripentonals.pdb #2/E ARG 172  
20250624_peripentonals.pdb #2/E ARG 185  
20250624_peripentonals.pdb #2/E ARG 190  
20250624_peripentonals.pdb #2/E ARG 200  
20250624_peripentonals.pdb #2/E ARG 208  
20250624_peripentonals.pdb #2/E TYR 221  
20250624_peripentonals.pdb #2/E TYR 255  
20250624_peripentonals.pdb #2/F TYR 14  
20250624_peripentonals.pdb #2/F TYR 33  
20250624_peripentonals.pdb #2/F ARG 39  
20250624_peripentonals.pdb #2/F ARG 44  
20250624_peripentonals.pdb #2/F ARG 56  
20250624_peripentonals.pdb #2/F ARG 79  
20250624_peripentonals.pdb #2/F TYR 84  
20250624_peripentonals.pdb #2/F ARG 127  
20250624_peripentonals.pdb #2/F ARG 132  
20250624_peripentonals.pdb #2/F ARG 137  
20250624_peripentonals.pdb #2/F TYR 145  
20250624_peripentonals.pdb #2/F TRP 168  
20250624_peripentonals.pdb #2/F ARG 172  
20250624_peripentonals.pdb #2/F ARG 185  
20250624_peripentonals.pdb #2/F ARG 190  
20250624_peripentonals.pdb #2/F ARG 200  
20250624_peripentonals.pdb #2/F ARG 208  
20250624_peripentonals.pdb #2/F TYR 221  
20250624_peripentonals.pdb #2/F TYR 255  
20250624_peripentonals.pdb #2/J TYR 14  
20250624_peripentonals.pdb #2/J TYR 33  
20250624_peripentonals.pdb #2/J ARG 39  
20250624_peripentonals.pdb #2/J ARG 44  
20250624_peripentonals.pdb #2/J ARG 56  
20250624_peripentonals.pdb #2/J ARG 79  
20250624_peripentonals.pdb #2/J TYR 84  
20250624_peripentonals.pdb #2/J ARG 127  
20250624_peripentonals.pdb #2/J ARG 132  
20250624_peripentonals.pdb #2/J ARG 137  
20250624_peripentonals.pdb #2/J TYR 145  
20250624_peripentonals.pdb #2/J TRP 168  
20250624_peripentonals.pdb #2/J ARG 172  
20250624_peripentonals.pdb #2/J ARG 185  
20250624_peripentonals.pdb #2/J ARG 190  
20250624_peripentonals.pdb #2/J ARG 200  
20250624_peripentonals.pdb #2/J ARG 208  
20250624_peripentonals.pdb #2/J TYR 221  
20250624_peripentonals.pdb #2/J TYR 255  
20250624_peripentonals.pdb #2/K TYR 14  
20250624_peripentonals.pdb #2/K TYR 33  
20250624_peripentonals.pdb #2/K ARG 39  
20250624_peripentonals.pdb #2/K ARG 44  
20250624_peripentonals.pdb #2/K ARG 56  
20250624_peripentonals.pdb #2/K ARG 79  
20250624_peripentonals.pdb #2/K TYR 84  
20250624_peripentonals.pdb #2/K ARG 127  
20250624_peripentonals.pdb #2/K ARG 132  
20250624_peripentonals.pdb #2/K ARG 137  
20250624_peripentonals.pdb #2/K TYR 145  
20250624_peripentonals.pdb #2/K TRP 168  
20250624_peripentonals.pdb #2/K ARG 172  
20250624_peripentonals.pdb #2/K ARG 185  
20250624_peripentonals.pdb #2/K ARG 190  
20250624_peripentonals.pdb #2/K ARG 200  
20250624_peripentonals.pdb #2/K ARG 208  
20250624_peripentonals.pdb #2/K TYR 221  
20250624_peripentonals.pdb #2/K TYR 255  
20250624_peripentonals.pdb #2/L TYR 14  
20250624_peripentonals.pdb #2/L TYR 33  
20250624_peripentonals.pdb #2/L ARG 39  
20250624_peripentonals.pdb #2/L ARG 44  
20250624_peripentonals.pdb #2/L ARG 56  
20250624_peripentonals.pdb #2/L ARG 79  
20250624_peripentonals.pdb #2/L TYR 84  
20250624_peripentonals.pdb #2/L ARG 127  
20250624_peripentonals.pdb #2/L ARG 132  
20250624_peripentonals.pdb #2/L ARG 137  
20250624_peripentonals.pdb #2/L TYR 145  
20250624_peripentonals.pdb #2/L TRP 168  
20250624_peripentonals.pdb #2/L ARG 172  
20250624_peripentonals.pdb #2/L ARG 185  
20250624_peripentonals.pdb #2/L ARG 190  
20250624_peripentonals.pdb #2/L ARG 200  
20250624_peripentonals.pdb #2/L ARG 208  
20250624_peripentonals.pdb #2/L TYR 221  
20250624_peripentonals.pdb #2/L TYR 255  
20250624_peripentonals.pdb #2/V TYR 14  
20250624_peripentonals.pdb #2/V TYR 33  
20250624_peripentonals.pdb #2/V ARG 39  
20250624_peripentonals.pdb #2/V ARG 44  
20250624_peripentonals.pdb #2/V ARG 56  
20250624_peripentonals.pdb #2/V ARG 79  
20250624_peripentonals.pdb #2/V TYR 84  
20250624_peripentonals.pdb #2/V ARG 127  
20250624_peripentonals.pdb #2/V ARG 132  
20250624_peripentonals.pdb #2/V ARG 137  
20250624_peripentonals.pdb #2/V TYR 145  
20250624_peripentonals.pdb #2/V TRP 168  
20250624_peripentonals.pdb #2/V ARG 172  
20250624_peripentonals.pdb #2/V ARG 185  
20250624_peripentonals.pdb #2/V ARG 190  
20250624_peripentonals.pdb #2/V ARG 200  
20250624_peripentonals.pdb #2/V ARG 208  
20250624_peripentonals.pdb #2/V TYR 221  
20250624_peripentonals.pdb #2/V TYR 255  
20250624_peripentonals.pdb #2/W TYR 14  
20250624_peripentonals.pdb #2/W TYR 33  
20250624_peripentonals.pdb #2/W ARG 39  
20250624_peripentonals.pdb #2/W ARG 44  
20250624_peripentonals.pdb #2/W ARG 56  
20250624_peripentonals.pdb #2/W ARG 79  
20250624_peripentonals.pdb #2/W TYR 84  
20250624_peripentonals.pdb #2/W ARG 127  
20250624_peripentonals.pdb #2/W ARG 132  
20250624_peripentonals.pdb #2/W ARG 137  
20250624_peripentonals.pdb #2/W TYR 145  
20250624_peripentonals.pdb #2/W TRP 168  
20250624_peripentonals.pdb #2/W ARG 172  
20250624_peripentonals.pdb #2/W ARG 185  
20250624_peripentonals.pdb #2/W ARG 190  
20250624_peripentonals.pdb #2/W ARG 200  
20250624_peripentonals.pdb #2/W ARG 208  
20250624_peripentonals.pdb #2/W TYR 221  
20250624_peripentonals.pdb #2/W TYR 255  
20250624_peripentonals.pdb #2/X TYR 14  
20250624_peripentonals.pdb #2/X TYR 33  
20250624_peripentonals.pdb #2/X ARG 39  
20250624_peripentonals.pdb #2/X ARG 44  
20250624_peripentonals.pdb #2/X ARG 56  
20250624_peripentonals.pdb #2/X ARG 79  
20250624_peripentonals.pdb #2/X TYR 84  
20250624_peripentonals.pdb #2/X ARG 127  
20250624_peripentonals.pdb #2/X ARG 132  
20250624_peripentonals.pdb #2/X ARG 137  
20250624_peripentonals.pdb #2/X TYR 145  
20250624_peripentonals.pdb #2/X TRP 168  
20250624_peripentonals.pdb #2/X ARG 172  
20250624_peripentonals.pdb #2/X ARG 185  
20250624_peripentonals.pdb #2/X ARG 190  
20250624_peripentonals.pdb #2/X ARG 200  
20250624_peripentonals.pdb #2/X ARG 208  
20250624_peripentonals.pdb #2/X TYR 221  
20250624_peripentonals.pdb #2/X TYR 255  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 20250624_peripentonals.pdb_A SES surface #2.1: minimum,
-17.55, mean -1.05, maximum 13.88  
Coulombic values for 20250624_peripentonals.pdb_B SES surface #2.2: minimum,
-23.86, mean -0.95, maximum 11.59  
Coulombic values for 20250624_peripentonals.pdb_C SES surface #2.3: minimum,
-20.53, mean -1.08, maximum 10.59  
Coulombic values for 20250624_peripentonals.pdb_D SES surface #2.4: minimum,
-17.77, mean -1.05, maximum 14.06  
Coulombic values for 20250624_peripentonals.pdb_E SES surface #2.5: minimum,
-19.20, mean -0.94, maximum 11.93  
Coulombic values for 20250624_peripentonals.pdb_F SES surface #2.6: minimum,
-21.27, mean -1.08, maximum 10.65  
Coulombic values for 20250624_peripentonals.pdb_J SES surface #2.7: minimum,
-17.39, mean -1.02, maximum 13.87  
Coulombic values for 20250624_peripentonals.pdb_K SES surface #2.8: minimum,
-21.69, mean -0.96, maximum 10.89  
Coulombic values for 20250624_peripentonals.pdb_L SES surface #2.9: minimum,
-22.66, mean -1.09, maximum 10.72  
Coulombic values for 20250624_peripentonals.pdb_V SES surface #2.10: minimum,
-17.69, mean -1.05, maximum 13.98  
Coulombic values for 20250624_peripentonals.pdb_W SES surface #2.11: minimum,
-21.57, mean -1.05, maximum 10.54  
Coulombic values for 20250624_peripentonals.pdb_X SES surface #2.12: minimum,
-18.14, mean -0.98, maximum 10.89  

> coulombic #3

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
20250624_capsomers2-4-5.pdb #3/J ARG 2  
20250624_capsomers2-4-5.pdb #3/J TYR 10  
20250624_capsomers2-4-5.pdb #3/J ARG 23  
20250624_capsomers2-4-5.pdb #3/J ARG 27  
20250624_capsomers2-4-5.pdb #3/J ARG 29  
20250624_capsomers2-4-5.pdb #3/J ARG 32  
20250624_capsomers2-4-5.pdb #3/J ARG 56  
20250624_capsomers2-4-5.pdb #3/J ARG 61  
20250624_capsomers2-4-5.pdb #3/J TYR 63  
20250624_capsomers2-4-5.pdb #3/J TYR 70  
20250624_capsomers2-4-5.pdb #3/J ARG 73  
20250624_capsomers2-4-5.pdb #3/J ARG 75  
20250624_capsomers2-4-5.pdb #3/J ARG 82  
20250624_capsomers2-4-5.pdb #3/J ARG 112  
20250624_capsomers2-4-5.pdb #3/J ARG 121  
20250624_capsomers2-4-5.pdb #3/J TYR 122  
20250624_capsomers2-4-5.pdb #3/J ARG 161  
20250624_capsomers2-4-5.pdb #3/J ARG 175  
20250624_capsomers2-4-5.pdb #3/J TRP 194  
20250624_capsomers2-4-5.pdb #3/K ARG 2  
20250624_capsomers2-4-5.pdb #3/K TYR 10  
20250624_capsomers2-4-5.pdb #3/K ARG 23  
20250624_capsomers2-4-5.pdb #3/K ARG 27  
20250624_capsomers2-4-5.pdb #3/K ARG 29  
20250624_capsomers2-4-5.pdb #3/K ARG 32  
20250624_capsomers2-4-5.pdb #3/K ARG 56  
20250624_capsomers2-4-5.pdb #3/K ARG 61  
20250624_capsomers2-4-5.pdb #3/K TYR 63  
20250624_capsomers2-4-5.pdb #3/K TYR 70  
20250624_capsomers2-4-5.pdb #3/K ARG 73  
20250624_capsomers2-4-5.pdb #3/K ARG 75  
20250624_capsomers2-4-5.pdb #3/K ARG 82  
20250624_capsomers2-4-5.pdb #3/K ARG 112  
20250624_capsomers2-4-5.pdb #3/K ARG 121  
20250624_capsomers2-4-5.pdb #3/K TYR 122  
20250624_capsomers2-4-5.pdb #3/K ARG 161  
20250624_capsomers2-4-5.pdb #3/K ARG 175  
20250624_capsomers2-4-5.pdb #3/K TRP 194  
20250624_capsomers2-4-5.pdb #3/L ARG 2  
20250624_capsomers2-4-5.pdb #3/L TYR 10  
20250624_capsomers2-4-5.pdb #3/L ARG 23  
20250624_capsomers2-4-5.pdb #3/L ARG 27  
20250624_capsomers2-4-5.pdb #3/L ARG 29  
20250624_capsomers2-4-5.pdb #3/L ARG 32  
20250624_capsomers2-4-5.pdb #3/L ARG 56  
20250624_capsomers2-4-5.pdb #3/L ARG 61  
20250624_capsomers2-4-5.pdb #3/L TYR 63  
20250624_capsomers2-4-5.pdb #3/L TYR 70  
20250624_capsomers2-4-5.pdb #3/L ARG 73  
20250624_capsomers2-4-5.pdb #3/L ARG 75  
20250624_capsomers2-4-5.pdb #3/L ARG 82  
20250624_capsomers2-4-5.pdb #3/L ARG 112  
20250624_capsomers2-4-5.pdb #3/L ARG 121  
20250624_capsomers2-4-5.pdb #3/L TYR 122  
20250624_capsomers2-4-5.pdb #3/L ARG 161  
20250624_capsomers2-4-5.pdb #3/L ARG 175  
20250624_capsomers2-4-5.pdb #3/L TRP 194  
20250624_capsomers2-4-5.pdb #3/M ARG 2  
20250624_capsomers2-4-5.pdb #3/M TYR 10  
20250624_capsomers2-4-5.pdb #3/M ARG 23  
20250624_capsomers2-4-5.pdb #3/M ARG 27  
20250624_capsomers2-4-5.pdb #3/M ARG 29  
20250624_capsomers2-4-5.pdb #3/M ARG 32  
20250624_capsomers2-4-5.pdb #3/M ARG 56  
20250624_capsomers2-4-5.pdb #3/M ARG 61  
20250624_capsomers2-4-5.pdb #3/M TYR 63  
20250624_capsomers2-4-5.pdb #3/M TYR 70  
20250624_capsomers2-4-5.pdb #3/M ARG 73  
20250624_capsomers2-4-5.pdb #3/M ARG 75  
20250624_capsomers2-4-5.pdb #3/M ARG 82  
20250624_capsomers2-4-5.pdb #3/M ARG 112  
20250624_capsomers2-4-5.pdb #3/M ARG 121  
20250624_capsomers2-4-5.pdb #3/M TYR 122  
20250624_capsomers2-4-5.pdb #3/M ARG 161  
20250624_capsomers2-4-5.pdb #3/M ARG 175  
20250624_capsomers2-4-5.pdb #3/M TRP 194  
20250624_capsomers2-4-5.pdb #3/N ARG 2  
20250624_capsomers2-4-5.pdb #3/N TYR 10  
20250624_capsomers2-4-5.pdb #3/N ARG 23  
20250624_capsomers2-4-5.pdb #3/N ARG 27  
20250624_capsomers2-4-5.pdb #3/N ARG 29  
20250624_capsomers2-4-5.pdb #3/N ARG 32  
20250624_capsomers2-4-5.pdb #3/N ARG 56  
20250624_capsomers2-4-5.pdb #3/N ARG 61  
20250624_capsomers2-4-5.pdb #3/N TYR 63  
20250624_capsomers2-4-5.pdb #3/N TYR 70  
20250624_capsomers2-4-5.pdb #3/N ARG 73  
20250624_capsomers2-4-5.pdb #3/N ARG 75  
20250624_capsomers2-4-5.pdb #3/N ARG 82  
20250624_capsomers2-4-5.pdb #3/N ARG 112  
20250624_capsomers2-4-5.pdb #3/N ARG 121  
20250624_capsomers2-4-5.pdb #3/N TYR 122  
20250624_capsomers2-4-5.pdb #3/N ARG 161  
20250624_capsomers2-4-5.pdb #3/N ARG 175  
20250624_capsomers2-4-5.pdb #3/N TRP 194  
20250624_capsomers2-4-5.pdb #3/O ARG 2  
20250624_capsomers2-4-5.pdb #3/O TYR 10  
20250624_capsomers2-4-5.pdb #3/O ARG 23  
20250624_capsomers2-4-5.pdb #3/O ARG 27  
20250624_capsomers2-4-5.pdb #3/O ARG 29  
20250624_capsomers2-4-5.pdb #3/O ARG 32  
20250624_capsomers2-4-5.pdb #3/O ARG 56  
20250624_capsomers2-4-5.pdb #3/O ARG 61  
20250624_capsomers2-4-5.pdb #3/O TYR 63  
20250624_capsomers2-4-5.pdb #3/O TYR 70  
20250624_capsomers2-4-5.pdb #3/O ARG 73  
20250624_capsomers2-4-5.pdb #3/O ARG 75  
20250624_capsomers2-4-5.pdb #3/O ARG 82  
20250624_capsomers2-4-5.pdb #3/O ARG 112  
20250624_capsomers2-4-5.pdb #3/O ARG 121  
20250624_capsomers2-4-5.pdb #3/O TYR 122  
20250624_capsomers2-4-5.pdb #3/O ARG 161  
20250624_capsomers2-4-5.pdb #3/O ARG 175  
20250624_capsomers2-4-5.pdb #3/O TRP 194  
20250624_capsomers2-4-5.pdb #3/S ARG 2  
20250624_capsomers2-4-5.pdb #3/S TYR 10  
20250624_capsomers2-4-5.pdb #3/S ARG 23  
20250624_capsomers2-4-5.pdb #3/S ARG 27  
20250624_capsomers2-4-5.pdb #3/S ARG 29  
20250624_capsomers2-4-5.pdb #3/S ARG 32  
20250624_capsomers2-4-5.pdb #3/S ARG 56  
20250624_capsomers2-4-5.pdb #3/S ARG 61  
20250624_capsomers2-4-5.pdb #3/S TYR 63  
20250624_capsomers2-4-5.pdb #3/S TYR 70  
20250624_capsomers2-4-5.pdb #3/S ARG 73  
20250624_capsomers2-4-5.pdb #3/S ARG 75  
20250624_capsomers2-4-5.pdb #3/S ARG 82  
20250624_capsomers2-4-5.pdb #3/S ARG 112  
20250624_capsomers2-4-5.pdb #3/S ARG 121  
20250624_capsomers2-4-5.pdb #3/S TYR 122  
20250624_capsomers2-4-5.pdb #3/S ARG 161  
20250624_capsomers2-4-5.pdb #3/S ARG 175  
20250624_capsomers2-4-5.pdb #3/S TRP 194  
20250624_capsomers2-4-5.pdb #3/T ARG 2  
20250624_capsomers2-4-5.pdb #3/T TYR 10  
20250624_capsomers2-4-5.pdb #3/T ARG 23  
20250624_capsomers2-4-5.pdb #3/T ARG 27  
20250624_capsomers2-4-5.pdb #3/T ARG 29  
20250624_capsomers2-4-5.pdb #3/T ARG 32  
20250624_capsomers2-4-5.pdb #3/T ARG 56  
20250624_capsomers2-4-5.pdb #3/T ARG 61  
20250624_capsomers2-4-5.pdb #3/T TYR 63  
20250624_capsomers2-4-5.pdb #3/T TYR 70  
20250624_capsomers2-4-5.pdb #3/T ARG 73  
20250624_capsomers2-4-5.pdb #3/T ARG 75  
20250624_capsomers2-4-5.pdb #3/T ARG 82  
20250624_capsomers2-4-5.pdb #3/T ARG 112  
20250624_capsomers2-4-5.pdb #3/T ARG 121  
20250624_capsomers2-4-5.pdb #3/T TYR 122  
20250624_capsomers2-4-5.pdb #3/T ARG 161  
20250624_capsomers2-4-5.pdb #3/T ARG 175  
20250624_capsomers2-4-5.pdb #3/T TRP 194  
20250624_capsomers2-4-5.pdb #3/U ARG 2  
20250624_capsomers2-4-5.pdb #3/U TYR 10  
20250624_capsomers2-4-5.pdb #3/U ARG 23  
20250624_capsomers2-4-5.pdb #3/U ARG 27  
20250624_capsomers2-4-5.pdb #3/U ARG 29  
20250624_capsomers2-4-5.pdb #3/U ARG 32  
20250624_capsomers2-4-5.pdb #3/U ARG 56  
20250624_capsomers2-4-5.pdb #3/U ARG 61  
20250624_capsomers2-4-5.pdb #3/U TYR 63  
20250624_capsomers2-4-5.pdb #3/U TYR 70  
20250624_capsomers2-4-5.pdb #3/U ARG 73  
20250624_capsomers2-4-5.pdb #3/U ARG 75  
20250624_capsomers2-4-5.pdb #3/U ARG 82  
20250624_capsomers2-4-5.pdb #3/U ARG 112  
20250624_capsomers2-4-5.pdb #3/U ARG 121  
20250624_capsomers2-4-5.pdb #3/U TYR 122  
20250624_capsomers2-4-5.pdb #3/U ARG 161  
20250624_capsomers2-4-5.pdb #3/U ARG 175  
20250624_capsomers2-4-5.pdb #3/U TRP 194  
20250624_capsomers2-4-5.pdb #3/j TYR 5  
20250624_capsomers2-4-5.pdb #3/j ARG 10  
20250624_capsomers2-4-5.pdb #3/j ARG 26  
20250624_capsomers2-4-5.pdb #3/j TYR 58  
20250624_capsomers2-4-5.pdb #3/j ARG 60  
20250624_capsomers2-4-5.pdb #3/j ARG 65  
20250624_capsomers2-4-5.pdb #3/j ARG 67  
20250624_capsomers2-4-5.pdb #3/j TYR 69  
20250624_capsomers2-4-5.pdb #3/j ARG 106  
20250624_capsomers2-4-5.pdb #3/j TYR 133  
20250624_capsomers2-4-5.pdb #3/j ARG 149  
20250624_capsomers2-4-5.pdb #3/j ARG 160  
20250624_capsomers2-4-5.pdb #3/j TRP 173  
20250624_capsomers2-4-5.pdb #3/j TRP 191  
20250624_capsomers2-4-5.pdb #3/j ARG 210  
20250624_capsomers2-4-5.pdb #3/k TYR 5  
20250624_capsomers2-4-5.pdb #3/k ARG 10  
20250624_capsomers2-4-5.pdb #3/k ARG 26  
20250624_capsomers2-4-5.pdb #3/k TYR 58  
20250624_capsomers2-4-5.pdb #3/k ARG 60  
20250624_capsomers2-4-5.pdb #3/k ARG 65  
20250624_capsomers2-4-5.pdb #3/k ARG 67  
20250624_capsomers2-4-5.pdb #3/k TYR 69  
20250624_capsomers2-4-5.pdb #3/k ARG 106  
20250624_capsomers2-4-5.pdb #3/k TYR 133  
20250624_capsomers2-4-5.pdb #3/k ARG 149  
20250624_capsomers2-4-5.pdb #3/k ARG 160  
20250624_capsomers2-4-5.pdb #3/k TRP 173  
20250624_capsomers2-4-5.pdb #3/k TRP 191  
20250624_capsomers2-4-5.pdb #3/k ARG 210  
20250624_capsomers2-4-5.pdb #3/l TYR 5  
20250624_capsomers2-4-5.pdb #3/l ARG 10  
20250624_capsomers2-4-5.pdb #3/l ARG 26  
20250624_capsomers2-4-5.pdb #3/l TYR 58  
20250624_capsomers2-4-5.pdb #3/l ARG 60  
20250624_capsomers2-4-5.pdb #3/l ARG 65  
20250624_capsomers2-4-5.pdb #3/l ARG 67  
20250624_capsomers2-4-5.pdb #3/l TYR 69  
20250624_capsomers2-4-5.pdb #3/l ARG 106  
20250624_capsomers2-4-5.pdb #3/l TYR 133  
20250624_capsomers2-4-5.pdb #3/l ARG 149  
20250624_capsomers2-4-5.pdb #3/l ARG 160  
20250624_capsomers2-4-5.pdb #3/l TRP 173  
20250624_capsomers2-4-5.pdb #3/l TRP 191  
20250624_capsomers2-4-5.pdb #3/l ARG 210  
20250624_capsomers2-4-5.pdb #3/m TYR 5  
20250624_capsomers2-4-5.pdb #3/m ARG 10  
20250624_capsomers2-4-5.pdb #3/m ARG 26  
20250624_capsomers2-4-5.pdb #3/m TYR 58  
20250624_capsomers2-4-5.pdb #3/m ARG 60  
20250624_capsomers2-4-5.pdb #3/m ARG 65  
20250624_capsomers2-4-5.pdb #3/m ARG 67  
20250624_capsomers2-4-5.pdb #3/m TYR 69  
20250624_capsomers2-4-5.pdb #3/m ARG 106  
20250624_capsomers2-4-5.pdb #3/m TYR 133  
20250624_capsomers2-4-5.pdb #3/m ARG 149  
20250624_capsomers2-4-5.pdb #3/m ARG 160  
20250624_capsomers2-4-5.pdb #3/m TRP 173  
20250624_capsomers2-4-5.pdb #3/m TRP 191  
20250624_capsomers2-4-5.pdb #3/m ARG 210  
20250624_capsomers2-4-5.pdb #3/n TYR 5  
20250624_capsomers2-4-5.pdb #3/n ARG 10  
20250624_capsomers2-4-5.pdb #3/n ARG 26  
20250624_capsomers2-4-5.pdb #3/n TYR 58  
20250624_capsomers2-4-5.pdb #3/n ARG 60  
20250624_capsomers2-4-5.pdb #3/n ARG 65  
20250624_capsomers2-4-5.pdb #3/n ARG 67  
20250624_capsomers2-4-5.pdb #3/n TYR 69  
20250624_capsomers2-4-5.pdb #3/n ARG 106  
20250624_capsomers2-4-5.pdb #3/n TYR 133  
20250624_capsomers2-4-5.pdb #3/n ARG 149  
20250624_capsomers2-4-5.pdb #3/n ARG 160  
20250624_capsomers2-4-5.pdb #3/n TRP 173  
20250624_capsomers2-4-5.pdb #3/n TRP 191  
20250624_capsomers2-4-5.pdb #3/n ARG 210  
20250624_capsomers2-4-5.pdb #3/o TYR 5  
20250624_capsomers2-4-5.pdb #3/o ARG 10  
20250624_capsomers2-4-5.pdb #3/o ARG 26  
20250624_capsomers2-4-5.pdb #3/o TYR 58  
20250624_capsomers2-4-5.pdb #3/o ARG 60  
20250624_capsomers2-4-5.pdb #3/o ARG 65  
20250624_capsomers2-4-5.pdb #3/o ARG 67  
20250624_capsomers2-4-5.pdb #3/o TYR 69  
20250624_capsomers2-4-5.pdb #3/o ARG 106  
20250624_capsomers2-4-5.pdb #3/o TYR 133  
20250624_capsomers2-4-5.pdb #3/o ARG 149  
20250624_capsomers2-4-5.pdb #3/o ARG 160  
20250624_capsomers2-4-5.pdb #3/o TRP 173  
20250624_capsomers2-4-5.pdb #3/o TRP 191  
20250624_capsomers2-4-5.pdb #3/o ARG 210  
20250624_capsomers2-4-5.pdb #3/s TYR 5  
20250624_capsomers2-4-5.pdb #3/s ARG 10  
20250624_capsomers2-4-5.pdb #3/s ARG 26  
20250624_capsomers2-4-5.pdb #3/s TYR 58  
20250624_capsomers2-4-5.pdb #3/s ARG 60  
20250624_capsomers2-4-5.pdb #3/s ARG 65  
20250624_capsomers2-4-5.pdb #3/s ARG 67  
20250624_capsomers2-4-5.pdb #3/s TYR 69  
20250624_capsomers2-4-5.pdb #3/s ARG 106  
20250624_capsomers2-4-5.pdb #3/s TYR 133  
20250624_capsomers2-4-5.pdb #3/s ARG 149  
20250624_capsomers2-4-5.pdb #3/s ARG 160  
20250624_capsomers2-4-5.pdb #3/s TRP 173  
20250624_capsomers2-4-5.pdb #3/s TRP 191  
20250624_capsomers2-4-5.pdb #3/s ARG 210  
20250624_capsomers2-4-5.pdb #3/t TYR 5  
20250624_capsomers2-4-5.pdb #3/t ARG 10  
20250624_capsomers2-4-5.pdb #3/t ARG 26  
20250624_capsomers2-4-5.pdb #3/t TYR 58  
20250624_capsomers2-4-5.pdb #3/t ARG 60  
20250624_capsomers2-4-5.pdb #3/t ARG 65  
20250624_capsomers2-4-5.pdb #3/t ARG 67  
20250624_capsomers2-4-5.pdb #3/t TYR 69  
20250624_capsomers2-4-5.pdb #3/t ARG 106  
20250624_capsomers2-4-5.pdb #3/t TYR 133  
20250624_capsomers2-4-5.pdb #3/t ARG 149  
20250624_capsomers2-4-5.pdb #3/t ARG 160  
20250624_capsomers2-4-5.pdb #3/t TRP 173  
20250624_capsomers2-4-5.pdb #3/t TRP 191  
20250624_capsomers2-4-5.pdb #3/t ARG 210  
20250624_capsomers2-4-5.pdb #3/u TYR 5  
20250624_capsomers2-4-5.pdb #3/u ARG 10  
20250624_capsomers2-4-5.pdb #3/u ARG 26  
20250624_capsomers2-4-5.pdb #3/u TYR 58  
20250624_capsomers2-4-5.pdb #3/u ARG 60  
20250624_capsomers2-4-5.pdb #3/u ARG 65  
20250624_capsomers2-4-5.pdb #3/u ARG 67  
20250624_capsomers2-4-5.pdb #3/u TYR 69  
20250624_capsomers2-4-5.pdb #3/u ARG 106  
20250624_capsomers2-4-5.pdb #3/u TYR 133  
20250624_capsomers2-4-5.pdb #3/u ARG 149  
20250624_capsomers2-4-5.pdb #3/u ARG 160  
20250624_capsomers2-4-5.pdb #3/u TRP 173  
20250624_capsomers2-4-5.pdb #3/u TRP 191  
20250624_capsomers2-4-5.pdb #3/u ARG 210  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 20250624_capsomers2-4-5.pdb_J SES surface #3.1: minimum,
-17.31, mean 0.67, maximum 16.08  
Coulombic values for 20250624_capsomers2-4-5.pdb_K SES surface #3.2: minimum,
-16.84, mean 0.45, maximum 24.10  
Coulombic values for 20250624_capsomers2-4-5.pdb_L SES surface #3.3: minimum,
-16.24, mean 0.67, maximum 16.34  
Coulombic values for 20250624_capsomers2-4-5.pdb_M SES surface #3.4: minimum,
-24.20, mean 0.02, maximum 16.55  
Coulombic values for 20250624_capsomers2-4-5.pdb_N SES surface #3.5: minimum,
-17.75, mean 0.07, maximum 17.22  
Coulombic values for 20250624_capsomers2-4-5.pdb_O SES surface #3.6: minimum,
-17.49, mean 0.34, maximum 16.52  
Coulombic values for 20250624_capsomers2-4-5.pdb_S SES surface #3.7: minimum,
-16.82, mean 0.29, maximum 15.48  
Coulombic values for 20250624_capsomers2-4-5.pdb_T SES surface #3.8: minimum,
-16.35, mean 0.41, maximum 16.10  
Coulombic values for 20250624_capsomers2-4-5.pdb_U SES surface #3.9: minimum,
-17.32, mean 0.11, maximum 16.58  
Coulombic values for 20250624_capsomers2-4-5.pdb_j SES surface #3.10: minimum,
-21.20, mean -3.44, maximum 20.06  
Coulombic values for 20250624_capsomers2-4-5.pdb_k SES surface #3.11: minimum,
-22.87, mean -3.53, maximum 14.65  
Coulombic values for 20250624_capsomers2-4-5.pdb_l SES surface #3.12: minimum,
-27.71, mean -3.23, maximum 16.88  
Coulombic values for 20250624_capsomers2-4-5.pdb_m SES surface #3.13: minimum,
-19.47, mean -3.47, maximum 18.67  
Coulombic values for 20250624_capsomers2-4-5.pdb_n SES surface #3.14: minimum,
-30.90, mean -3.27, maximum 17.94  
Coulombic values for 20250624_capsomers2-4-5.pdb_o SES surface #3.15: minimum,
-19.92, mean -3.31, maximum 10.95  
Coulombic values for 20250624_capsomers2-4-5.pdb_s SES surface #3.16: minimum,
-23.16, mean -3.47, maximum 11.73  
Coulombic values for 20250624_capsomers2-4-5.pdb_t SES surface #3.17: minimum,
-21.19, mean -3.14, maximum 16.05  
Coulombic values for 20250624_capsomers2-4-5.pdb_u SES surface #3.18: minimum,
-21.80, mean -3.45, maximum 17.71  

> coulombic #4

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
20250624_pseudo3-fold.pdb #4/J ARG 2  
20250624_pseudo3-fold.pdb #4/J TYR 10  
20250624_pseudo3-fold.pdb #4/J ARG 23  
20250624_pseudo3-fold.pdb #4/J ARG 27  
20250624_pseudo3-fold.pdb #4/J ARG 29  
20250624_pseudo3-fold.pdb #4/J ARG 32  
20250624_pseudo3-fold.pdb #4/J ARG 56  
20250624_pseudo3-fold.pdb #4/J ARG 61  
20250624_pseudo3-fold.pdb #4/J TYR 63  
20250624_pseudo3-fold.pdb #4/J TYR 70  
20250624_pseudo3-fold.pdb #4/J ARG 73  
20250624_pseudo3-fold.pdb #4/J ARG 75  
20250624_pseudo3-fold.pdb #4/J ARG 82  
20250624_pseudo3-fold.pdb #4/J ARG 112  
20250624_pseudo3-fold.pdb #4/J ARG 121  
20250624_pseudo3-fold.pdb #4/J TYR 122  
20250624_pseudo3-fold.pdb #4/J ARG 161  
20250624_pseudo3-fold.pdb #4/J ARG 175  
20250624_pseudo3-fold.pdb #4/J TRP 194  
20250624_pseudo3-fold.pdb #4/K ARG 2  
20250624_pseudo3-fold.pdb #4/K TYR 10  
20250624_pseudo3-fold.pdb #4/K ARG 23  
20250624_pseudo3-fold.pdb #4/K ARG 27  
20250624_pseudo3-fold.pdb #4/K ARG 29  
20250624_pseudo3-fold.pdb #4/K ARG 32  
20250624_pseudo3-fold.pdb #4/K ARG 56  
20250624_pseudo3-fold.pdb #4/K ARG 61  
20250624_pseudo3-fold.pdb #4/K TYR 63  
20250624_pseudo3-fold.pdb #4/K TYR 70  
20250624_pseudo3-fold.pdb #4/K ARG 73  
20250624_pseudo3-fold.pdb #4/K ARG 75  
20250624_pseudo3-fold.pdb #4/K ARG 82  
20250624_pseudo3-fold.pdb #4/K ARG 112  
20250624_pseudo3-fold.pdb #4/K ARG 121  
20250624_pseudo3-fold.pdb #4/K TYR 122  
20250624_pseudo3-fold.pdb #4/K ARG 161  
20250624_pseudo3-fold.pdb #4/K ARG 175  
20250624_pseudo3-fold.pdb #4/K TRP 194  
20250624_pseudo3-fold.pdb #4/L ARG 2  
20250624_pseudo3-fold.pdb #4/L TYR 10  
20250624_pseudo3-fold.pdb #4/L ARG 23  
20250624_pseudo3-fold.pdb #4/L ARG 27  
20250624_pseudo3-fold.pdb #4/L ARG 29  
20250624_pseudo3-fold.pdb #4/L ARG 32  
20250624_pseudo3-fold.pdb #4/L ARG 56  
20250624_pseudo3-fold.pdb #4/L ARG 61  
20250624_pseudo3-fold.pdb #4/L TYR 63  
20250624_pseudo3-fold.pdb #4/L TYR 70  
20250624_pseudo3-fold.pdb #4/L ARG 73  
20250624_pseudo3-fold.pdb #4/L ARG 75  
20250624_pseudo3-fold.pdb #4/L ARG 82  
20250624_pseudo3-fold.pdb #4/L ARG 112  
20250624_pseudo3-fold.pdb #4/L ARG 121  
20250624_pseudo3-fold.pdb #4/L TYR 122  
20250624_pseudo3-fold.pdb #4/L ARG 161  
20250624_pseudo3-fold.pdb #4/L ARG 175  
20250624_pseudo3-fold.pdb #4/L TRP 194  
20250624_pseudo3-fold.pdb #4/P ARG 2  
20250624_pseudo3-fold.pdb #4/P TYR 10  
20250624_pseudo3-fold.pdb #4/P ARG 23  
20250624_pseudo3-fold.pdb #4/P ARG 27  
20250624_pseudo3-fold.pdb #4/P ARG 29  
20250624_pseudo3-fold.pdb #4/P ARG 32  
20250624_pseudo3-fold.pdb #4/P ARG 56  
20250624_pseudo3-fold.pdb #4/P ARG 61  
20250624_pseudo3-fold.pdb #4/P TYR 63  
20250624_pseudo3-fold.pdb #4/P TYR 70  
20250624_pseudo3-fold.pdb #4/P ARG 73  
20250624_pseudo3-fold.pdb #4/P ARG 75  
20250624_pseudo3-fold.pdb #4/P ARG 82  
20250624_pseudo3-fold.pdb #4/P ARG 112  
20250624_pseudo3-fold.pdb #4/P ARG 121  
20250624_pseudo3-fold.pdb #4/P TYR 122  
20250624_pseudo3-fold.pdb #4/P ARG 161  
20250624_pseudo3-fold.pdb #4/P ARG 175  
20250624_pseudo3-fold.pdb #4/P TRP 194  
20250624_pseudo3-fold.pdb #4/Q ARG 2  
20250624_pseudo3-fold.pdb #4/Q TYR 10  
20250624_pseudo3-fold.pdb #4/Q ARG 23  
20250624_pseudo3-fold.pdb #4/Q ARG 27  
20250624_pseudo3-fold.pdb #4/Q ARG 29  
20250624_pseudo3-fold.pdb #4/Q ARG 32  
20250624_pseudo3-fold.pdb #4/Q ARG 56  
20250624_pseudo3-fold.pdb #4/Q ARG 61  
20250624_pseudo3-fold.pdb #4/Q TYR 63  
20250624_pseudo3-fold.pdb #4/Q TYR 70  
20250624_pseudo3-fold.pdb #4/Q ARG 73  
20250624_pseudo3-fold.pdb #4/Q ARG 75  
20250624_pseudo3-fold.pdb #4/Q ARG 82  
20250624_pseudo3-fold.pdb #4/Q ARG 112  
20250624_pseudo3-fold.pdb #4/Q ARG 121  
20250624_pseudo3-fold.pdb #4/Q TYR 122  
20250624_pseudo3-fold.pdb #4/Q ARG 161  
20250624_pseudo3-fold.pdb #4/Q ARG 175  
20250624_pseudo3-fold.pdb #4/Q TRP 194  
20250624_pseudo3-fold.pdb #4/R ARG 2  
20250624_pseudo3-fold.pdb #4/R TYR 10  
20250624_pseudo3-fold.pdb #4/R ARG 23  
20250624_pseudo3-fold.pdb #4/R ARG 27  
20250624_pseudo3-fold.pdb #4/R ARG 29  
20250624_pseudo3-fold.pdb #4/R ARG 32  
20250624_pseudo3-fold.pdb #4/R ARG 56  
20250624_pseudo3-fold.pdb #4/R ARG 61  
20250624_pseudo3-fold.pdb #4/R TYR 63  
20250624_pseudo3-fold.pdb #4/R TYR 70  
20250624_pseudo3-fold.pdb #4/R ARG 73  
20250624_pseudo3-fold.pdb #4/R ARG 75  
20250624_pseudo3-fold.pdb #4/R ARG 82  
20250624_pseudo3-fold.pdb #4/R ARG 112  
20250624_pseudo3-fold.pdb #4/R ARG 121  
20250624_pseudo3-fold.pdb #4/R TYR 122  
20250624_pseudo3-fold.pdb #4/R ARG 161  
20250624_pseudo3-fold.pdb #4/R ARG 175  
20250624_pseudo3-fold.pdb #4/R TRP 194  
20250624_pseudo3-fold.pdb #4/S ARG 2  
20250624_pseudo3-fold.pdb #4/S TYR 10  
20250624_pseudo3-fold.pdb #4/S ARG 23  
20250624_pseudo3-fold.pdb #4/S ARG 27  
20250624_pseudo3-fold.pdb #4/S ARG 29  
20250624_pseudo3-fold.pdb #4/S ARG 32  
20250624_pseudo3-fold.pdb #4/S ARG 56  
20250624_pseudo3-fold.pdb #4/S ARG 61  
20250624_pseudo3-fold.pdb #4/S TYR 63  
20250624_pseudo3-fold.pdb #4/S TYR 70  
20250624_pseudo3-fold.pdb #4/S ARG 73  
20250624_pseudo3-fold.pdb #4/S ARG 75  
20250624_pseudo3-fold.pdb #4/S ARG 82  
20250624_pseudo3-fold.pdb #4/S ARG 112  
20250624_pseudo3-fold.pdb #4/S ARG 121  
20250624_pseudo3-fold.pdb #4/S TYR 122  
20250624_pseudo3-fold.pdb #4/S ARG 161  
20250624_pseudo3-fold.pdb #4/S ARG 175  
20250624_pseudo3-fold.pdb #4/S TRP 194  
20250624_pseudo3-fold.pdb #4/T ARG 2  
20250624_pseudo3-fold.pdb #4/T TYR 10  
20250624_pseudo3-fold.pdb #4/T ARG 23  
20250624_pseudo3-fold.pdb #4/T ARG 27  
20250624_pseudo3-fold.pdb #4/T ARG 29  
20250624_pseudo3-fold.pdb #4/T ARG 32  
20250624_pseudo3-fold.pdb #4/T ARG 56  
20250624_pseudo3-fold.pdb #4/T ARG 61  
20250624_pseudo3-fold.pdb #4/T TYR 63  
20250624_pseudo3-fold.pdb #4/T TYR 70  
20250624_pseudo3-fold.pdb #4/T ARG 73  
20250624_pseudo3-fold.pdb #4/T ARG 75  
20250624_pseudo3-fold.pdb #4/T ARG 82  
20250624_pseudo3-fold.pdb #4/T ARG 112  
20250624_pseudo3-fold.pdb #4/T ARG 121  
20250624_pseudo3-fold.pdb #4/T TYR 122  
20250624_pseudo3-fold.pdb #4/T ARG 161  
20250624_pseudo3-fold.pdb #4/T ARG 175  
20250624_pseudo3-fold.pdb #4/T TRP 194  
20250624_pseudo3-fold.pdb #4/U ARG 2  
20250624_pseudo3-fold.pdb #4/U TYR 10  
20250624_pseudo3-fold.pdb #4/U ARG 23  
20250624_pseudo3-fold.pdb #4/U ARG 27  
20250624_pseudo3-fold.pdb #4/U ARG 29  
20250624_pseudo3-fold.pdb #4/U ARG 32  
20250624_pseudo3-fold.pdb #4/U ARG 56  
20250624_pseudo3-fold.pdb #4/U ARG 61  
20250624_pseudo3-fold.pdb #4/U TYR 63  
20250624_pseudo3-fold.pdb #4/U TYR 70  
20250624_pseudo3-fold.pdb #4/U ARG 73  
20250624_pseudo3-fold.pdb #4/U ARG 75  
20250624_pseudo3-fold.pdb #4/U ARG 82  
20250624_pseudo3-fold.pdb #4/U ARG 112  
20250624_pseudo3-fold.pdb #4/U ARG 121  
20250624_pseudo3-fold.pdb #4/U TYR 122  
20250624_pseudo3-fold.pdb #4/U ARG 161  
20250624_pseudo3-fold.pdb #4/U ARG 175  
20250624_pseudo3-fold.pdb #4/U TRP 194  
20250624_pseudo3-fold.pdb #4/j TYR 5  
20250624_pseudo3-fold.pdb #4/j ARG 10  
20250624_pseudo3-fold.pdb #4/j ARG 26  
20250624_pseudo3-fold.pdb #4/j TYR 58  
20250624_pseudo3-fold.pdb #4/j ARG 60  
20250624_pseudo3-fold.pdb #4/j ARG 65  
20250624_pseudo3-fold.pdb #4/j ARG 67  
20250624_pseudo3-fold.pdb #4/j TYR 69  
20250624_pseudo3-fold.pdb #4/j ARG 106  
20250624_pseudo3-fold.pdb #4/j TYR 133  
20250624_pseudo3-fold.pdb #4/j ARG 149  
20250624_pseudo3-fold.pdb #4/j ARG 160  
20250624_pseudo3-fold.pdb #4/j TRP 173  
20250624_pseudo3-fold.pdb #4/j TRP 191  
20250624_pseudo3-fold.pdb #4/j ARG 210  
20250624_pseudo3-fold.pdb #4/k TYR 5  
20250624_pseudo3-fold.pdb #4/k ARG 10  
20250624_pseudo3-fold.pdb #4/k ARG 26  
20250624_pseudo3-fold.pdb #4/k TYR 58  
20250624_pseudo3-fold.pdb #4/k ARG 60  
20250624_pseudo3-fold.pdb #4/k ARG 65  
20250624_pseudo3-fold.pdb #4/k ARG 67  
20250624_pseudo3-fold.pdb #4/k TYR 69  
20250624_pseudo3-fold.pdb #4/k ARG 106  
20250624_pseudo3-fold.pdb #4/k TYR 133  
20250624_pseudo3-fold.pdb #4/k ARG 149  
20250624_pseudo3-fold.pdb #4/k ARG 160  
20250624_pseudo3-fold.pdb #4/k TRP 173  
20250624_pseudo3-fold.pdb #4/k TRP 191  
20250624_pseudo3-fold.pdb #4/k ARG 210  
20250624_pseudo3-fold.pdb #4/l TYR 5  
20250624_pseudo3-fold.pdb #4/l ARG 10  
20250624_pseudo3-fold.pdb #4/l ARG 26  
20250624_pseudo3-fold.pdb #4/l TYR 58  
20250624_pseudo3-fold.pdb #4/l ARG 60  
20250624_pseudo3-fold.pdb #4/l ARG 65  
20250624_pseudo3-fold.pdb #4/l ARG 67  
20250624_pseudo3-fold.pdb #4/l TYR 69  
20250624_pseudo3-fold.pdb #4/l ARG 106  
20250624_pseudo3-fold.pdb #4/l TYR 133  
20250624_pseudo3-fold.pdb #4/l ARG 149  
20250624_pseudo3-fold.pdb #4/l ARG 160  
20250624_pseudo3-fold.pdb #4/l TRP 173  
20250624_pseudo3-fold.pdb #4/l TRP 191  
20250624_pseudo3-fold.pdb #4/l ARG 210  
20250624_pseudo3-fold.pdb #4/p TYR 5  
20250624_pseudo3-fold.pdb #4/p ARG 10  
20250624_pseudo3-fold.pdb #4/p ARG 26  
20250624_pseudo3-fold.pdb #4/p TYR 58  
20250624_pseudo3-fold.pdb #4/p ARG 60  
20250624_pseudo3-fold.pdb #4/p ARG 65  
20250624_pseudo3-fold.pdb #4/p ARG 67  
20250624_pseudo3-fold.pdb #4/p TYR 69  
20250624_pseudo3-fold.pdb #4/p ARG 106  
20250624_pseudo3-fold.pdb #4/p TYR 133  
20250624_pseudo3-fold.pdb #4/p ARG 149  
20250624_pseudo3-fold.pdb #4/p ARG 160  
20250624_pseudo3-fold.pdb #4/p TRP 173  
20250624_pseudo3-fold.pdb #4/p TRP 191  
20250624_pseudo3-fold.pdb #4/p ARG 210  
20250624_pseudo3-fold.pdb #4/q TYR 5  
20250624_pseudo3-fold.pdb #4/q ARG 10  
20250624_pseudo3-fold.pdb #4/q ARG 26  
20250624_pseudo3-fold.pdb #4/q TYR 58  
20250624_pseudo3-fold.pdb #4/q ARG 60  
20250624_pseudo3-fold.pdb #4/q ARG 65  
20250624_pseudo3-fold.pdb #4/q ARG 67  
20250624_pseudo3-fold.pdb #4/q TYR 69  
20250624_pseudo3-fold.pdb #4/q ARG 106  
20250624_pseudo3-fold.pdb #4/q TYR 133  
20250624_pseudo3-fold.pdb #4/q ARG 149  
20250624_pseudo3-fold.pdb #4/q ARG 160  
20250624_pseudo3-fold.pdb #4/q TRP 173  
20250624_pseudo3-fold.pdb #4/q TRP 191  
20250624_pseudo3-fold.pdb #4/q ARG 210  
20250624_pseudo3-fold.pdb #4/r TYR 5  
20250624_pseudo3-fold.pdb #4/r ARG 10  
20250624_pseudo3-fold.pdb #4/r ARG 26  
20250624_pseudo3-fold.pdb #4/r TYR 58  
20250624_pseudo3-fold.pdb #4/r ARG 60  
20250624_pseudo3-fold.pdb #4/r ARG 65  
20250624_pseudo3-fold.pdb #4/r ARG 67  
20250624_pseudo3-fold.pdb #4/r TYR 69  
20250624_pseudo3-fold.pdb #4/r ARG 106  
20250624_pseudo3-fold.pdb #4/r TYR 133  
20250624_pseudo3-fold.pdb #4/r ARG 149  
20250624_pseudo3-fold.pdb #4/r ARG 160  
20250624_pseudo3-fold.pdb #4/r TRP 173  
20250624_pseudo3-fold.pdb #4/r TRP 191  
20250624_pseudo3-fold.pdb #4/r ARG 210  
20250624_pseudo3-fold.pdb #4/s TYR 5  
20250624_pseudo3-fold.pdb #4/s ARG 10  
20250624_pseudo3-fold.pdb #4/s ARG 26  
20250624_pseudo3-fold.pdb #4/s TYR 58  
20250624_pseudo3-fold.pdb #4/s ARG 60  
20250624_pseudo3-fold.pdb #4/s ARG 65  
20250624_pseudo3-fold.pdb #4/s ARG 67  
20250624_pseudo3-fold.pdb #4/s TYR 69  
20250624_pseudo3-fold.pdb #4/s ARG 106  
20250624_pseudo3-fold.pdb #4/s TYR 133  
20250624_pseudo3-fold.pdb #4/s ARG 149  
20250624_pseudo3-fold.pdb #4/s ARG 160  
20250624_pseudo3-fold.pdb #4/s TRP 173  
20250624_pseudo3-fold.pdb #4/s TRP 191  
20250624_pseudo3-fold.pdb #4/s ARG 210  
20250624_pseudo3-fold.pdb #4/t TYR 5  
20250624_pseudo3-fold.pdb #4/t ARG 10  
20250624_pseudo3-fold.pdb #4/t ARG 26  
20250624_pseudo3-fold.pdb #4/t TYR 58  
20250624_pseudo3-fold.pdb #4/t ARG 60  
20250624_pseudo3-fold.pdb #4/t ARG 65  
20250624_pseudo3-fold.pdb #4/t ARG 67  
20250624_pseudo3-fold.pdb #4/t TYR 69  
20250624_pseudo3-fold.pdb #4/t ARG 106  
20250624_pseudo3-fold.pdb #4/t TYR 133  
20250624_pseudo3-fold.pdb #4/t ARG 149  
20250624_pseudo3-fold.pdb #4/t ARG 160  
20250624_pseudo3-fold.pdb #4/t TRP 173  
20250624_pseudo3-fold.pdb #4/t TRP 191  
20250624_pseudo3-fold.pdb #4/t ARG 210  
20250624_pseudo3-fold.pdb #4/u TYR 5  
20250624_pseudo3-fold.pdb #4/u ARG 10  
20250624_pseudo3-fold.pdb #4/u ARG 26  
20250624_pseudo3-fold.pdb #4/u TYR 58  
20250624_pseudo3-fold.pdb #4/u ARG 60  
20250624_pseudo3-fold.pdb #4/u ARG 65  
20250624_pseudo3-fold.pdb #4/u ARG 67  
20250624_pseudo3-fold.pdb #4/u TYR 69  
20250624_pseudo3-fold.pdb #4/u ARG 106  
20250624_pseudo3-fold.pdb #4/u TYR 133  
20250624_pseudo3-fold.pdb #4/u ARG 149  
20250624_pseudo3-fold.pdb #4/u ARG 160  
20250624_pseudo3-fold.pdb #4/u TRP 173  
20250624_pseudo3-fold.pdb #4/u TRP 191  
20250624_pseudo3-fold.pdb #4/u ARG 210  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 20250624_pseudo3-fold.pdb_J SES surface #4.1: minimum,
-17.31, mean 0.67, maximum 16.08  
Coulombic values for 20250624_pseudo3-fold.pdb_K SES surface #4.2: minimum,
-16.84, mean 0.45, maximum 24.10  
Coulombic values for 20250624_pseudo3-fold.pdb_L SES surface #4.3: minimum,
-16.24, mean 0.67, maximum 16.34  
Coulombic values for 20250624_pseudo3-fold.pdb_P SES surface #4.4: minimum,
-18.22, mean 0.02, maximum 16.77  
Coulombic values for 20250624_pseudo3-fold.pdb_Q SES surface #4.5: minimum,
-17.31, mean 0.33, maximum 17.49  
Coulombic values for 20250624_pseudo3-fold.pdb_R SES surface #4.6: minimum,
-17.28, mean 0.25, maximum 24.62  
Coulombic values for 20250624_pseudo3-fold.pdb_S SES surface #4.7: minimum,
-16.82, mean 0.29, maximum 15.48  
Coulombic values for 20250624_pseudo3-fold.pdb_T SES surface #4.8: minimum,
-16.35, mean 0.41, maximum 16.10  
Coulombic values for 20250624_pseudo3-fold.pdb_U SES surface #4.9: minimum,
-17.32, mean 0.11, maximum 16.58  
Coulombic values for 20250624_pseudo3-fold.pdb_j SES surface #4.10: minimum,
-21.20, mean -3.44, maximum 20.06  
Coulombic values for 20250624_pseudo3-fold.pdb_k SES surface #4.11: minimum,
-22.87, mean -3.53, maximum 14.65  
Coulombic values for 20250624_pseudo3-fold.pdb_l SES surface #4.12: minimum,
-27.71, mean -3.23, maximum 16.88  
Coulombic values for 20250624_pseudo3-fold.pdb_p SES surface #4.13: minimum,
-19.63, mean -3.49, maximum 11.68  
Coulombic values for 20250624_pseudo3-fold.pdb_q SES surface #4.14: minimum,
-20.90, mean -3.44, maximum 12.92  
Coulombic values for 20250624_pseudo3-fold.pdb_r SES surface #4.15: minimum,
-24.12, mean -3.75, maximum 16.22  
Coulombic values for 20250624_pseudo3-fold.pdb_s SES surface #4.16: minimum,
-23.16, mean -3.47, maximum 11.73  
Coulombic values for 20250624_pseudo3-fold.pdb_t SES surface #4.17: minimum,
-21.19, mean -3.14, maximum 16.05  
Coulombic values for 20250624_pseudo3-fold.pdb_u SES surface #4.18: minimum,
-21.80, mean -3.45, maximum 17.71  

> close

> open /old-home/euribe/EM/ssip-1/COM/20250312_facet.pdb

Chain information for 20250312_facet.pdb #1  
---  
Chain | Description  
? | No description available  
A F Q W | No description available  
B C D H J K L P Y v | No description available  
E | No description available  
G I M N O R S T U x z | No description available  
V Z a c f r | No description available  
X b d e g h i j k l m n o p q s t u w y | No description available  
  

> coulombic #1


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 575.57.08
OpenGL renderer: NVIDIA T400 4GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
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=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:2
Manufacturer: HP
Model: HP Z4 G5 Workstation Desktop PC
OS: Rocky Linux 9.6 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) w3-2425
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           124Gi       8.8Gi       4.0Gi        62Mi       113Gi       116Gi
	Swap:          2.0Gi       0.0Ki       2.0Gi

Graphics:
	47:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GL [T400 4GB / T400E] [10de:1ff2] (rev a1)	
	Subsystem: Hewlett-Packard Company Device [103c:1613]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 4 months ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 4 months ago

Resolution: → duplicate
Status: accepted → closed
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