delete all: OSError: exception: access violation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\Destiny\\\Desktop\\\42sa\\\42sa.pdb

Chain information for 42sa.pdb #1  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open "H:/研究生课题/羰基还原酶课题/目的基因序列/序列挖掘和结构进化/序列祖先酶结构/afd3 结构/186.pdb"

Chain information for 186.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> matchmaker #1 to #2

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 186.pdb, chain A (#2) with 42sa.pdb, chain (blank) (#1), sequence
alignment score = 1305.1  
RMSD between 306 pruned atom pairs is 0.720 angstroms; (across all 336 pairs:
1.360)  
  

> view

[Repeated 1 time(s)]

> set bgColor gray

> set bgColor white

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> lighting flat

> mlp

Map values for surface "42sa.pdb_ SES surface": minimum -28.53, mean -3.918,
maximum 24.41  
Map values for surface "186.pdb_A SES surface": minimum -28.9, mean -4.783,
maximum 24.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #1.1 models

> show #1.1 models

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> hide #1.1 models

> hide #2.1 models

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> hide #!2 models

Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid  

> matchmaker #1 to #2 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 186.pdb, chain A (#2) with 42sa.pdb, chain (blank) (#1), sequence
alignment score = 1305.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 42sa.pdb #1/?, 186.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 306 pruned atom pairs is 0.720 angstroms; (across all 336 pairs:
1.360)  
  

> select #1/?:2 #2/A:2

17 atoms, 15 bonds, 2 residues, 2 models selected  

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #1.1 models

> show #2.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #!1 models

> show #1.1 models

> hide #2.1 models

> hide #!2 models

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.2
which is incompatible.  
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.2.2 which is incompatible.  
\---  

pip standard output:  
\---  
\---  

> kvfinder #1

13 cavities found for 42sa.pdb #1  
42sa.pdb Cavities  
---  
ID |  | Volume | Area | Points  
1.2.4 |  | 769.61 | 659.38 | 3563  
1.2.10 |  | 81.65 | 74.47 | 378  
1.2.5 |  | 42.98 | 64.13 | 199  
1.2.7 |  | 19.87 | 36.19 | 92  
1.2.2 |  | 17.71 | 31.93 | 82  
1.2.13 |  | 16.42 | 30.1 | 76  
1.2.6 |  | 12.31 | 29.54 | 57  
1.2.8 |  | 12.31 | 29.54 | 57  
1.2.9 |  | 12.31 | 29.54 | 57  
1.2.1 |  | 9.07 | 18.95 | 42  
1.2.12 |  | 7.56 | 15.24 | 35  
1.2.3 |  | 6.7 | 11.9 | 31  
1.2.11 |  | 5.83 | 11.14 | 27  
  

> view #1.2.4 @< 3.5

> zoom 0.75

moved plane near -72.51055873867432 [-0.82764558 0.3829862 0.41027352]  
moved plane far -72.51055873867432 [-0.82764558 0.3829862 0.41027352]  

> surface #1.2

> transparency #1.2 50

> ~surface #1.2

> surface #1.2.4

> show #!1 & (#1.2.4 :< 3.5)

> view #!1.2.5 @< 3.5

> zoom 0.75

moved plane near -35.16614731754637 [-0.90835211 0.21193086 0.36052982]  
moved plane far -35.16614731754637 [-0.90835211 0.21193086 0.36052982]  

> ~surface #1.2

> surface #!1.2.5

> show #!1 & (#!1.2.5 :< 3.5)

> view #!1.2.4 @< 3.5

> zoom 0.75

moved plane near -81.94294163100507 [-0.96701903 0.12072461 0.22427609]  
moved plane far -81.94294163100507 [-0.96701903 0.12072461 0.22427609]  

> ~surface #1.2

> surface #!1.2.4

> show #!1 & (#!1.2.4 :< 3.5)

> ui tool show "Find Cavities"

> kvfinder

13 cavities found for 42sa.pdb #!1  
42sa.pdb Cavities  
---  
ID |  | Volume | Area | Points  
1.3.4 |  | 769.61 | 659.38 | 3563  
1.3.10 |  | 81.65 | 74.47 | 378  
1.3.5 |  | 42.98 | 64.13 | 199  
1.3.7 |  | 19.87 | 36.19 | 92  
1.3.2 |  | 17.71 | 31.93 | 82  
1.3.13 |  | 16.42 | 30.1 | 76  
1.3.6 |  | 12.31 | 29.54 | 57  
1.3.8 |  | 12.31 | 29.54 | 57  
1.3.9 |  | 12.31 | 29.54 | 57  
1.3.1 |  | 9.07 | 18.95 | 42  
1.3.12 |  | 7.56 | 15.24 | 35  
1.3.3 |  | 6.7 | 11.9 | 31  
1.3.11 |  | 5.83 | 11.14 | 27  
  
10 cavities found for 186.pdb #2  
186.pdb Cavities  
---  
ID |  | Volume | Area | Points  
2.2.2 |  | 662.69 | 550.38 | 3068  
2.2.1 |  | 68.04 | 88.39 | 315  
2.2.9 |  | 41.69 | 49.09 | 193  
2.2.6 |  | 24.41 | 34.45 | 113  
2.2.8 |  | 19.44 | 31.66 | 90  
2.2.4 |  | 17.28 | 36.68 | 80  
2.2.5 |  | 12.31 | 29.54 | 57  
2.2.3 |  | 7.78 | 14.07 | 36  
2.2.10 |  | 5.62 | 9.56 | 26  
2.2.7 |  | 5.18 | 8.77 | 24  
  

> view #2.2.2 @< 3.5

> zoom 0.75

moved plane near -70.08300318745404 [-0.6311082 0.46630985 0.61988512]  
moved plane far -70.08300318745404 [-0.6311082 0.46630985 0.61988512]  

> surface #2.2

> transparency #2.2 50

> ~surface #2.2

> surface #2.2.2

> show #!2 & (#2.2.2 :< 3.5)

> hide #1.1 models

> hide #!1 models

> show #!1 models

> hide #!2.2 models

> show #!2.2 models

> hide #!1 models

> hide #!1.2 models

> hide #!2.2 models

> hide #!1.3 models

> show #!1 models

> show #!1.2 models

> hide #1.3.1 models

> show #1.3.1 models

> hide #1.3.1 models

> hide #1.3.2 models

> show #1.3.2 models

> show #1.3.1 models

> hide #!1.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> delete all

Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\cmd_line\tool.py", line
319, in execute  
cmd.run(cmd_text)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\std_commands\delete.py",
line 33, in delete  
delete_atoms(session, atoms, attached_hyds=attached_hyds)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\std_commands\delete.py",
line 50, in delete_atoms  
atoms.delete()  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molarray.py", line
818, in delete  
c_function('atom_delete',  
OSError: exception: access violation writing 0x00007FFCD1A5CAC8  
  
OSError: exception: access violation writing 0x00007FFCD1A5CAC8  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molarray.py", line
818, in delete  
c_function('atom_delete',  
  
See log for complete Python traceback.  
  

> open 1fpp

Summary of feedback from opening 1fpp fetched from pdb  
---  
notes | Fetching compressed mmCIF 1fpp from http://files.rcsb.org/download/1fpp.cif  
Fetching CCD FPP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/FPP/FPP.cif  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
1fpp title:  
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]  
  
Chain information for 1fpp #1  
---  
Chain | Description | UniProt  
A | PROTEIN FARNESYLTRANSFERASE | PFTA_RAT 1-377  
B | PROTEIN FARNESYLTRANSFERASE | PFTB_RAT 1-437  
  
Non-standard residues in 1fpp #1  
---  
FPP — farnesyl diphosphate  
PO4 — phosphate ion  
ZN — zinc ion  
  

> mlp

Map values for surface "1fpp_A SES surface": minimum -28.46, mean -4.976,
maximum 24.73  
Map values for surface "1fpp_B SES surface": minimum -27.83, mean -4.111,
maximum 22.2  

> lighting flat

> surface zone #1 nearAtoms :fpp distance 8 maxComponents 1

> surface zone #1 nearAtoms :fpp distance 3 maxComponents 1

> surface zone #1 nearAtoms :fpp distance 10 maxComponents 1

> surface zone #1 nearAtoms :fpp distance 10 maxComponents 2

> surface zone #1 nearAtoms :fpp distance 10

> surface zone #1 nearAtoms :fpp distance 10 maxComponents 6

> surface zone #1 nearAtoms :fpp distance 8 maxComponents 6

> surface zone #1 nearAtoms :fpp distance 8 maxComponents 1

> surface zone #1 nearAtoms :fpp distance 8 maxComponents 8

> hide ~:fpp target ar

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> lighting soft

> hide ~:fpp

> ui windowfill toggle

[Repeated 1 time(s)]

> show

> show cartoons

> hide atoms

> show :fpp

> hide :fpp

> show ~:fpp

> show :fpp

> hide !:fpp

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide ~:fpp

> hide ~:fpp targer c

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide ~:fpp target c

> surface

> show all

> surface

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete atoms

> open 1fpp format mmcif fromDatabase pdb

1fpp title:  
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]  
  
Chain information for 1fpp #1  
---  
Chain | Description | UniProt  
A | PROTEIN FARNESYLTRANSFERASE | PFTA_RAT 1-377  
B | PROTEIN FARNESYLTRANSFERASE | PFTB_RAT 1-437  
  
Non-standard residues in 1fpp #1  
---  
FPP — farnesyl diphosphate  
PO4 — phosphate ion  
ZN — zinc ion  
  

> surface

> clip

> clip model #!1 false

> clip model #1 false

> clip off

> clip ff

Expected a keyword  

> clip

> clip

[Repeated 1 time(s)]

> hide #1.3 models

> hide #1.2 models

> clip

> delete atoms

> open 1fpp format mmcif fromDatabase pdb

1fpp title:  
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]  
  
Chain information for 1fpp #1  
---  
Chain | Description | UniProt  
A | PROTEIN FARNESYLTRANSFERASE | PFTA_RAT 1-377  
B | PROTEIN FARNESYLTRANSFERASE | PFTB_RAT 1-437  
  
Non-standard residues in 1fpp #1  
---  
FPP — farnesyl diphosphate  
PO4 — phosphate ion  
ZN — zinc ion  
  

> clip

> clip off

> clip

> clip off

> surface

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

Alignment identifier is 1/B  
Alignment identifier is 1/A  

> clip

> clip model #!1 false

> clip model #1 false

[Repeated 1 time(s)]

> clip model #1 true

> clip model #!1 false

> hide ~:fpp target ar

> color :fpp & C green

> lighting soft

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right zone

> zone /B:386

> zone label false

> ui mousemode right zone

> zone /B:248

> zone /B:248 residueDistance 3.82 labelDistance 3.06 surfaceDistance 6.11

> zone label false

> zone /B:248 residueDistance 2.93 labelDistance 2.34 surfaceDistance 4.68

> ui mousemode right zone

> undo

[Repeated 8 time(s)]Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\undo.py", line 196,
in undo  
inst.undo()  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\undo.py", line 407,
in undo  
self._update_owner(owner, attribute, old_value, option, deleted_check)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\undo.py", line 439,
in _update_owner  
setattr(owner, attribute, value)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line
234, in set_prop  
cset(self._c_pointers, n, v)  
OSError: exception: access violation reading 0x0000000000000000  
  
undo failed: exception: access violation reading 0x0000000000000000:  
OSError: exception: access violation reading 0x0000000000000000  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line
234, in set_prop  
cset(self._c_pointers, n, v)  
  
See log for complete Python traceback.  
  

> delete all

Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1069, in proxy_handler  
s._changes_cb(*args)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1069, in proxy_handler  
s._changes_cb(*args)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> open 1fpp format mmcif fromDatabase pdb

1fpp title:  
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]  
  
Chain information for 1fpp #1  
---  
Chain | Description | UniProt  
A | PROTEIN FARNESYLTRANSFERASE | PFTA_RAT 1-377  
B | PROTEIN FARNESYLTRANSFERASE | PFTB_RAT 1-437  
  
Non-standard residues in 1fpp #1  
---  
FPP — farnesyl diphosphate  
PO4 — phosphate ion  
ZN — zinc ion  
  
Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1069, in proxy_handler  
s._changes_cb(*args)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1069, in proxy_handler  
s._changes_cb(*args)  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "F:\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line 91,
in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 566.14
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: TUF Gaming FX505GT_FX95GT
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 17,024,634,880
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-9300H CPU @ 2.40GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.0
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1