Opened 2 years ago

Last modified 2 years ago

#10123 assigned defect

Problem reading XYZ file: invalid literal for int() with base 10

Reported by: giuso@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Opened an xyz file

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "P:\\__Work\\_others\TTY Si Zr
> Hf\\_SiNHC\TTY122Me_VAC_TD-S1_opt_EDDM.cub" format cube

Opened TTY122Me_VAC_TD-S1_opt_EDDM.cub as #1, grid size 113,94,89, pixel
0.176, shown at level -0.000636,0.000636, step 1, values float32  

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 559, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1922, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  

> close

> close #

Expected a models specifier or a keyword  

> open "P:\\__Work\\_others\TTY Si Zr
> Hf\\_SiNHC\TTY122Me_VAC_TD-S1_opt_EDDM.cub" format cube

Opened TTY122Me_VAC_TD-S1_opt_EDDM.cub as #1, grid size 113,94,89, pixel
0.176, shown at level -0.000636,0.000636, step 1, values float32  

> close

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  

> open "P:\\__Work\\_others\TTY Si Zr
> Hf\\_SiNHC\TTY122Me_VAC_TD-S1_opt_EDDM.cub" format cube

Opened TTY122Me_VAC_TD-S1_opt_EDDM.cub as #1, grid size 113,94,89, pixel
0.176, shown at level -0.000636,0.000636, step 1, values float32  

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  

> open "P:/__Work/_others/TTY Si Zr Hf/_SiNHC/TTY122Me_VAC_TD-S1_opt_EDDM.xyz"

Traceback (most recent call last):  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 253, in open_xyz  
n_atoms = int(line)  
ValueError: invalid literal for int() with base 10: 'TTY122Me TD-S1 C1\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\\__init__.py", line 481, in open  
return open_xyz(  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 311, in open_xyz  
raise e  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
UnboundLocalError: local variable 'eles' referenced before assignment  
  
File "C:\Users\giuso\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\SEQCROW\io.py", line 259, in open_xyz  
eles,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 369.39
OpenGL renderer: Quadro K420/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision Tower 3620
OS: Microsoft Windows 10 Professionnel (Build 19045)
Memory: 8,476,569,600
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7500 CPU @ 3.40GHz
OSLanguage: fr-FR

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    argcomplete: 3.0.5
    asttokens: 2.1.0
    attrs: 23.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    basis-set-exchange: 0.9
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jsonschema: 4.17.3
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyrsistent: 0.19.3
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    regex: 2023.3.23
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.6.5
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Attachments (1)

benzene.xyz​ (545 bytes ) - added by Tony Schaefer 2 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem reading XYZ file: invalid literal for int() with base 10

Reported by Valerio Giuso

comment:2 by Tony Schaefer, 2 years ago 

Valerio,

I've attached an example of the style of XYZ files that can be parsed. In
general, it expects

number of atoms
one comment line
element1 x1 y1 z1
element2 x2 y2 z2
...

For trajectories/animations, the next structure should be right after the
last atom. It looks like there might be a comment in the right spot, but
this error message doesn't have much info. The error message might be more
detailed on the newer versions of seqcrow.

It looks like you're trying to show the structure from a cube file. Tom
Goddard has written this Python script to load the atom data from all
opened cube files:
https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html

Best,

Tony

On Thu, Nov 9, 2023 at 11:29 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

benzene.xyz​

by Tony Schaefer, 2 years ago

Attachment: benzene.xyz​ added

Added by email2trac

comment:3 by valerio.giuso@…, 2 years ago 

Hello, 

I am a complete neophite on any of these things, but the issue
was resolved by opening the xyz with Mercury, saving it in a new file
and opening it again. I fear I cannot send you the xyz files as the
article is currently being reviewed.

Valerio GIUSO 

Institut de
Physique et de Chimie des Matériaux de Strasbourg (IPCMS) 

Departement
des Matériaux Organiques (DMO) 
23 rue du Loess 
67034, STRASBOURG Cedex
2, France

Il 2023-11-09 19:50 ChimeraX ha scritto:

reading XYZ file: invalid literal for int() with base 10
>
----------------------------------+---------------------------
>
Reporter:  giuso@\u2026      |      Owner:  Tony Schaefer
 |     Status:  assigned
>
Component:  Third Party  |    Version:
Keywords:
closed:               |   Platform:  all
>
----------------------------------+---------------------------
(by Tony Schaefer):
the style of XYZ files that can be parsed. In
>
number of atoms
z2
right after the
the right spot, but
error message might be more
seqcrow.
cube file. Tom
data from all
>
https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html
>

<ChimeraX-bugs-
>>
>>
>>
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>
[attachment:"benzene.xyz"]
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