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#8096 closed defect

Antechamber on M2: Bad CPU type in executable — at Version 9

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

Description (last modified by Tom Goddard)

The following bug report has been submitted:
Platform:        macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202211290133 (2022-11-29 01:33:01 UTC)
Description
When protein structure is loaded, pressing electrostatic under the "coloring" option results in an error message

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.dev202211290133 (2022-11-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/alexsestok/Alex/UMB
> SOP/Research/F32/Figures/Snail1_3W5K_ZF4_CCHC_Colored.py"

Failed opening file /Users/alexsestok/Alex/UMB
SOP/Research/F32/Figures/Snail1_3W5K_ZF4_CCHC_Colored.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera  
to ChimeraX is being worked on but only handles molecules and molecular
surfaces  
(not volumes) at this time. If that is sufficient, use the latest Chimera  
daily build and its File->Export Scene menu item, and change the resulting  
dialog's "File Type" to ChimeraX.  

> open "/Users/alexsestok/Alex/UMB
> SOP/Research/F32/Figures/Snail1_3W5K_ZF4_CCHC_Colored.py"

ChimeraX cannot open a regular Chimera session. An exporter from Chimera  
to ChimeraX is being worked on but only handles molecules and molecular
surfaces  
(not volumes) at this time. If that is sufficient, use the latest Chimera  
daily build and its File->Export Scene menu item, and change the resulting  
dialog's "File Type" to ChimeraX.  

> open /Users/alexsestok/Downloads/3w5k.pdb

3w5k.pdb title:  
Crystal structure of SNAIL1 and importin β complex [more info...]  
  
Chain information for 3w5k.pdb #1  
---  
Chain | Description | UniProt  
A | importin subunit β-1 | IMB1_HUMAN  
B | zinc finger protein SNAI1 | SNAI1_HUMAN  
  
Non-standard residues in 3w5k.pdb #1  
---  
ZN — zinc ion  
  

> select /A

6725 atoms, 6785 bonds, 1 pseudobond, 908 residues, 2 models selected  

> hide (#!1 & sel) target a

> cartoon hide (#!1 & sel)

Drag select of 2 residues  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:259

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /B:259

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /B:254-255

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /B:254-255

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /B:252

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:252

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:254

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:254

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select add #1

7588 atoms, 7654 bonds, 19 pseudobonds, 1033 residues, 3 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select /A

6725 atoms, 6785 bonds, 1 pseudobond, 908 residues, 2 models selected  

> hide sel cartoons

> select /B

863 atoms, 869 bonds, 18 pseudobonds, 125 residues, 3 models selected  

> show (#!1 & sel) target ab

> hide (#!1 & sel) target a

> select ::name="ZN"

4 atoms, 4 residues, 1 model selected  

> show sel cartoons

[Repeated 2 time(s)]

> show sel target ab

> select /B

863 atoms, 869 bonds, 18 pseudobonds, 125 residues, 3 models selected  

> style sel stick

Changed 863 atom styles  

> style sel stick

Changed 863 atom styles  

> style sel sphere

Changed 863 atom styles  

> style sel ball

Changed 863 atom styles  

> style sel sphere

Changed 863 atom styles  

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

[Repeated 4 time(s)]

> style sel stick

Changed 863 atom styles  

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 863 atom styles  

> style sel sphere

Changed 863 atom styles  

> style sel ball

Changed 863 atom styles  

> style sel sphere

Changed 863 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel sphere

Changed 863 atom styles  

> style sel ball

Changed 863 atom styles  

> style sel sphere

Changed 863 atom styles  

> color sel byhetero

[Repeated 3 time(s)]

> color sel bychain

> color sel bypolymer

> rainbow sel

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B ASP 232  
/B VAL 233  
/B LYS 235  
/B HIS 252  
/B ARG 264  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmppncu6lcx/ante.in.mol2 -fi
mol2 -o
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmppncu6lcx/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 88, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 318, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 571, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 951, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B ASP 232  
/B VAL 233  
/B LYS 235  
/B HIS 252  
/B ARG 264  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmp9oje853i/ante.in.mol2 -fi
mol2 -o
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmp9oje853i/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 88, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 318, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 571, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 951, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  

> color sel byhetero

> color sel bychain

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B ASP 232  
/B VAL 233  
/B LYS 235  
/B HIS 252  
/B ARG 264  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmp92rz0fio/ante.in.mol2 -fi
mol2 -o
/var/folders/k1/_zs6ytcn45v0zvp4bbrvcdhr0000gn/T/tmp92rz0fio/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 88, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 318, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 571, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 951, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py",
line 1821, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 3 days, 17 hours, 7 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.7
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.4
    ChimeraX-AtomicLibrary: 8.0.4
    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: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202211290133
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.1
    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: 1.0.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 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: 2.9
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.7
    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: 1.9.3
    ChimeraX-PDB: 2.6.9
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    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: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8
    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: 1.10.1
    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-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.25.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    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
    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
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    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
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (9)

comment:1 by Eric Pettersen, 3 years ago

Cc:	chimera-programmers added
Component:	Unassigned → Build System
Owner:	set to Tom Goddard
Platform:	→ all
Priority:	normal → high
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Antechamber on M2: Bad CPU type in executable

No email provided, but name supplied as Alex Sestok

comment:2 by Tom Goddard, 3 years ago

It looks like Rosetta, the Intel emulation on Apple Silicon is not installed by default. According to the following page the user is asked to install it the first time it is needed.

https://support.apple.com/en-us/HT211861

My guess is that with the ChimeraX Antechamber subprocess it does not ask and Rosetta has never been installed by the user so it gives this error. Maybe the interactive prompt to install is only when launching a desktop app directly. The following page suggests that code needs to test if Rosetta is available, although this page is about running Intel binaries in a Linux VM on Mac.

https://developer.apple.com/documentation/virtualization/running_intel_binaries_in_linux_vms_with_rosetta

comment:3 by Tom Goddard, 3 years ago

This may be a rare problem. It probably is not new to macOS 13, and anyone running our universal build release candidate on Mac M1 or M2 machines could encounter it, but it has not been reported until now because most users have already run an Intel application and installed Rosetta.

We could add to the ChimeraX 1.5 release notes that Rosetta is needed for Coulombic, movie recording, and whatever other Intel subprocesses are in our ARM Mac build. Of course most user will not find that.

We could probably add some coded that checks if Rosetta is installed and warns if it is not and explains how to install it.

We might be able to build the Intel binaries we are using (Antechamber, ffmpeg, others?) for Mac ARM.

comment:4 by Tom Goddard, 3 years ago

I don't think we need to fix this in ChimeraX 1.5. If Rosetta was not installed in macOS 12 then the problem has only been reported once in about 3 months of availability of the Mac universal build, and longer for the Mac ARM build. But if Rosetta was installed by default on macOS 12 and it is only in macOS 13 where it has to be installed separately then it might be a bigger problem, because macOS 13 just came out a month ago.

comment:5 by Tom Goddard, 3 years ago

It appears Rosetta was not installed by default in macOS 12

https://support.apple.com/en-us/HT211861

But a user would have been asked to install it with Intel ChimeraX. So the problem is new with ARM ChimeraX.

comment:6 by Tom Goddard, 3 years ago

It is somewhat painful to uninstall Rosetta because it is necessary to disable Mac security to do it. This could be done to test that we correctly understand the problem.

https://iboysoft.com/news/uninstall-rosetta-2.html

comment:7 by Tom Goddard, 3 years ago

Component:	Build System → Platform
Priority:	high → moderate

Possibly the user was asked to install Rosetta and declined. We would have to uninstall Rosetta on a Mac ARM machine to see what happens. I did not see anything online that says whether an Intel subprocess of an ARM desktop app would cause it to ask to install Rosetta.

To install Rosetta without having an intel app to launch apparently requires typing a command at the terminal.

https://iboysoft.com/news/how-to-install-rosetta-on-mac-m1.html

comment:8 by Tom Goddard, 3 years ago

I'm inclined to wait and see if this is ever reported again before taking any steps to fix it.

It would be nice to replace Intel binaries in Mac ARM ChimeraX with ARM binaries if the are available.

comment:9 by Tom Goddard, 2 years ago

Description:	modified (diff)

We have now had 3 reports of this error. #8893 was also Antechamber, and #10132 was ffmpeg. All 3 are on M2 CPUs. It may be that the newer Apple M2 machines do not have Rosetta installed by default.

In any case we are probably going to have to replace all our Intel-only third-party binaries with universal binaries (or ARM only) in the future when Apple drops Intel support. That could be the distant future, and if we wait until Apple drops Intel support, we may also drop ChimeraX on Mac Intel and then we would only need ARM binaries which would be simpler.

Should probably survey what Mac Intel-only binaries we are including in the distribution. Possibly the universal build lipo script logs all those and we could find them by looking at the lipo script log.

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