Opened 2 years ago

Closed 2 years ago

#8893 closed defect (fixed)

antechamber: Bad CPU type in executable

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 UTC)
Description
(Describe the actions that caused this problem to occur here)

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: 1.6rc202304202331 (2023-04-20)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /Users/jo_air/Documents/ChimeraX

Current working directory is: /Users/jo_air/Documents/ChimeraX  

> open /Users/jo_air/Downloads/8d81.pdb

8d81.pdb title:  
Cereblon~DDB1 bound to pomalidomide [more info...]  
  
Chain information for 8d81.pdb #1  
---  
Chain | Description | UniProt  
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-699 706-1140  
B | protein cereblon | CRBN_HUMAN 1-442  
  
Non-standard residues in 8d81.pdb #1  
---  
Y70 — S-pomalidomide  
ZN — zinc ion  
  

> volume style surface

No volumes specified  

> select

9248 atoms, 9433 bonds, 6 pseudobonds, 1200 residues, 3 models selected  

> volume style surface

No volumes specified  

> surface (#!1 & sel)

> transparency sel 50

> volume style mesh

No volumes specified  

> volume style image

No volumes specified  

> transparency sel 0

> transparency sel 50

> transparency sel 0

> volume showOutlineBox true

No volumes specified  

> volume showOutlineBox true

No volumes specified  

> volume style mesh

No volumes specified  

> volume style mesh

No volumes specified  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> volume hide

No volumes specified  

> transparency sel 50

> transparency sel 0

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> select /A

6290 atoms, 6404 bonds, 2 pseudobonds, 817 residues, 2 models selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A GLU 27  
/A ASP 99  
/A ARG 114  
/A ARG 129  
/A ARG 147  
/A LYS 153  
/A GLN 186  
/A LYS 204  
/A LYS 208  
/A GLN 209  
/A ILE 237  
/A LYS 287  
/A GLU 288  
/A GLU 289  
/A GLN 290  
/A MET 291  
/A ASP 292  
/A THR 294  
/A VAL 295  
/A LYS 298  
/A ARG 369  
/A GLN 370  
/A LYS 709  
/A LYS 769  
/A LYS 823  
/A SER 955  
/A SER 981  
/A GLU 1019  
/A ASN 1111  
/A ASP 1116  
/A SER 1118  
/A MET 1120  
/A ARG 1122  
/A GLU 1123  
/A THR 1125  
/A LYS 1131  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 8d81.pdb_A SES surface #1.3: minimum, -19.27, mean -5.07,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for 8d81.pdb_A SES surface #1.3: minimum, -19.27, mean -5.07,
maximum 10.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow sel

> color bfactor sel

6290 atoms, 817 residues, 1 surfaces, atom bfactor range 0 to 0  

> color bfactor sel

6290 atoms, 817 residues, 1 surfaces, atom bfactor range 0 to 0  

> select /A

6290 atoms, 6404 bonds, 2 pseudobonds, 817 residues, 2 models selected  

> select /B

2958 atoms, 3029 bonds, 4 pseudobonds, 383 residues, 2 models selected  

> color bfactor sel

2958 atoms, 383 residues, 1 surfaces, atom bfactor range 0 to 0  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B ASN 45  
/B ILE 46  
/B ASP 63  
/B GLU 65  
/B GLU 66  
/B HIS 68  
/B ASP 75  
/B ASP 76  
/B GLN 86  
/B MET 88  
/B PRO 98  
/B MET 109  
/B LYS 116  
/B ASN 127  
/B VAL 128  
/B GLN 129  
/B GLU 130  
/B ARG 131  
/B GLU 132  
/B GLU 146  
/B ASP 149  
/B PHE 150  
/B GLU 153  
/B LYS 166  
/B GLN 183  
/B GLU 216  
/B ASN 267  
/B LYS 269  
/B ASP 292  
/B LYS 317  
/B LYS 324  
/B GLN 325  
/B GLN 327  
/B GLU 328  
/B LYS 364  
/B LYS 392  
/B LYS 413  

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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmpeqij19m8/ante.in.mol2 -fi
mol2 -o
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmpeqij19m8/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1335, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 570, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 513, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 572, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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.  
  

> undo

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B ASN 45  
/B ILE 46  
/B ASP 63  
/B GLU 65  
/B GLU 66  
/B HIS 68  
/B ASP 75  
/B ASP 76  
/B GLN 86  
/B MET 88  
/B PRO 98  
/B MET 109  
/B LYS 116  
/B ASN 127  
/B VAL 128  
/B GLN 129  
/B GLU 130  
/B ARG 131  
/B GLU 132  
/B GLU 146  
/B ASP 149  
/B PHE 150  
/B GLU 153  
/B LYS 166  
/B GLN 183  
/B GLU 216  
/B ASN 267  
/B LYS 269  
/B ASP 292  
/B LYS 317  
/B LYS 324  
/B GLN 325  
/B GLN 327  
/B GLU 328  
/B LYS 364  
/B LYS 392  
/B LYS 413  

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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmp1oqqpiqj/ante.in.mol2 -fi
mol2 -o
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmp1oqqpiqj/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1335, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 570, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 513, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 572, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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.  
  

> mlp sel

Map values for surface "8d81.pdb_B SES surface": minimum -27.3, mean -3.266,
maximum 24.05  
To also show corresponding color key, enter the above mlp command and add key
true  

> select ::name="Y70"

20 atoms, 22 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 20 atom styles  

> mlp sel

mlp: no amino acids specified  

> show sel surfaces

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> hide sel surfaces

> select /B

2958 atoms, 3029 bonds, 4 pseudobonds, 383 residues, 2 models selected  

> style sel ball

Changed 2958 atom styles  

> transparency (#!1 & sel) 40

> color (#!1 & sel) cornflower blue

> undo

> select /B

2958 atoms, 3029 bonds, 4 pseudobonds, 383 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> undo

> select protein

9227 atoms, 9411 bonds, 2 pseudobonds, 1198 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> transparency (#!1 & sel) 40

> color (#!1 & sel) byhetero

> undo

> hide sel surfaces

> select protein

9227 atoms, 9411 bonds, 2 pseudobonds, 1198 residues, 2 models selected  

> color (#!1 & sel) byhetero

> select sideonly

4434 atoms, 3455 bonds, 1122 residues, 1 model selected  

> select ~sel

4814 atoms, 4811 bonds, 2 pseudobonds, 1200 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> style sel sphere

Changed 4814 atom styles  

> undo

> select ::name="Y70"

20 atoms, 22 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) light gray

> color (#!1 & sel) byhetero

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B PRO 98 N  

2 hydrogen bonds found  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select /B

2958 atoms, 3029 bonds, 6 pseudobonds, 383 residues, 3 models selected  

> surface (#!1 & sel)

> mlp sel

Map values for surface "8d81.pdb_B SES surface": minimum -27.3, mean -3.266,
maximum 24.05  
To also show corresponding color key, enter the above mlp command and add key
true  

> transparency (#!1 & sel) 40

> select clear

> save /Users/jo_air/Desktop/image1.png supersample 3

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> ui tool show "Selection Inspector"

> lighting soft

> lighting full

> lighting simple

> ui mousemode right clip

> undo

> ui mousemode right "map eraser"

Can only have one displayed volume when erasing  

> ui mousemode right "pick blobs"

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> open /Users/jo_air/Downloads/8d81.pdb

8d81.pdb title:  
Cereblon~DDB1 bound to pomalidomide [more info...]  
  
Chain information for 8d81.pdb #3  
---  
Chain | Description | UniProt  
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-699 706-1140  
B | protein cereblon | CRBN_HUMAN 1-442  
  
Non-standard residues in 8d81.pdb #3  
---  
Y70 — S-pomalidomide  
ZN — zinc ion  
  

> close session

> open /Users/jo_air/Downloads/8d81.pdb format pdb

8d81.pdb title:  
Cereblon~DDB1 bound to pomalidomide [more info...]  
  
Chain information for 8d81.pdb #1  
---  
Chain | Description | UniProt  
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-699 706-1140  
B | protein cereblon | CRBN_HUMAN 1-442  
  
Non-standard residues in 8d81.pdb #1  
---  
Y70 — S-pomalidomide  
ZN — zinc ion  
  

> color byhetero

> color bychain

> color bypolymer

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A GLU 27  
/A ASP 99  
/A ARG 114  
/A ARG 129  
/A ARG 147  
/A LYS 153  
/A GLN 186  
/A LYS 204  
/A LYS 208  
/A GLN 209  
/A ILE 237  
/A LYS 287  
/A GLU 288  
/A GLU 289  
/A GLN 290  
/A MET 291  
/A ASP 292  
/A THR 294  
/A VAL 295  
/A LYS 298  
/A ARG 369  
/A GLN 370  
/A LYS 709  
/A LYS 769  
/A LYS 823  
/A SER 955  
/A SER 981  
/A GLU 1019  
/A ASN 1111  
/A ASP 1116  
/A SER 1118  
/A MET 1120  
/A ARG 1122  
/A GLU 1123  
/A THR 1125  
/A LYS 1131  
/B ASN 45  
/B ILE 46  
/B ASP 63  
/B GLU 65  
/B GLU 66  
/B HIS 68  
/B ASP 75  
/B ASP 76  
/B GLN 86  
/B MET 88  
/B PRO 98  
/B MET 109  
/B LYS 116  
/B ASN 127  
/B VAL 128  
/B GLN 129  
/B GLU 130  
/B ARG 131  
/B GLU 132  
/B GLU 146  
/B ASP 149  
/B PHE 150  
/B GLU 153  
/B LYS 166  
/B GLN 183  
/B GLU 216  
/B ASN 267  
/B LYS 269  
/B ASP 292  
/B LYS 317  
/B LYS 324  
/B GLN 325  
/B GLN 327  
/B GLU 328  
/B LYS 364  
/B LYS 392  
/B LYS 413  

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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmpn4k89is7/ante.in.mol2 -fi
mol2 -o
/var/folders/rf/5nxwwkb11ysb9yxk85xpbv940000gn/T/tmpn4k89is7/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1335, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 570, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 513, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 572, in nonstd_charge  
ante_messages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=temp_dir, bufsize=1,  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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-1.6-rc2023.04.20.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-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
OSError: [Errno 86] Bad CPU type in executable:
'/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/bin/amber20/bin/antechamber'  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.20.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 - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z161000GJY/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (22E261)
      Kernel Version: Darwin 22.4.0
      Time since boot: 4 hours, 6 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 Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304202331
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-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: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (7)

comment:1 by pett, 2 years ago

Cc: chimera-programmers added
Component: Unassigned → Build System
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → antechamber: Bad CPU type in executable

Seems like the correct CPU type AFAICT. I downloaded both the 1.6 universal and ARM candidates onto Elaine's M! laptop and antechamber ran fine in both.

comment:2 by pett, 2 years ago

"M1 laptop", not "M! laptop", lol

comment:3 by Greg Couch, 2 years ago

I've seen this on Linux when the 32-bit compatibility libraries weren't installed and tried to run a 32-bit binary. Is that possible on the mac?

comment:4 by pett, 2 years ago

I think you're on the right track. I think the real problem is that this user has never installed Rosetta, and the fact that ChimeraX is running the Intel antechamber as a subprocess isn't triggering the "you need to install Rosetta" dialog that comes up if you run an Intel binary directly. For reference, the user needs to run "softwareupdate --install-rosetta" in a terminal window.

Is this something we should put in the installation notes?

comment:5 by Greg Couch, 2 years ago

Either in the installation notes, or catch the error and say what to do in a dialog.

comment:6 by pett, 2 years ago

Owner: changed from Zach Pearson to pett

Catching the exception sounds like a good plan.

comment:7 by pett, 2 years ago

Resolution: → fixed
Status: assigned → closed

Exception now caught in both branches

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