Hi Pavel
I got Phenix-2.1 to work well with Coot 1.2.x well, however, there appears to
be issues with Coot 1 (1.x-pre b3be01)+ Phenix-2.2. I emailed phenix online
about this but haven’t heard back.
It was this error attached (Phenix opens coot, loads the clash dots, but cannot
load PDB or MTZ from Phenix)
I also cant find where Phenix is installing its instance of Coot to see if I
can resolve this by pointing to this executable. Do you know the path?
On 24.08.2026, 16:49, "CCP4 bulletin board" <[email protected]> wrote:
Hi,
I have not figure out how to do it for coot 1.x yet.
there is no need to figure that out. Phenix now comes bundled with Coot 1.3x.
Pavel
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RuntimeError : XMLRPC error: <Fault 1: '<class \'Exception\'>:[Errno 2] No such
file or directory: \'ls -l
/Users/kelvinlau/Documents/Facility/Crystallography/Gregoire/20260715-mx2738-id30b/design-Gregoire-Bcatenin-HIT-5/phenix/Refine_19/\'\nOriginal
traceback: File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 175, in _dispatch\n result = func(*params)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 571, in load_phenix_refine_final_files\n
self.load_phenix_refine_final_pdb(output_dir, file_base)\n
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 557, in load_phenix_refine_final_pdb\n subprocess.call("ls -l %s/" %
to_str(output_dir))\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n
File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 396, in call\n with Popen(*popenargs, **kwargs) as p:\n
~~~~~^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1039, in __init__\n self._execute_child(args, executable, preexec_fn,
close_fds,\n ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n
pass_fds, cwd, env,\n
^^^^^^^^^^^^^^^^^^^\n ...<5 lines>...\n gid, gids,
uid, umask,\n ^^^^^^^^^^^^^^^^^^^^^^\n
start_new_session, process_group)\n
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1990, in _execute_child\n raise child_exception_type(errno_num,
err_msg, err_filename)\n'>
Method: load_phenix_refine_final_files
Params:
/Users/kelvinlau/Documents/Facility/Crystallography/Gregoire/20260715-mx2738-id30b/design-Gregoire-Bcatenin-HIT-5/phenix/Refine_19,
Gregoire-catenin-HIT-5_refine_019
Traceback (most recent call last):
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/libtbx/xmlrpc_utils.py",
line 163, in flush_requests
response = self.__transport.request(
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/xmlrpc/client.py",
line 1166, in request
return self.single_request(host, handler, request_body, verbose)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/xmlrpc/client.py",
line 1182, in single_request
return self.parse_response(resp)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/xmlrpc/client.py",
line 1354, in parse_response
return u.close()
^^^^^^^^^
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/xmlrpc/client.py",
line 668, in close
raise Fault(**self._stack[0])
xmlrpc.client.Fault: <Fault 1: '<class \'Exception\'>:[Errno 2] No such file or
directory: \'ls -l
/Users/kelvinlau/Documents/Facility/Crystallography/Gregoire/20260715-mx2738-id30b/design-Gregoire-Bcatenin-HIT-5/phenix/Refine_19/\'\nOriginal
traceback: File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 175, in _dispatch\n result = func(*params)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 571, in load_phenix_refine_final_files\n
self.load_phenix_refine_final_pdb(output_dir, file_base)\n
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 557, in load_phenix_refine_final_pdb\n subprocess.call("ls -l %s/" %
to_str(output_dir))\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n
File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 396, in call\n with Popen(*popenargs, **kwargs) as p:\n
~~~~~^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1039, in __init__\n self._execute_child(args, executable, preexec_fn,
close_fds,\n ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n
pass_fds, cwd, env,\n
^^^^^^^^^^^^^^^^^^^\n ...<5 lines>...\n gid, gids,
uid, umask,\n ^^^^^^^^^^^^^^^^^^^^^^\n
start_new_session, process_group)\n
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1990, in _execute_child\n raise child_exception_type(errno_num,
err_msg, err_filename)\n'>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/wxGUI2/App.py",
line 945, in OnTimer
self.coot_server.flush_requests()
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/libtbx/xmlrpc_utils.py",
line 310, in flush_requests
return self._server.flush_requests(*args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/libtbx/xmlrpc_utils.py",
line 197, in flush_requests
raise RuntimeError(msg)
RuntimeError: XMLRPC error: <Fault 1: '<class \'Exception\'>:[Errno 2] No such
file or directory: \'ls -l
/Users/kelvinlau/Documents/Facility/Crystallography/Gregoire/20260715-mx2738-id30b/design-Gregoire-Bcatenin-HIT-5/phenix/Refine_19/\'\nOriginal
traceback: File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 175, in _dispatch\n result = func(*params)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 571, in load_phenix_refine_final_files\n
self.load_phenix_refine_final_pdb(output_dir, file_base)\n
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 137, in log_wrapper\n return f(self, *args, **kwds)\n\n File
"/Users/kelvinlau/Applications/phenix-2.2-6143/lib/python3.11/site-packages/phenix/wxGUI2/Coot.py",
line 557, in load_phenix_refine_final_pdb\n subprocess.call("ls -l %s/" %
to_str(output_dir))\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n
File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 396, in call\n with Popen(*popenargs, **kwargs) as p:\n
~~~~~^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1039, in __init__\n self._execute_child(args, executable, preexec_fn,
close_fds,\n ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n
pass_fds, cwd, env,\n
^^^^^^^^^^^^^^^^^^^\n ...<5 lines>...\n gid, gids,
uid, umask,\n ^^^^^^^^^^^^^^^^^^^^^^\n
start_new_session, process_group)\n
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File
"/opt/homebrew/Cellar/[email protected]/3.14.7/Frameworks/Python.framework/Versions/3.14/lib/python3.14/subprocess.py",
line 1990, in _execute_child\n raise child_exception_type(errno_num,
err_msg, err_filename)\n'>
Method: load_phenix_refine_final_files
Params:
/Users/kelvinlau/Documents/Facility/Crystallography/Gregoire/20260715-mx2738-id30b/design-Gregoire-Bcatenin-HIT-5/phenix/Refine_19,
Gregoire-catenin-HIT-5_refine_019
Platform info:
__FILE__ =
/Users/runner/miniforge3/conda-bld/phenix_1785829213003/work/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Aug 4 2026
__TIME__ = 08:07:40
__TIMESTAMP__ = Tue Aug 4 04:33:16 2026
__APPLE_CC__ = 6000
__GNUC__ = 4
__GNUC_MINOR__ = 2
__GNUC_PATCHLEVEL__ = 1
__clang__
__clang_major__ = 19
__clang_minor__ = 1
__clang_patchlevel__ = 7
__clang_version__ = 19.1.7
__llvm__
__GXX_WEAK__ = 1
__LP64__ = 1
__VERSION__ = Clang 19.1.7
FE_INEXACT = 16
FE_DIVBYZERO = 2
FE_UNDERFLOW = 8
FE_OVERFLOW = 4
FE_INVALID = 1
FE_ALL_EXCEPT = 159
BOOST_LIB_VERSION = 1_88
PY_VERSION = 3.11.15
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 8
sizeof(std::size_t) = 8
sizeof(void*) = 8
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 8
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 4
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: None
os.name: posix
sys.platform: darwin
sys.byteorder: little
platform.platform(): macOS-26.5.2-arm64-arm-64bit
platform.architecture(): ('64bit', '')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 10
Memory total: 34,359,738,368
Memory free: unknown
import thread: NO
"hello" = ['h', 'e', 'l', 'l', 'o']
u"hello" = ['h', 'e', 'l', 'l', 'o']
u"Ã
" = Ã
as utf-8 = b'\xc3\x85'
LATIN CAPITAL LETTER A WITH RING ABOVE = b'\xc3\x85'
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