Dear All,
By clicking "phenix" in my centos 8 terminal, the phenix GUI can be launched, but in the terminal there were messages "Gtk-Message: 11:08:21.204: Failed to load module "pk-gtk-module" and message "Gtk-Message: 11:08:21.205: Failed to load module "canberra-gtk-module". Does this mean I have failed for something for my phenix installation? Which phenix functions it affects? Is any way I install these uninstalled modules at this stage and how to install?
Next, when I run the phenix.real_space_refine as command line in the terminal, it wroks fine. However when I run it in the phenix GUI, I got the following assertion error message (see following between "----").
I am looking forward to getting your reply to have the above issues solved.
Best wishes,
Smith
----
AssertionError :
Traceback:
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py", line 181, in run
return_value = self.target()
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py", line 76, in __call__
result = self.run()
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py", line 52, in run
self.result.validation_cryoem = self.run_validation()
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py", line 113, in run_validation
task.validate()
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/programs/validation_cryoem.py", line 476, in validate
self.params.map_model_cc.ignore_symmetry_conflicts)
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py", line 302, in __init__
mmmn.shift_origin()
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py", line 7837, in shift_origin
assert approx_equal(existing_shift_cart, expected_model_shift_cart)
Platform info:
__FILE__ = /dev/shm/bkpoon/software/release/patch/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Jan 21 2021
__TIME__ = 11:15:23
__TIMESTAMP__ = Mon Oct 5 22:43:41 2020
__x86_64__
__linux
__GNUC__ = 4
__GNUC_MINOR__ = 4
__GNUC_PATCHLEVEL__ = 7
__GXX_WEAK__ = 1
__LP64__ = 1
__VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-23)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
__SSE2__ = 1
BOOST_LIB_VERSION = 1_70
PY_VERSION = 2.7.15
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) = 16
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 4
_OPENMP = 200805
gnu libc version: 2.28
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: None
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): Linux-4.18.0-193.28.1.el8_2.x86_64-x86_64-with-centos-8.2.2004-Core
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: 12
Memory total: 134,367,047,680
Memory free: 124,477,964,288
import thread: OK
"hello" = ['h', 'e', 'l', 'l', 'o']
u"hello" = ['h', '\x00', '\x00', '\x00', 'e', '\x00', '\x00', '\x00', 'l', '\x00', '\x00', '\x00', 'l', '\x00', '\x00', '\x00', 'o', '\x00', '\x00', '\x00']
u"\u00C5" = ['\xc5', '\x00', '\x00', '\x00'] as utf-8 = ['\xc3', '\x85']
LATIN CAPITAL LETTER A WITH RING ABOVE = Å
On Thursday, March 18, 2021, 6:36:32 AM GMT+8, Pavel Afonine