[phenixbb] on "Tutorial: Solving a structure with cryo-EM data using docking"
smith_lee123 at yahoo.com
Fri Mar 19 08:27:22 PDT 2021
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.
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
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/programs/validation_cryoem.py", line 476, in validate
File "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py", line 302, in __init__
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)
__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
__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
sizeof(PY_UNICODE_TYPE) = 4
_OPENMP = 200805
gnu libc version: 2.28
platform.architecture(): ('64bit', '')
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 <pafonine at lbl.gov> wrote:
all data files that are used in tutorials are shipped with Phenix. So you don't need to download anything additionally. If you want to use your own data, just do it and follow the tutorial script. In this case your files have the same property as in the tutorial (for example, have symmetry if it is used as part of the tutorial).
Hope this helps!
On 3/13/21 18:29, Smith Lee wrote:
For "Tutorial: Solving a structure with cryo-EM data using docking", it is easy to download the emd_20026_half_map_1_box.ccp4 and emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but will you please let me know step by step how to get the tutorial used seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? Cannot find the exact name file in emd_20026 depositation), apoferritin_chainA_rsr.pdb (it mentioned "model refined against sharpened map", which sharpened map, and what was the refinement method ued?), run_denmod_dock.csh?
I am looking forward to getting your reply.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb