[phenixbb] on "Tutorial: Solving a structure with cryo-EM data using docking"

[Smith Lee]

 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 <pafonine at lbl.gov> wrote:  
 
  
Hi Smith,
 
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!
 
Pavel
 
 On 3/13/21 18:29, Smith Lee wrote:
  
 
 Dear All, 
   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. 
  Best wishes, 
  Smith
  
    
   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210319/b0750abe/attachment.htm>