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

Hi Smith,

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?

it's just noise. Don't worry about it. Things should work, normally.

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.

We fixed this problem already. Please use the most recent version of Phenix located in usual place: http://phenix-online.org/download/nightly_builds.cgi Let us know of any other issues! Pavel

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 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